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- Committer: Bazaar Package Importer
- Author(s): Aaron M. Ucko
- Date: 2008-07-14 19:43:15 UTC
- mfrom: (2.1.12 intrepid)
- Revision ID: james.westby@ubuntu.com-20080714194315-ed44u9ek7txva2rz
Tags: 6.1.20080302-3
tools/readdb.c: enable madvise()-based code on all glibc (hence all
Debian) systems, not just Linux. (Closes: #490437.)
Debian) systems, not just Linux. (Closes: #490437.)
- files added:
- access/mla2.asn
- make/msvc800_prj/demo/asnbarval
- make/msvc800_prj/demo/asndisc
- make/msvc800_prj/demo/asnstrip
- make/msvc800_prj/demo/raw2delt
- make/msvc_prj/demo/asnbarval
- make/msvc_prj/demo/asndisc
- make/msvc_prj/demo/asnmacro
- make/msvc_prj/demo/asnstrip
- make/msvc_prj/demo/cleanasn
- make/msvc_prj/demo/cspeedtest
- make/msvc_prj/demo/raw2delt
- make/xCode/ncbicguiapp
- make/xCode/ncbicguiapp/English.lproj
- make/xCode/ncbicguiapp/ncbicguiapp.xcodeproj
- make/xCode/ncbictoolkit
- make/xCode/ncbictoolkit/English.lproj
- make/xCode/ncbictoolkit/ncbictoolkit.xcodeproj
- files removed:
- algo/blast/core/blast_dust.c
- debian/man.unused
- debian/old-blast-man
- make/msvc800_prj/demo/entrezcf
- make/msvc800_prj/demo/getseq
- make/msvc_prj/demo/entrezcf
- make/msvc_prj/demo/getseq
- files modified:
- VERSION
- biostruc/RESEARCH/res.shtml *
- biostruc/RESEARCH/threading.shtml *
- biostruc/VastAlign/Makefile *
- biostruc/cblast/cblast.h *
- biostruc/newVSch/Makefile *
- biostruc/pdbeast/interface.c *
- biostruc/pdbeast/interface.h *
- biostruc/pdbeast/mmdborgcpy.c *
- biostruc/pdbeast/orgmatch.c *
- biostruc/pdbeast/para.h *
- biostruc/pdbeast/pdbeast.c *
- biostruc/pdbeast/pdbeast.h *
- biostruc/pdbeast/tax_index.c *
- cn3d/cn3dmatn.c *
- cn3d/cn3dmsg.c *
- cn3d/cn3dmsg.h *
- corelib/tsprintf.h *
- doc/images/affil.png *
- doc/images/annot.png *
- doc/images/authors.png *
- doc/images/cds_edit.png *
- doc/images/contact.png *
- doc/images/desktop.png *
- doc/images/format.png *
- doc/images/genbank.png *
- doc/images/graphic.png *
- doc/images/net_cfg.png *
- doc/images/nucset.png *
- doc/images/nucsing1.png *
- doc/images/nucsing2.png *
- doc/images/organism.png *
- doc/images/protein1.png *
- doc/images/protein2.png *
- doc/images/sequence.png *
- doc/images/update.png *
- doc/images/validate.png *
- doc/images/welcome.png *
- link/macmet/MW-BSD-limits-fix.h *
- sequin/sbtedit.c *
- vibrant/vibrgb.h *
- webdesign/designs/cubby/storedsearch/Templates/edit.gif *
- webdesign/designs/cubby/storedsearch/Templates/mail.gif *
- webdesign/designs/cubby/storedsearch/Templates/plus.gif *
- webdesign/designs/cubby/storedsearch/Templates/run.gif *
- webdesign/designs/cubby/storedsearch/Templates/whatsnew.gif *
- webdesign/designs/cubby/storedsearch/Templates/x.gif *
- webdesign/designs/pmc/layout.css *
added
removed
sequin/sequin5.c
29
29
*
30
30
* Version Creation Date: 8/26/97
31
31
*
32
* $Revision: 6.470 $
32
* $Revision: 6.637 $
33
33
*
34
34
* File Description:
35
35
*
72
72
#include <salutil.h>
73
73
74
74
#include <asn2gnbp.h> /* added for parse to flatfile */
75
#include <seqpanel.h> /* added to include SeqEdTranslateOneCDS */
75
#include <sqnutils.h> /* added to include SeqEdTranslateOneCDS */
76
#include <seqpanel.h>
76
77
#include <salpanel.h>
78
#include <tax3api.h> /* added for specific-host corrections */
79
#include <findrepl.h>
80
#include <valid.h> /* added for latloncountry conflict checking */
77
81
78
82
static void CommonLaunchBioseqViewer (SeqEntryPtr sep, CharPtr path, Boolean directToEditor)
79
83
2164
2168
return;
2165
2169
}
2166
2170
2167
static void FeatConvertImpToSpecialRNA (SeqFeatPtr sfp,
2168
Int2 toFeatSubType)
2171
static Boolean ConvertImpToSpecialRNA
2172
(SeqFeatPtr sfp,
2173
Uint2 featdef_to,
2174
Pointer extradata)
2169
2175
{
2170
2176
RnaRefPtr rrp;
2171
2177
2178
if (sfp == NULL || sfp->data.choice != SEQFEAT_IMP)
2179
{
2180
return FALSE;
2181
}
2172
2182
rrp = RnaRefNew ();
2173
2183
if (rrp != NULL) {
2174
2184
sfp->data.value.ptrvalue = ImpFeatFree ((ImpFeatPtr) sfp->data.value.ptrvalue);
2175
2185
sfp->data.choice = SEQFEAT_RNA;
2176
2186
sfp->data.value.ptrvalue = (Pointer) rrp;
2177
if (toFeatSubType == FEATDEF_precursor_RNA) {
2187
if (featdef_to == FEATDEF_precursor_RNA) {
2178
2188
rrp->type = 1;
2179
2189
} else {
2180
2190
rrp->type = 255;
2181
2191
}
2182
2192
}
2183
}
2184
2185
static void FeatConvertRegionToImp (SeqFeatPtr sfp,
2186
Int2 toFeatSubType,
2187
EnumFieldAssoc PNTR alist)
2188
{
2189
EnumFieldAssocPtr ap;
2190
GBQualPtr gbqual;
2191
Int2 i;
2192
ImpFeatPtr ifp;
2193
CharPtr str;
2194
2195
ifp = ImpFeatNew ();
2196
if (NULL == ifp)
2197
return;
2198
2199
str = (CharPtr) sfp->data.value.ptrvalue;
2200
sfp->data.choice = SEQFEAT_IMP;
2201
sfp->data.value.ptrvalue = (Pointer) ifp;
2202
for (i = 1, ap = alist; ap->name != NULL; i++, ap++) {
2203
if (ap->value == toFeatSubType) {
2204
ifp->key = MemFree (ifp->key);
2205
ifp->key = StringSave (ap->name);
2206
}
2207
}
2208
2209
if (ifp->key == NULL) {
2210
ifp->key = StringSave ("misc_feature");
2211
}
2212
2213
if (! StringHasNoText (str)) {
2214
gbqual = GBQualNew ();
2215
if (gbqual != NULL) {
2216
gbqual->qual = StringSave ("note");
2217
gbqual->val = str;
2218
gbqual->next = sfp->qual;
2219
sfp->qual = gbqual;
2220
}
2221
}
2222
2223
}
2224
2225
static void FeatConvertRegionToRNA (SeqFeatPtr sfp,
2226
Int2 toFeatSubType)
2193
return TRUE;
2194
}
2195
2196
static Boolean ConvertRegionToRNA
2197
(SeqFeatPtr sfp,
2198
Uint2 featdef_to,
2199
Pointer extradata)
2227
2200
{
2228
2201
RnaRefPtr rrp;
2229
2202
CharPtr str;
2230
2203
2204
if (sfp == NULL || sfp->data.choice != SEQFEAT_REGION)
2205
{
2206
return FALSE;
2207
}
2208
2231
2209
rrp = RnaRefNew ();
2232
2210
if (NULL == rrp)
2233
return;
2211
{
2212
return FALSE;
2213
}
2234
2214
2235
2215
str = (CharPtr) sfp->data.value.ptrvalue;
2236
2216
sfp->data.choice = SEQFEAT_RNA;
2237
2217
sfp->data.value.ptrvalue = (Pointer) rrp;
2238
2218
2239
if (toFeatSubType == FEATDEF_precursor_RNA) {
2219
if (featdef_to == FEATDEF_precursor_RNA) {
2240
2220
rrp->type = 1;
2241
2221
} else {
2242
2222
rrp->type = 255;
2246
2226
rrp->ext.choice = 1;
2247
2227
rrp->ext.value.ptrvalue = str;
2248
2228
}
2249
2229
return TRUE;
2250
2230
}
2251
2231
2252
static void FeatConvertImpToRNA (SeqFeatPtr sfp,
2253
Int2 toFeatSubType)
2232
static Boolean ConvertImpToRNA
2233
(SeqFeatPtr sfp,
2234
Uint2 featdef_to,
2235
Pointer extradata)
2254
2236
{
2255
2237
RnaRefPtr rrp;
2256
2238
2239
if (sfp == NULL || sfp->data.choice != SEQFEAT_IMP)
2240
{
2241
return FALSE;
2242
}
2243
2257
2244
rrp = RnaRefNew ();
2258
2245
if (NULL == rrp)
2259
return;
2246
return FALSE;
2260
2247
2261
2248
sfp->data.value.ptrvalue =
2262
2249
ImpFeatFree ((ImpFeatPtr) sfp->data.value.ptrvalue);
2263
2250
sfp->data.choice = SEQFEAT_RNA;
2264
2251
sfp->data.value.ptrvalue = (Pointer) rrp;
2265
2252
2266
switch (toFeatSubType) {
2253
switch (featdef_to) {
2267
2254
case FEATDEF_preRNA :
2268
2255
rrp->type = 1;
2269
2256
break;
2285
2272
case FEATDEF_snoRNA :
2286
2273
rrp->type = 7;
2287
2274
break;
2275
case FEATDEF_ncRNA :
2276
rrp->type = 255;
2277
rrp->ext.choice = 1;
2278
rrp->ext.value.ptrvalue = StringSave ("ncRNA");
2279
break;
2288
2280
case FEATDEF_otherRNA :
2289
2281
rrp->type = 255;
2290
2282
break;
2291
2283
default :
2292
2284
break;
2293
2285
}
2294
2286
return TRUE;
2295
2287
}
2296
2288
2297
static void FeatConvertCommentToMiscFeature (SeqFeatPtr sfp)
2289
static Boolean ConvertCommentToMiscFeat (SeqFeatPtr sfp, Uint2 featdef_to, Pointer extradata)
2298
2290
{
2299
2291
ImpFeatPtr ifp;
2300
2292
2301
if (sfp->data.value.ptrvalue == NULL) {
2302
ifp = ImpFeatNew ();
2303
if (ifp != NULL) {
2304
ifp->key = StringSave ("misc_feature");
2305
sfp->data.choice = SEQFEAT_IMP;
2306
sfp->data.value.ptrvalue = (Pointer) ifp;
2307
}
2308
}
2293
if (sfp == NULL || sfp->data.choice != SEQFEAT_COMMENT || sfp->data.value.ptrvalue != NULL)
2294
{
2295
return FALSE;
2296
}
2297
2298
ifp = ImpFeatNew ();
2299
if (ifp != NULL) {
2300
ifp->key = StringSave ("misc_feature");
2301
sfp->data.choice = SEQFEAT_IMP;
2302
sfp->data.value.ptrvalue = (Pointer) ifp;
2303
return TRUE;
2304
}
2305
return FALSE;
2309
2306
}
2310
2307
2311
static void FeatConvertGeneToMiscFeature (SeqFeatPtr sfp)
2308
static Boolean ConvertGeneToMiscFeat
2309
(SeqFeatPtr sfp,
2310
Uint2 featdef_to,
2311
Pointer extradata)
2312
2312
{
2313
2313
ImpFeatPtr ifp;
2314
GBQualPtr gbqual;
2315
CharPtr genelocus;
2314
CharPtr new_comment;
2316
2315
GeneRefPtr grp;
2316
Int4 comment_len = 0;
2317
2317
2318
if (sfp == NULL || sfp->data.choice != SEQFEAT_GENE)
2319
{
2320
return FALSE;
2321
}
2318
2322
ifp = ImpFeatNew ();
2319
2323
if (NULL == ifp)
2320
return;
2324
{
2325
return FALSE;
2326
}
2321
2327
2322
genelocus = NULL;
2323
2328
grp = (GeneRefPtr) sfp->data.value.ptrvalue;
2324
if (grp != NULL) {
2325
genelocus = grp->locus;
2326
grp->locus = NULL;
2329
if (grp != NULL)
2330
{
2331
if (!StringHasNoText (grp->locus))
2332
{
2333
comment_len += StringLen (grp->locus) + 2;
2334
}
2335
if (!StringHasNoText (grp->desc))
2336
{
2337
comment_len += StringLen (grp->desc) + 2;
2338
}
2339
}
2340
if (comment_len == 0)
2341
{
2342
/* nothing to add to comment */
2343
}
2344
else
2345
{
2346
/* add one for terminating NULL */
2347
comment_len++;
2348
if (!StringHasNoText (sfp->comment))
2349
{
2350
comment_len += StringLen (sfp->comment) + 2;
2351
}
2352
2353
new_comment = (CharPtr) MemNew (sizeof (Char) * comment_len);
2354
/* NOTE - I don't have to check for grp == NULL because
2355
* comment_len would only have been > 0 if grp had existed
2356
* and had nonempty fields.
2357
*/
2358
if (!StringHasNoText (grp->desc))
2359
{
2360
StringCat (new_comment, grp->desc);
2361
StringCat (new_comment, "; ");
2362
}
2363
if (!StringHasNoText (grp->locus))
2364
{
2365
StringCat (new_comment, grp->locus);
2366
StringCat (new_comment, "; ");
2367
}
2368
if (!StringHasNoText (sfp->comment))
2369
{
2370
StringCat (new_comment, sfp->comment);
2371
StringCat (new_comment, "; ");
2372
}
2373
/* remove last semicolon */
2374
new_comment[StringLen (new_comment) - 2] = 0;
2375
sfp->comment = MemFree (sfp->comment);
2376
sfp->comment = new_comment;
2327
2377
}
2328
2378
2329
2379
sfp->data.value.ptrvalue =
2331
2381
sfp->data.choice = SEQFEAT_IMP;
2332
2382
sfp->data.value.ptrvalue = (Pointer) ifp;
2333
2383
ifp->key = StringSave ("misc_feature");
2334
2335
if (! StringHasNoText (genelocus)) {
2336
gbqual = GBQualNew ();
2337
if (gbqual != NULL) {
2338
gbqual->qual = StringSave ("gene");
2339
gbqual->val = genelocus;
2340
gbqual->next = sfp->qual;
2341
sfp->qual = gbqual;
2342
}
2343
}
2344
2384
return TRUE;
2345
2385
}
2346
2386
2347
static void FeatConvertRNAToMiscFeature (SeqFeatPtr sfp)
2387
static Boolean ConvertRNAToMiscFeat
2388
(SeqFeatPtr sfp,
2389
Uint2 featdef_to,
2390
Pointer extradata)
2348
2391
{
2349
GBQualPtr gbqual;
2392
GBQualPtr gbqual, q_p, q_n;
2350
2393
ImpFeatPtr ifp;
2351
CharPtr rnaname;
2394
CharPtr rnaname, newnote;
2352
2395
RnaRefPtr rrp;
2396
Int4 note_len = 0;
2397
2398
if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA)
2399
{
2400
return FALSE;
2401
}
2353
2402
2354
2403
ifp = ImpFeatNew ();
2355
2404
if (NULL == ifp)
2356
return;
2405
{
2406
return FALSE;
2407
}
2357
2408
2358
2409
rnaname = NULL;
2359
2410
rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
2360
if (rrp != NULL) {
2411
if (rrp != NULL && rrp->type != 255 && rrp->ext.choice == 1) {
2361
2412
if (rrp->ext.choice == 1) {
2362
2413
rnaname = (CharPtr) rrp->ext.value.ptrvalue;
2363
2414
rrp->ext.value.ptrvalue = NULL;
2415
note_len = StringLen (rnaname) + 2;
2364
2416
}
2365
2417
}
2366
2418
2370
2422
sfp->data.value.ptrvalue = (Pointer) ifp;
2371
2423
ifp->key = StringSave ("misc_feature");
2372
2424
2373
if (! StringHasNoText (rnaname)) {
2374
gbqual = GBQualNew ();
2375
if (gbqual != NULL) {
2376
gbqual->qual = StringSave ("product");
2377
gbqual->val = rnaname;
2378
gbqual->next = sfp->qual;
2379
sfp->qual = gbqual;
2380
}
2425
for (gbqual = sfp->qual; gbqual != NULL; gbqual = gbqual->next) {
2426
if (StringCmp (gbqual->qual, "product") == 0) {
2427
note_len += StringLen (gbqual->val) + 2;
2428
}
2429
}
2430
2431
if (note_len > 0) {
2432
if (!StringHasNoText (sfp->comment)) {
2433
note_len += StringLen (sfp->comment) + 2;
2434
}
2435
newnote = (CharPtr) MemNew (sizeof (Char) * (note_len + 1));
2436
if (!StringHasNoText (sfp->comment)) {
2437
StringCpy (newnote, sfp->comment);
2438
StringCat (newnote, "; ");
2439
}
2440
if (rnaname != NULL) {
2441
StringCat (newnote, rnaname);
2442
StringCat (newnote, "; ");
2443
rnaname = MemFree (rnaname);
2444
}
2445
gbqual = sfp->qual;
2446
q_p = NULL;
2447
while (gbqual != NULL) {
2448
q_n = gbqual->next;
2449
if (StringCmp (gbqual->qual, "product") == 0) {
2450
StringCat (newnote, gbqual->val);
2451
if (q_p == NULL) {
2452
sfp->qual = q_n;
2453
} else {
2454
q_p->next = q_n;
2455
}
2456
gbqual->next = NULL;
2457
gbqual = GBQualFree (gbqual);
2458
} else {
2459
q_p = gbqual;
2460
}
2461
gbqual = q_n;
2462
}
2463
/* trim trailing semicolon */
2464
newnote[note_len - 2] = 0;
2465
sfp->comment = MemFree (sfp->comment);
2466
sfp->comment = newnote;
2381
2467
}
2382
2468
2469
return TRUE;
2383
2470
}
2384
2471
2385
static void FeatConvertSiteToMiscFeature (SeqFeatPtr sfp)
2472
static Boolean ConvertSiteToMiscFeat
2473
(SeqFeatPtr sfp,
2474
Uint2 featdef_to,
2475
Pointer extradata)
2386
2476
{
2387
2477
GBQualPtr gbqual;
2388
2478
ImpFeatPtr ifp;
2389
2479
Int2 sitetype;
2390
2480
2481
if (sfp == NULL || sfp->data.choice != SEQFEAT_SITE)
2482
{
2483
return FALSE;
2484
}
2485
2391
2486
ifp = ImpFeatNew ();
2392
2487
if (NULL == ifp)
2393
return;
2488
{
2489
return FALSE;
2490
}
2394
2491
2395
2492
sitetype = (Int2) sfp->data.value.intvalue;
2396
2493
sfp->data.choice = SEQFEAT_IMP;
2405
2502
sfp->qual = gbqual;
2406
2503
}
2407
2504
}
2408
2505
return TRUE;
2409
2506
}
2410
2507
2411
static void FeatConvertPeptideToRegion (SeqFeatPtr sfp)
2508
static Boolean ConvertProtToRegion
2509
(SeqFeatPtr sfp,
2510
Uint2 featdef_to,
2511
Pointer extradata)
2412
2512
{
2413
2513
ProtRefPtr prp;
2414
2514
ValNodePtr vnp;
2415
2515
CharPtr str;
2416
2516
2517
if (sfp == NULL || sfp->data.choice != SEQFEAT_PROT)
2518
{
2519
return FALSE;
2520
}
2417
2521
prp = (ProtRefPtr) sfp->data.value.ptrvalue;
2418
2522
if (NULL == prp)
2419
return;
2523
{
2524
return FALSE;
2525
}
2420
2526
2421
2527
vnp = prp->name;
2422
2528
if (vnp != NULL && vnp->next == NULL) {
2428
2534
sfp->data.value.ptrvalue = (Pointer) str;
2429
2535
}
2430
2536
}
2431
2432
}
2433
2434
2435
static void FeatConvertImpToImp (SeqFeatPtr sfp,
2436
Int2 toFeatSubType,
2437
EnumFieldAssoc PNTR alist)
2438
{
2439
EnumFieldAssocPtr ap;
2440
Int2 i;
2441
ImpFeatPtr ifp;
2442
2443
ifp = (ImpFeatPtr) sfp->data.value.ptrvalue;
2444
if (NULL == ifp)
2537
return TRUE;
2538
}
2539
2540
static Boolean ConvertRNAToNcRNA
2541
(SeqFeatPtr sfp)
2542
{
2543
RnaRefPtr rrp;
2544
GBQualPtr gbq;
2545
tRNAPtr trp;
2546
2547
if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA) return FALSE;
2548
2549
rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
2550
if (NULL == rrp) {
2551
rrp = RnaRefNew ();
2552
sfp->data.value.ptrvalue = rrp;
2553
}
2554
2555
if (rrp->ext.choice == 2) {
2556
trp = (tRNAPtr) rrp->ext.value.ptrvalue;
2557
if (trp != NULL) {
2558
trp->anticodon = SeqLocFree (trp->anticodon);
2559
trp = MemFree (trp);
2560
rrp->ext.value.ptrvalue = trp;
2561
}
2562
rrp->ext.choice = 0;
2563
}
2564
2565
/* might be converting from other ncRNA, tmRNA, or misc_RNA */
2566
if (rrp->ext.choice == 1) {
2567
if (StringCmp (rrp->ext.value.ptrvalue, "ncRNA") == 0) {
2568
/* already ncRNA */
2569
} else if (StringCmp (rrp->ext.value.ptrvalue, "tmRNA") == 0) {
2570
rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
2571
rrp->ext.value.ptrvalue = StringSave ("ncRNA");
2572
} else if (StringCmp (rrp->ext.value.ptrvalue, "misc_RNA") == 0) {
2573
rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
2574
rrp->ext.value.ptrvalue = StringSave ("ncRNA");
2575
} else {
2576
/* not one of the specified types, copy to product gbqual */
2577
gbq = GBQualNew ();
2578
gbq->qual = StringSave ("product");
2579
gbq->val = rrp->ext.value.ptrvalue;
2580
gbq->next = sfp->qual;
2581
sfp->qual = gbq;
2582
rrp->ext.value.ptrvalue = StringSave ("ncRNA");
2583
}
2584
} else {
2585
rrp->ext.choice = 1;
2586
rrp->ext.value.ptrvalue = StringSave ("ncRNA");
2587
}
2588
2589
if (rrp->type == 5) {
2590
gbq = GBQualNew ();
2591
gbq->qual = StringSave ("ncRNA_class");
2592
gbq->val = StringSave ("snRNA");
2593
gbq->next = sfp->qual;
2594
sfp->qual = gbq;
2595
} else if (rrp->type == 6) {
2596
gbq = GBQualNew ();
2597
gbq->qual = StringSave ("ncRNA_class");
2598
gbq->val = StringSave ("scRNA");
2599
gbq->next = sfp->qual;
2600
sfp->qual = gbq;
2601
} else if (rrp->type == 7) {
2602
gbq = GBQualNew ();
2603
gbq->qual = StringSave ("ncRNA_class");
2604
gbq->val = StringSave ("snoRNA");
2605
gbq->next = sfp->qual;
2606
sfp->qual = gbq;
2607
}
2608
2609
rrp->type = 255;
2610
return TRUE;
2611
}
2612
2613
2614
static void ConvertFromncRNAtoMiscRNA (SeqFeatPtr sfp)
2615
{
2616
RnaRefPtr rrp;
2617
GBQualPtr gbq, gbq_prev = NULL;
2618
CharPtr tmp;
2619
2620
if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA) return;
2621
rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
2622
if (rrp == NULL || rrp->ext.choice != 1 || StringCmp (rrp->ext.value.ptrvalue, "ncRNA") != 0) {
2445
2623
return;
2446
2447
for (i = 1, ap = alist; ap->name != NULL; i++, ap++) {
2448
if (ap->value == toFeatSubType) {
2449
ifp->key = MemFree (ifp->key);
2450
ifp->key = StringSave (ap->name);
2451
}
2452
}
2453
2624
}
2625
rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
2626
rrp->ext.choice = 0;
2627
/* find new value for product */
2628
gbq = sfp->qual;
2629
while (gbq != NULL && StringCmp (gbq->qual, "product") != 0) {
2630
gbq_prev = gbq;
2631
gbq = gbq->next;
2632
}
2633
2634
if (gbq != NULL) {
2635
rrp->ext.choice = 1;
2636
rrp->ext.value.ptrvalue = StringSave (gbq->val);
2637
if (gbq_prev == NULL) {
2638
sfp->qual = gbq->next;
2639
} else {
2640
gbq_prev->next = gbq->next;
2641
}
2642
gbq->next = NULL;
2643
gbq = GBQualFree (gbq);
2644
} else if (!StringHasNoText (sfp->comment)) {
2645
rrp->ext.choice = 1;
2646
rrp->ext.value.ptrvalue = StringSave (sfp->comment);
2647
sfp->comment = MemFree (sfp->comment);
2648
}
2649
2650
/* move ncRNA_class elsewhere */
2651
gbq = sfp->qual;
2652
gbq_prev = NULL;
2653
while (gbq != NULL && StringCmp (gbq->qual, "ncRNA_class") != 0) {
2654
gbq_prev = gbq;
2655
gbq = gbq->next;
2656
}
2657
2658
if (gbq != NULL) {
2659
if (StringCmp (gbq->val, "other") != 0) {
2660
if (rrp->ext.choice == 0) {
2661
rrp->ext.choice = 1;
2662
rrp->ext.value.ptrvalue = StringSave (gbq->val);
2663
} else {
2664
if (StringHasNoText (sfp->comment)) {
2665
sfp->comment = MemFree (sfp->comment);
2666
sfp->comment = StringSave (gbq->val);
2667
} else {
2668
tmp = (CharPtr) MemNew (sizeof (Char) * (StringLen (sfp->comment) + StringLen (gbq->val) + 3));
2669
sprintf (tmp, "%s; %s", sfp->comment, gbq->val);
2670
sfp->comment = MemFree (sfp->comment);
2671
sfp->comment = tmp;
2672
}
2673
}
2674
}
2675
if (gbq_prev == NULL) {
2676
sfp->qual = gbq->next;
2677
} else {
2678
gbq_prev->next = gbq->next;
2679
}
2680
gbq->next = NULL;
2681
gbq = GBQualFree (gbq);
2682
}
2454
2683
}
2455
2684
2456
static void FeatConvertRNAToRNA (SeqFeatPtr sfp,
2457
Int2 toFeatSubType)
2685
2686
static Boolean ConvertRNAToRNA
2687
(SeqFeatPtr sfp,
2688
Uint2 featdef_to,
2689
Pointer extradata)
2458
2690
{
2459
2691
RnaRefPtr rrp;
2692
Boolean from_misc = FALSE, to_misc = FALSE;
2693
GBQualPtr gbq, gbq_p = NULL;
2460
2694
2461
2695
rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
2462
2696
if (NULL == rrp)
2463
return;
2464
2465
switch (toFeatSubType) {
2466
case FEATDEF_preRNA :
2467
rrp->type = 1;
2468
break;
2469
case FEATDEF_mRNA :
2470
rrp->type = 2;
2471
break;
2472
case FEATDEF_tRNA :
2473
rrp->type = 3;
2474
break;
2475
case FEATDEF_rRNA :
2476
rrp->type = 4;
2477
break;
2478
case FEATDEF_snRNA :
2479
rrp->type = 5;
2480
break;
2481
case FEATDEF_scRNA :
2482
rrp->type = 6;
2483
break;
2484
case FEATDEF_snoRNA :
2485
rrp->type = 7;
2486
break;
2487
case FEATDEF_otherRNA :
2488
rrp->type = 255;
2489
break;
2490
default:
2491
break;
2492
}
2493
2697
return FALSE;
2698
2699
if (rrp->type == 255) {
2700
from_misc = TRUE;
2701
}
2702
2703
switch (featdef_to) {
2704
case FEATDEF_preRNA :
2705
rrp->type = 1;
2706
break;
2707
case FEATDEF_mRNA :
2708
rrp->type = 2;
2709
break;
2710
case FEATDEF_tRNA :
2711
rrp->type = 3;
2712
break;
2713
case FEATDEF_rRNA :
2714
rrp->type = 4;
2715
break;
2716
case FEATDEF_snRNA :
2717
rrp->type = 5;
2718
to_misc = TRUE;
2719
break;
2720
case FEATDEF_scRNA :
2721
rrp->type = 6;
2722
to_misc = TRUE;
2723
break;
2724
case FEATDEF_snoRNA :
2725
rrp->type = 7;
2726
to_misc = TRUE;
2727
break;
2728
case FEATDEF_ncRNA :
2729
return ConvertRNAToNcRNA (sfp);
2730
break;
2731
case FEATDEF_otherRNA :
2732
rrp->type = 255;
2733
ConvertFromncRNAtoMiscRNA (sfp);
2734
break;
2735
default:
2736
break;
2737
}
2738
if (from_misc && !to_misc && rrp->ext.choice == 1 && StringCmp (rrp->ext.value.ptrvalue, "misc_RNA") == 0) {
2739
/* move product qual to string */
2740
gbq = sfp->qual;
2741
while (gbq != NULL && StringCmp (gbq->qual, "product") != 0) {
2742
gbq_p = gbq;
2743
gbq = gbq->next;
2744
}
2745
if (gbq == NULL) {
2746
rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
2747
rrp->ext.choice = 0;
2748
} else {
2749
rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
2750
rrp->ext.value.ptrvalue = gbq->val;
2751
gbq->val = NULL;
2752
if (gbq_p == NULL) {
2753
sfp->qual = gbq->next;
2754
} else {
2755
gbq_p->next = gbq->next;
2756
}
2757
gbq->next = NULL;
2758
gbq = GBQualFree (gbq);
2759
}
2760
}
2761
return TRUE;
2494
2762
}
2495
2763
2496
static void FeatConvertProtToProt (SeqFeatPtr sfp,
2497
Int2 toFeatSubType)
2764
static Boolean ConvertProtToProt
2765
(SeqFeatPtr sfp,
2766
Uint2 featdef_to,
2767
Pointer extradata)
2498
2768
{
2499
2769
ProtRefPtr prp;
2500
2770
2501
2771
prp = (ProtRefPtr) sfp->data.value.ptrvalue;
2502
2772
if (NULL == prp)
2503
return;
2773
return FALSE;
2504
2774
2505
switch (toFeatSubType) {
2506
case FEATDEF_PROT :
2507
prp->processed = 0;
2508
break;
2509
case FEATDEF_preprotein :
2510
prp->processed = 1;
2511
break;
2512
case FEATDEF_mat_peptide_aa :
2513
prp->processed = 2;
2514
break;
2515
case FEATDEF_sig_peptide_aa :
2516
prp->processed = 3;
2517
break;
2518
case FEATDEF_transit_peptide_aa :
2519
prp->processed = 4;
2520
break;
2521
default :
2522
break;
2775
switch (featdef_to) {
2776
case FEATDEF_PROT :
2777
prp->processed = 0;
2778
break;
2779
case FEATDEF_preprotein :
2780
prp->processed = 1;
2781
break;
2782
case FEATDEF_mat_peptide_aa :
2783
prp->processed = 2;
2784
break;
2785
case FEATDEF_sig_peptide_aa :
2786
prp->processed = 3;
2787
break;
2788
case FEATDEF_transit_peptide_aa :
2789
prp->processed = 4;
2790
break;
2791
default :
2792
break;
2523
2793
}
2524
2525
}
2526
2794
return TRUE;
2795
}
2796
2797
/* copied from seqport.c, for the benefit of load_fuzz_to_DNA */
2798
static Boolean add_fuzziness_to_loc (SeqLocPtr slp, Boolean less)
2799
{
2800
IntFuzzPtr ifp;
2801
SeqIntPtr sint;
2802
SeqPntPtr spnt;
2803
2804
sint = NULL;
2805
spnt = NULL;
2806
2807
if(slp->choice == SEQLOC_INT)
2808
sint = (SeqIntPtr) slp->data.ptrvalue;
2809
else
2810
{
2811
if(slp->choice == SEQLOC_PNT)
2812
spnt = (SeqPntPtr) slp->data.ptrvalue;
2813
else
2814
return FALSE;
2815
}
2816
ifp = IntFuzzNew();
2817
ifp->choice = 4;
2818
ifp->a = less ? 2 : 1;
2819
2820
if(spnt != NULL)
2821
spnt->fuzz = ifp;
2822
else
2823
{
2824
if(less)
2825
sint->if_from = ifp;
2826
else
2827
sint->if_to = ifp;
2828
}
2829
2830
return TRUE;
2831
}
2832
2833
2834
/* copied from seqport.c, for the benefit of MYdnaLoc_to_aaLoc */
2835
static Boolean load_fuzz_to_DNA(SeqLocPtr dnaLoc, SeqLocPtr aaLoc, Boolean
2836
first)
2837
{
2838
Uint1 strand;
2839
SeqPntPtr spnt;
2840
SeqIntPtr sint;
2841
IntFuzzPtr ifp;
2842
Boolean load, less;
2843
2844
load = FALSE;
2845
strand = SeqLocStrand(aaLoc);
2846
if(aaLoc->choice == SEQLOC_INT)
2847
{
2848
sint = (SeqIntPtr) aaLoc->data.ptrvalue;
2849
if((first && strand != Seq_strand_minus ) ||
2850
(!first && strand == Seq_strand_minus)) /*the first
2851
Seq-loc*/
2852
{
2853
ifp = sint->if_from;
2854
if(ifp && ifp->choice == 4 )
2855
load = (ifp->a == 2);
2856
}
2857
else
2858
{
2859
ifp = sint->if_to;
2860
if(ifp && ifp->choice == 4)
2861
load = (ifp->a == 1);
2862
}
2863
}
2864
else if(aaLoc->choice == SEQLOC_PNT)
2865
{
2866
spnt = (SeqPntPtr) aaLoc->data.ptrvalue;
2867
ifp = spnt->fuzz;
2868
if(ifp && ifp->choice == 4)
2869
{
2870
if(first)
2871
load = (ifp->a == 2);
2872
else
2873
load = (ifp->a == 1);
2874
}
2875
}
2876
2877
if(load)
2878
{
2879
if(SeqLocStrand(dnaLoc) == Seq_strand_minus)
2880
less = (first == FALSE);
2881
else
2882
less = first;
2883
add_fuzziness_to_loc (dnaLoc, less);
2884
return TRUE;
2885
}
2886
else
2887
return FALSE;
2888
}
2889
2890
static SeqLocPtr MYdnaLoc_to_aaLoc(SeqFeatPtr sfp,
2891
SeqLocPtr location_loc,
2892
Boolean merge,
2893
Int4Ptr frame,
2894
Boolean allowTerminator)
2895
{
2896
SeqLocPtr aa_loc = NULL, loc;
2897
CdRegionPtr crp;
2898
Int4 product_len, end_pos, frame_offset;
2899
GatherRange gr;
2900
Int4 a_left = 0, a_right, last_aa = -20, aa_from, aa_to;
2901
SeqLocPtr slp, slp1, slp2;
2902
Int2 cmpval;
2903
SeqIdPtr aa_sip;
2904
BioseqPtr bsp;
2905
2906
if ((sfp == NULL) || (location_loc == NULL)) return aa_loc;
2907
if (sfp->data.choice != 3) return aa_loc;
2908
if (sfp->product == NULL) return aa_loc;
2909
2910
crp = (CdRegionPtr) sfp->data.value.ptrvalue;
2911
if(crp == NULL) return aa_loc;
2912
2913
/* each interval of location_loc must be equal to or contained in
2914
* an interval of sfp->location
2915
*/
2916
slp1 = SeqLocFindNext (sfp->location, NULL);
2917
slp2 = SeqLocFindNext (location_loc, NULL);
2918
while (slp2 != NULL && slp1 != NULL) {
2919
cmpval = SeqLocCompare (slp2, slp1);
2920
if (cmpval == SLC_A_IN_B || cmpval == SLC_A_EQ_B) {
2921
slp2 = SeqLocFindNext (location_loc, slp2);
2922
} else {
2923
slp1 = SeqLocFindNext (sfp->location, slp1);
2924
}
2925
}
2926
if (slp1 == NULL) return aa_loc;
2927
2928
aa_sip = SeqLocId(sfp->product);
2929
if (aa_sip == NULL) return aa_loc;
2930
bsp = BioseqLockById(aa_sip);
2931
if (bsp == NULL) return aa_loc;
2932
end_pos = bsp->length - 1;
2933
BioseqUnlock(bsp);
2934
2935
if(crp->frame == 0)
2936
frame_offset = 0;
2937
else
2938
frame_offset = (Int4)crp->frame-1;
2939
2940
slp = NULL;
2941
product_len = 0;
2942
loc = NULL;
2943
while ((slp = SeqLocFindNext(sfp->location, slp))!=NULL)
2944
{
2945
if (SeqLocOffset(location_loc, slp, &gr, 0))
2946
{
2947
SeqLocOffset(slp, location_loc, &gr, 0);
2948
2949
a_left = gr.left + product_len - frame_offset;
2950
a_right = gr.right + product_len - frame_offset;
2951
2952
aa_from = a_left / 3;
2953
aa_to = a_right / 3;
2954
2955
if (aa_from < 0)
2956
aa_from = 0;
2957
if (aa_to > end_pos)
2958
aa_to = end_pos;
2959
2960
if (merge)
2961
{
2962
if (aa_from <= last_aa) /* overlap due to
2963
codons */
2964
aa_from = last_aa+1; /* set up to merge
2965
*/
2966
}
2967
2968
if (aa_from <= aa_to || (allowTerminator && aa_from == aa_to + 1))
2969
{
2970
if(loc != NULL)
2971
{
2972
if(aa_loc == NULL)
2973
load_fuzz_to_DNA(loc, location_loc,
2974
TRUE);
2975
SeqLocAdd(&aa_loc, loc, merge, FALSE);
2976
}
2977
loc = SeqLocIntNew(aa_from, aa_to, 0, aa_sip);
2978
last_aa = aa_to;
2979
}
2980
}
2981
2982
product_len += SeqLocLen(slp);
2983
}
2984
2985
if(loc != NULL)
2986
{
2987
if(aa_loc == NULL)
2988
load_fuzz_to_DNA(loc, location_loc, TRUE);
2989
load_fuzz_to_DNA(loc, location_loc, FALSE);
2990
SeqLocAdd(&aa_loc, loc, merge, FALSE);
2991
}
2992
if (frame != NULL)
2993
*frame = a_left % 3;
2994
2995
return SeqLocPackage(aa_loc);
2996
}
2527
2997
2528
2998
static SeqLocPtr BuildProtLoc (SeqFeatPtr overlapping_cds, SeqLocPtr slp, Int4Ptr frame)
2529
2999
{
2544
3014
is_ordered = TRUE;
2545
3015
} else {
2546
3016
if (first) {
2547
aa_loc = dnaLoc_to_aaLoc (overlapping_cds, tmp_loc, FALSE, frame, FALSE);
3017
aa_loc = MYdnaLoc_to_aaLoc (overlapping_cds, tmp_loc, FALSE, frame, FALSE);
2548
3018
first = FALSE;
2549
3019
} else {
2550
aa_loc = dnaLoc_to_aaLoc (overlapping_cds, tmp_loc, FALSE, NULL, FALSE);
3020
aa_loc = MYdnaLoc_to_aaLoc (overlapping_cds, tmp_loc, FALSE, NULL, FALSE);
2551
3021
}
2552
3022
}
2553
3023
if (last_loc == NULL) {
2581
3051
2582
3052
/*---------------------------------------------------------------------*/
2583
3053
/* */
2584
/* FeatConvertImpToPeptide () - Convert a given import feature to a */
3054
/* ConvertImpToProt () - Convert a given import feature to a */
2585
3055
/* protein feature. */
2586
3056
/* */
2587
3057
/* Note : Any of the Import feature's gbquals that can be converted */
2591
3061
/* */
2592
3062
/*---------------------------------------------------------------------*/
2593
3063
2594
static void FeatConvertImpToPeptide (SeqFeatPtr sfp,
2595
Uint1 toFeatSubType,
2596
Uint2 entityID)
3064
static Boolean ConvertImpToProt
3065
(SeqFeatPtr sfp,
3066
Uint2 featdef_to,
3067
Pointer extradata)
2597
3068
{
2598
3069
ImpFeatPtr ifp;
2599
3070
SeqFeatPtr cds;
2603
3074
ProtRefPtr prp;
2604
3075
SeqIdPtr sip;
2605
3076
BioseqPtr bsp;
3077
SeqMgrFeatContext fcontext;
2606
3078
3079
if (sfp == NULL || sfp->data.choice != SEQFEAT_IMP)
3080
{
3081
return FALSE;
3082
}
2607
3083
/* Get the Import Feature */
2608
3084
2609
3085
ifp = (ImpFeatPtr) sfp->data.value.ptrvalue;
2610
3086
if (NULL == ifp)
2611
return;
3087
{
3088
return FALSE;
3089
}
2612
3090
2613
3091
/* Convert the location to a protein location */
2614
2615
cds = FindBestCds (entityID, sfp->location, NULL, NULL);
3092
cds = SeqMgrGetOverlappingCDS (sfp->location, &fcontext);
2616
3093
if (cds == NULL)
2617
return;
3094
{
3095
return FALSE;
3096
}
2618
3097
2619
3098
slp = BuildProtLoc (cds, sfp->location, &frame);
2620
3099
if (slp == NULL)
2621
return;
3100
{
3101
return FALSE;
3102
}
2622
3103
2623
3104
/* Create a new generic feature */
2624
3105
2625
3106
sip = SeqLocId (cds->product);
2626
3107
if (sip == NULL)
2627
return;
3108
{
3109
slp = SeqLocFree (slp);
3110
return FALSE;
3111
}
2628
3112
2629
3113
bsp = BioseqLockById (sip);
2630
3114
if (bsp == NULL)
2631
return;
3115
{
3116
slp = SeqLocFree (slp);
3117
return FALSE;
3118
}
2632
3119
2633
3120
newSfp = CreateNewFeatureOnBioseq (bsp, SEQFEAT_PROT, slp);
2634
3121
BioseqUnlock (bsp);
2635
3122
if (newSfp == NULL)
2636
return;
3123
{
3124
slp = SeqLocFree (slp);
3125
return FALSE;
3126
}
2637
3127
2638
3128
/* Make it into a protein feature */
2639
3129
2640
3130
prp = ProtRefNew ();
2641
3131
newSfp->data.value.ptrvalue = (Pointer) prp;
2642
3132
if (NULL == prp)
2643
return;
3133
{
3134
slp = SeqLocFree (slp);
3135
newSfp = SeqFeatFree (newSfp);
3136
return FALSE;
3137
}
2644
3138
2645
switch (toFeatSubType) {
3139
switch (featdef_to) {
2646
3140
case FEATDEF_mat_peptide_aa :
2647
3141
prp->processed = 2;
2648
3142
break;
2654
3148
break;
2655
3149
}
2656
3150
2657
sfp->idx.subtype = toFeatSubType;
2658
2659
3151
/* Transfer unchanged fields from old feature */
2660
3152
2661
3153
newSfp->partial = sfp->partial;
2686
3178
/* Mark the old feature for deletion */
2687
3179
2688
3180
sfp->idx.deleteme = TRUE;
2689
}
2690
2691
/*---------------------------------------------------------------------*/
2692
/* */
2693
/* FeatConvertPeptideToImp () - */
2694
/* */
2695
/*---------------------------------------------------------------------*/
2696
2697
static void FeatConvertPeptideToImp (SeqFeatPtr sfp, Uint2 entityID)
3181
return TRUE;
3182
}
3183
3184
3185
static SeqLocPtr FindNucleotideLocationForProteinFeatureConversion (SeqLocPtr slp, Uint2 entityID)
3186
{
3187
SeqFeatPtr cds;
3188
3189
cds = FindBestCds (entityID, NULL, slp, NULL);
3190
if (NULL == cds)
3191
{
3192
return NULL;
3193
}
3194
3195
return aaLoc_to_dnaLoc (cds, slp);
3196
}
3197
3198
/*---------------------------------------------------------------------*/
3199
/* */
3200
/* ConvertProtToImp () - */
3201
/* */
3202
/*---------------------------------------------------------------------*/
3203
3204
static Boolean ConvertProtToImp (SeqFeatPtr sfp, Uint2 featdef_to, Pointer extradata)
2698
3205
{
2699
3206
ProtRefPtr prp;
2700
SeqFeatPtr cds;
2701
3207
SeqLocPtr slp;
2702
3208
ImpFeatPtr ifp;
2703
3209
CharPtr name;
2710
3216
DbtagPtr dbt;
2711
3217
Char idStr[64];
2712
3218
ObjectIdPtr oip;
3219
Uint2 entityID;
2713
3220
2714
3221
/* Make sure that we have a matching peptide feature */
2715
3222
2716
if (sfp->data.choice != SEQFEAT_PROT)
2717
return;
3223
if (sfp == NULL || sfp->data.choice != SEQFEAT_PROT)
3224
{
3225
return FALSE;
3226
}
3227
entityID = sfp->idx.entityID;
2718
3228
2719
3229
prp = (ProtRefPtr) sfp->data.value.ptrvalue;
2720
3230
if (NULL == prp)
2721
return;
3231
{
3232
return FALSE;
3233
}
2722
3234
2723
3235
switch (sfp->idx.subtype) {
2724
3236
case FEATDEF_mat_peptide_aa :
2725
3237
if (2 != prp->processed)
2726
return;
3238
return FALSE;
2727
3239
break;
2728
3240
case FEATDEF_sig_peptide_aa :
2729
3241
if (3 != prp->processed)
2730
return;
3242
return FALSE;
2731
3243
break;
2732
3244
case FEATDEF_transit_peptide_aa :
2733
3245
if (4 != prp->processed)
2734
return;
3246
return FALSE;
2735
3247
break;
2736
3248
}
2737
3249
2738
3250
/* Convert the location from the protein */
2739
3251
/* to the nucleotide Bioseq. */
2740
3252
2741
cds = FindBestCds (entityID, NULL, sfp->location, NULL);
2742
if (NULL == cds)
2743
return;
3253
slp = FindNucleotideLocationForProteinFeatureConversion (sfp->location, entityID);
2744
3254
2745
slp = aaLoc_to_dnaLoc (cds, sfp->location);
2746
3255
if (NULL == slp)
2747
return;
3256
return FALSE;
2748
3257
sfp->location = SeqLocFree (sfp->location);
2749
3258
sfp->location = slp;
2750
3259
2753
3262
2754
3263
ifp = ImpFeatNew ();
2755
3264
if (NULL == ifp)
2756
return;
3265
{
3266
return FALSE;
3267
}
2757
3268
2758
3269
switch (sfp->idx.subtype) {
2759
3270
case FEATDEF_mat_peptide_aa :
2783
3294
if (name != NULL) {
2784
3295
gbqual = GBQualNew ();
2785
3296
if (NULL == gbqual)
2786
return;
3297
return FALSE;
2787
3298
topOfGbqList = gbqual;
2788
3299
gbqual->qual = StringSave ("product");
2789
3300
gbqual->val = StringSave (name);
2799
3310
if (ec != NULL) {
2800
3311
gbqual = GBQualNew ();
2801
3312
if (NULL == gbqual)
2802
return;
3313
return FALSE;
2803
3314
prevGbq->next = gbqual;
2804
3315
gbqual->qual = StringSave ("EC_number");
2805
3316
gbqual->val = StringSave (ec);
2815
3326
if (NULL != activity) {
2816
3327
gbqual = GBQualNew ();
2817
3328
if (NULL == gbqual)
2818
return;
3329
return FALSE;
2819
3330
prevGbq->next = gbqual;
2820
3331
gbqual->qual = StringSave ("function");
2821
3332
gbqual->val = StringSave (activity);
2826
3337
for (vnp = prp->db; vnp != NULL; vnp = vnp->next) {
2827
3338
dbt = (DbtagPtr) vnp->data.ptrvalue;
2828
3339
if (NULL == dbt )
2829
return;
3340
continue;
2830
3341
if (! StringHasNoText (dbt->db)) {
2831
3342
gbqual = GBQualNew ();
2832
3343
if (NULL == gbqual)
2833
return;
3344
continue;
2834
3345
prevGbq->next = gbqual;
2835
3346
oip = dbt->tag;
2836
3347
if (oip->str != NULL && (! StringHasNoText (oip->str))) {
2837
sprintf (idStr, "%s:%s", (CharPtr)dbt->tag, oip->str);
2838
gbqual->qual = StringSave ("db_xref");
2839
gbqual->val = StringSave (idStr);
3348
sprintf (idStr, "%s:%s", (CharPtr)dbt->tag, oip->str);
3349
gbqual->qual = StringSave ("db_xref");
3350
gbqual->val = StringSave (idStr);
2840
3351
} else {
2841
sprintf (idStr, "%s:%ld", (CharPtr)dbt->tag, (long) oip->id);
2842
gbqual->qual = StringSave ("db_xref");
2843
gbqual->val = StringSave (idStr);
3352
sprintf (idStr, "%s:%ld", (CharPtr)dbt->tag, (long) oip->id);
3353
gbqual->qual = StringSave ("db_xref");
3354
gbqual->val = StringSave (idStr);
2844
3355
}
2845
3356
prevGbq = gbqual;
2846
3357
}
2854
3365
/* Free the obsolete Protein reference */
2855
3366
2856
3367
ProtRefFree (prp);
3368
return TRUE;
3369
}
3370
3371
static CharPtr SubSourceText (BioSourcePtr biop, Uint1 subtype, BoolPtr found)
3372
{
3373
Int4 subtype_len = 0;
3374
SubSourcePtr ssp;
3375
CharPtr subtype_txt = NULL;
3376
3377
if (biop == NULL || biop->subtype == NULL) return NULL;
3378
for (ssp = biop->subtype; ssp != NULL; ssp = ssp->next) {
3379
if (ssp->subtype == subtype) {
3380
if (found != NULL) *found = TRUE;
3381
if (!StringHasNoText (ssp->name)) {
3382
subtype_len += StringLen (ssp->name) + 1;
3383
}
3384
}
3385
}
3386
if (subtype_len == 0) return NULL;
3387
subtype_txt = (CharPtr) MemNew (sizeof (Char) * subtype_len);
3388
for (ssp = biop->subtype; ssp != NULL; ssp = ssp->next) {
3389
if (ssp->subtype == subtype && !StringHasNoText (ssp->name)) {
3390
if (!StringHasNoText (subtype_txt)) {
3391
StringCat (subtype_txt, ";");
3392
}
3393
StringCat (subtype_txt, ssp->name);
3394
}
3395
}
3396
return subtype_txt;
3397
}
3398
3399
static CharPtr OrgModText (BioSourcePtr biop, Uint1 subtype, BoolPtr found)
3400
{
3401
Int4 subtype_len = 0;
3402
OrgModPtr omp;
3403
CharPtr subtype_txt = NULL;
3404
3405
if (biop == NULL
3406
|| biop->org == NULL
3407
|| biop->org->orgname == NULL
3408
|| biop->org->orgname->mod == NULL) {
3409
return NULL;
3410
}
3411
3412
for (omp = biop->org->orgname->mod; omp != NULL; omp = omp->next) {
3413
if (omp->subtype == subtype) {
3414
if (found != NULL) *found = TRUE;
3415
if (!StringHasNoText (omp->subname)) {
3416
subtype_len += StringLen (omp->subname) + 1;
3417
}
3418
}
3419
}
3420
if (subtype_len == 0) return NULL;
3421
subtype_txt = (CharPtr) MemNew (sizeof (Char) * subtype_len);
3422
for (omp = biop->org->orgname->mod; omp != NULL; omp = omp->next) {
3423
if (omp->subtype == subtype && !StringHasNoText (omp->subname)) {
3424
if (!StringHasNoText (subtype_txt)) {
3425
StringCat (subtype_txt, ";");
3426
}
3427
StringCat (subtype_txt, omp->subname);
3428
}
3429
}
3430
return subtype_txt;
3431
}
3432
3433
static CharPtr NoteText (BioSourcePtr biop, CharPtr comment)
3434
{
3435
CharPtr orgmod_note, subsource_note;
3436
Int4 text_len = 0;
3437
CharPtr note_text = NULL;
3438
3439
orgmod_note = OrgModText(biop, ORGMOD_other, NULL);
3440
if (!StringHasNoText (orgmod_note)) {
3441
text_len += StringLen (orgmod_note) + 1;
3442
}
3443
subsource_note = SubSourceText (biop, SUBSRC_other, NULL);
3444
if (!StringHasNoText (subsource_note)) {
3445
text_len += StringLen (subsource_note) + 1;
3446
}
3447
if (!StringHasNoText (comment)) {
3448
text_len += StringLen (comment) + 1;
3449
}
3450
3451
if (text_len == 0) return NULL;
3452
3453
note_text = (CharPtr) MemNew (sizeof(Char) * text_len);
3454
if (!StringHasNoText (orgmod_note)) {
3455
StringCat (note_text, orgmod_note);
3456
}
3457
orgmod_note = MemFree (orgmod_note);
3458
if (!StringHasNoText (subsource_note)) {
3459
if (!StringHasNoText (note_text)) {
3460
StringCat (note_text, ";");
3461
}
3462
StringCat (note_text, subsource_note);
3463
}
3464
subsource_note = MemFree (subsource_note);
3465
3466
if (!StringHasNoText (comment)) {
3467
if (!StringHasNoText (note_text)) {
3468
StringCat (note_text, ";");
3469
}
3470
StringCat (note_text, comment);
3471
}
3472
return note_text;
2857
3473
}
2858
3474
2859
3475
/*---------------------------------------------------------------------*/
2860
3476
/* */
2861
/* FeatConvertBioSrcToRepeatRegion () */
3477
/* ConvertBioSrcToRepeatRegion () */
2862
3478
/* */
2863
3479
/* 9/28/2004: Changed to convert all BioSource features with notes */
2864
3480
/* instead of ones with transposon or insertion_seq qualifiers. */
2865
3481
/*---------------------------------------------------------------------*/
2866
3482
2867
static void FeatConvertBioSrcToRepeatRegion (SeqFeatPtr sfp)
3483
static Boolean ConvertBioSrcToRepeatRegion (SeqFeatPtr sfp, Uint2 featdef_to, Pointer extradata)
2868
3484
{
2869
3485
BioSourcePtr biop;
2870
3486
GBQualPtr gbqual;
2871
3487
ImpFeatPtr ifp;
2872
OrgModPtr omp = NULL;
2873
SubSourcePtr ssp = NULL;
2874
CharPtr text_to_use = NULL;
2875
Int4 text_len = 0;
3488
CharPtr transposon_txt, insertion_seq_txt, note_txt;
3489
Boolean is_transposon = FALSE, is_insertion_seq = FALSE;
2876
3490
2877
/* Only convert transposon and insertion_seq features */
3491
if (sfp == NULL || sfp->idx.subtype != FEATDEF_BIOSRC) return FALSE;
2878
3492
2879
3493
biop = (BioSourcePtr) sfp->data.value.ptrvalue;
2880
for (ssp = biop->subtype;
2881
ssp != NULL && ssp->subtype != SUBSRC_other;
2882
ssp = ssp->next)
2883
{
2884
}
2885
if (biop->org != NULL && biop->org->orgname != NULL)
2886
{
2887
for (omp = biop->org->orgname->mod;
2888
omp != NULL && omp->subtype != ORGMOD_other;
2889
omp = omp->next)
2890
{
2891
}
2892
}
2893
3494
3495
transposon_txt = SubSourceText (biop, SUBSRC_transposon_name, &is_transposon);
3496
insertion_seq_txt = SubSourceText (biop, SUBSRC_insertion_seq_name, &is_insertion_seq);
3497
note_txt = NoteText (biop, sfp->comment);
3498
2894
3499
2895
3500
/* Create a new Import Feature */
2896
3501
2897
3502
ifp = ImpFeatNew ();
2898
3503
if (NULL == ifp)
2899
return;
3504
return FALSE;
2900
3505
ifp->key = StringSave ("repeat_region");
2901
3506
2902
3507
/* Copy relevant info from the BioSource */
2903
3508
/* feature to the Import feature. */
2904
3509
2905
if (ssp != NULL)
2906
{
2907
text_len += StringLen (ssp->name) + 1;
2908
}
2909
if (omp != NULL)
2910
{
2911
text_len += StringLen (omp->subname) + 1;
2912
}
2913
if (text_len > 0)
2914
{
2915
text_to_use = (CharPtr) MemNew (text_len * sizeof (Char));
2916
if (text_to_use != NULL)
2917
{
2918
text_to_use [0] = 0;
2919
if (ssp != NULL)
2920
{
2921
StringCat (text_to_use, ssp->name);
2922
}
2923
if (omp != NULL)
2924
{
2925
if (!StringHasNoText (text_to_use))
2926
{
2927
StringCat (text_to_use, ";");
2928
}
2929
StringCat (text_to_use, omp->subname);
2930
}
2931
gbqual = GBQualNew ();
2932
if (gbqual != NULL)
2933
{
2934
gbqual->qual = StringSave ("note");
2935
gbqual->val = text_to_use;
2936
gbqual->next = sfp->qual;
2937
sfp->qual = gbqual;
2938
}
2939
}
2940
}
2941
3510
2942
3511
/* Delete the old BioSource feature */
2943
3512
2947
3516
2948
3517
sfp->data.choice = SEQFEAT_IMP;
2949
3518
sfp->data.value.ptrvalue = ifp;
3519
3520
if (is_transposon) {
3521
gbqual = GBQualNew ();
3522
gbqual->qual = StringSave ("mobile_element");
3523
gbqual->val = (CharPtr) MemNew (sizeof(Char) * (StringLen (transposon_txt) + 12));
3524
StringCat (gbqual->val, "transposon:");
3525
StringCat (gbqual->val, transposon_txt);
3526
gbqual->next = sfp->qual;
3527
sfp->qual = gbqual;
3528
}
3529
transposon_txt = MemFree (transposon_txt);
3530
3531
if (is_insertion_seq) {
3532
gbqual = GBQualNew ();
3533
gbqual->qual = StringSave ("mobile_element");
3534
gbqual->val = (CharPtr) MemNew (sizeof(Char) * (StringLen (insertion_seq_txt) + 19));
3535
StringCat (gbqual->val, "insertion sequence:");
3536
StringCat (gbqual->val, insertion_seq_txt);
3537
gbqual->next = sfp->qual;
3538
sfp->qual = gbqual;
3539
}
3540
insertion_seq_txt = MemFree (insertion_seq_txt);
3541
3542
sfp->comment = MemFree (sfp->comment);
3543
sfp->comment = note_txt;
3544
return TRUE;
2950
3545
}
2951
3546
2952
3547
2953
static void FeatConvertRegionToProt (SeqFeatPtr sfp, Int2 toFeatSubType)
3548
static Boolean ConvertRegionToProt (SeqFeatPtr sfp, Uint2 featdef_to, Pointer extradata)
2954
3549
{
2955
3550
BioseqPtr bsp;
2956
3551
ProtRefPtr prp;
2959
3554
2960
3555
if (sfp == NULL || sfp->data.choice != SEQFEAT_REGION)
2961
3556
{
2962
return;
3557
return FALSE;
2963
3558
}
2964
3559
2965
3560
/* only convert features that are on protein sequences */
2969
3564
cds = SeqMgrGetOverlappingCDS (sfp->location, NULL);
2970
3565
if (cds == NULL)
2971
3566
{
2972
return;
3567
return FALSE;
2973
3568
}
2974
3569
else
2975
3570
{
2987
3582
{
2988
3583
/* use region name for protein name */
2989
3584
prp->name->data.ptrvalue = sfp->data.value.ptrvalue;
2990
switch (toFeatSubType)
3585
switch (featdef_to)
2991
3586
{
2992
3587
case FEATDEF_PROT :
2993
3588
prp->processed = 0;
3012
3607
sfp->data.choice = SEQFEAT_PROT;
3013
3608
}
3014
3609
}
3610
return TRUE;
3015
3611
}
3016
3612
3017
3613
extern EnumFieldAssoc enum_bond_alist [];
3038
3634
{"function", Class_text},
3039
3635
{"gene", Class_text},
3040
3636
{"gdb_xref", Class_text},
3041
{"insertion_seq", Class_text},
3042
3637
{"label", Class_token},
3043
3638
{"map", Class_text},
3639
{"mobile_element", Class_text},
3044
3640
{"mod_base", Class_token}, {"note", Class_note},
3045
3641
{"number", Class_number},
3046
3642
#ifdef INTERNAL_NCBI_SEQUIN
3047
3643
{"old_locus_tag", Class_text},
3048
3644
#endif
3645
{"operon", Class_text},
3049
3646
{"organism", Class_text},
3050
3647
{"partial", Class_none}, {"PCR_conditions", Class_text},
3051
3648
{"phenotype", Class_text},
3057
3654
{"sequenced_mol", Class_text},
3058
3655
{"standard_name", Class_text},
3059
3656
{"translation", Class_text}, {"transl_except", Class_pos_aa},
3060
{"transl_table", Class_int}, {"transposon", Class_text},
3657
{"transl_table", Class_int},
3061
3658
{"usedin", Class_token},
3062
3659
{"focus", Class_none},
3063
3660
{"protein_id", Class_text},
3071
3668
#define QUAL_EVIDENCE 13
3072
3669
#define QUAL_EXPERIMENT 15
3073
3670
3074
static ENUM_ALIST(subsource_and_orgmod_subtype_alistX)
3075
{" ", 0},
3076
{"Acronym", 19},
3077
{"Anamorph", 29},
3078
{"Authority", 24},
3079
{"Biotype", 14},
3080
{"Biovar", 13},
3081
{"Breed", 31},
3082
{"Cell-line", 108},
3083
{"Cell-type", 109},
3084
{"Chemovar", 12},
3085
{"Chromosome", 101},
3086
{"Clone", 103},
3087
{"Clone-lib", 111},
3088
{"Collected-by", 131},
3089
{"Collection-date", 130},
3090
{"Common", 18},
3091
{"Country", 123},
3092
{"Cultivar", 10},
3093
{"Dev-stage", 112},
3094
{"Dosage", 20},
3095
{"Ecotype", 27},
3096
{"Endogenous-virus-name", 125},
3097
{"Environmental-sample", 127},
3098
{"Forma", 25},
3099
{"Forma-specialis", 26},
3100
{"Frequency", 113},
3101
{"Fwd-PCR-primer-name", 135},
3102
{"Fwd-PCR-primer-seq", 133},
3103
{"Genotype", 106},
3104
{"Germline", 114},
3105
{"Group", 15},
3106
{"Haplotype", 105},
3107
{"Identified_by", 132},
3108
{"Ins-seq-name", 121},
3109
{"Isolate", 17},
3110
{"Isolation-source", 128},
3111
{"Lab-host", 116},
3112
{"Lat-lon", 129},
3113
{"Map", 102},
3114
{"Note - OrgMod", 55},
3115
{"Note - SubSource", 155},
3116
{"Old Lineage", 53}, /* 253 */
3117
{"Old Name", 54}, /* 254 */
3118
{"Pathovar", 11},
3119
{"Plasmid-name", 119},
3120
{"Plastid-name", 122},
3121
{"Pop-variant", 117},
3122
{"Rearranged", 115},
3123
{"Rev-PCR-primer-name", 136},
3124
{"Rev-PCR-primer-seq", 134},
3125
{"Segment", 124},
3126
{"Serogroup", 8},
3127
{"Serotype", 7},
3128
{"Serovar", 9},
3129
{"Sex", 107},
3130
{"Specific-host", 21},
3131
{"Specimen-voucher", 23},
3132
{"Strain", 2},
3133
{"Sub-species", 22},
3134
{"Subclone", 104},
3135
{"Subgroup", 16},
3136
{"Substrain", 3},
3137
{"Subtype", 5},
3138
{"Synonym", 28},
3139
{"Teleomorph", 30},
3140
{"Tissue-lib", 118},
3141
{"Tissue-type", 110},
3142
{"Transgenic", 126},
3143
{"Transposon-name", 120},
3144
{"Type", 4},
3145
{"Variety", 6},
3146
END_ENUM_ALIST
3147
3671
3148
3672
static ENUM_ALIST(biosource_genome_alistX)
3149
3673
{" ", 0},
3294
3818
3295
3819
extern Uint1 FindTypeForModNameText (CharPtr cp)
3296
3820
{
3297
EnumFieldAssocPtr ap;
3298
3299
for (ap = subsource_and_orgmod_subtype_alistX; ap->name != NULL; ap++)
3300
{
3301
if (DoModNamesMatch (ap->name, cp))
3302
{
3303
return ap->value;
3821
Uint1 subtype;
3822
3823
subtype = EquivalentSubSource (cp);
3824
if (subtype == 0) {
3825
subtype = EquivalentOrgMod (cp);
3826
if (subtype > 200) {
3827
/* function that calls this expects less than 100 vals for orgmod */
3828
/* need to adjust for old-lineage and old-name */
3829
subtype -= 200;
3304
3830
}
3305
}
3306
return 255;
3831
} else {
3832
/* function that calls this uses >100 to decide if subsource */
3833
subtype += 100;
3834
}
3835
if (subtype == 0) {
3836
subtype = SUBSRC_other;
3837
}
3838
return subtype;
3307
3839
}
3308
3840
3309
3841
static CharPtr GetValueNameFromEnum (Int4 val, EnumFieldAssocPtr list)
3447
3979
}
3448
3980
}
3449
3981
3450
static void LocationConstraintClearText (LocationConstraintPtr lcp)
3982
static void LocationConstraintXClearText (LocationConstraintXPtr lcp)
3451
3983
{
3452
3984
if (lcp != NULL)
3453
3985
{
3456
3988
}
3457
3989
}
3458
3990
3459
static LocationConstraintPtr LocationConstraintFree (LocationConstraintPtr lcp)
3991
static LocationConstraintXPtr LocationConstraintXFree (LocationConstraintXPtr lcp)
3460
3992
{
3461
3993
lcp = MemFree (lcp);
3462
3994
return lcp;
3463
3995
}
3464
3996
3465
static LocationConstraintPtr LocationConstraintCopy (LocationConstraintPtr lcp)
3997
static LocationConstraintXPtr LocationConstraintXCopy (LocationConstraintXPtr lcp)
3466
3998
{
3467
LocationConstraintPtr lcp_new;
3999
LocationConstraintXPtr lcp_new;
3468
4000
if (lcp == NULL)
3469
4001
{
3470
4002
return NULL;
3471
4003
}
3472
lcp_new = (LocationConstraintPtr) MemNew (sizeof (LocationConstraintData));
4004
lcp_new = (LocationConstraintXPtr) MemNew (sizeof (LocationConstraintXData));
3473
4005
if (lcp_new != NULL)
3474
4006
{
3475
4007
lcp_new->left = lcp->left;
3482
4014
return lcp_new;
3483
4015
}
3484
4016
3485
extern StringConstraintPtr StringConstraintFree (StringConstraintPtr scp)
4017
extern StringConstraintXPtr StringConstraintXFree (StringConstraintXPtr scp)
3486
4018
{
3487
4019
if (scp == NULL) return NULL;
3488
4020
scp->match_text = MemFree (scp->match_text);
3490
4022
return scp;
3491
4023
}
3492
4024
3493
static void StringConstraintClearText (StringConstraintPtr scp)
4025
static void StringConstraintClearText (StringConstraintXPtr scp)
3494
4026
{
3495
4027
if (scp != NULL)
3496
4028
{
3498
4030
}
3499
4031
}
3500
4032
3501
static StringConstraintPtr StringConstraintCopy (StringConstraintPtr scp)
4033
static StringConstraintXPtr StringConstraintCopy (StringConstraintXPtr scp)
3502
4034
{
3503
StringConstraintPtr scp_new;
4035
StringConstraintXPtr scp_new;
3504
4036
if (scp == NULL)
3505
4037
{
3506
4038
return NULL;
3507
4039
}
3508
4040
3509
scp_new = (StringConstraintPtr) MemNew (sizeof (StringConstraintData));
4041
scp_new = (StringConstraintXPtr) MemNew (sizeof (StringConstraintData));
3510
4042
if (scp_new != NULL)
3511
4043
{
3512
4044
scp_new->match_text = StringSave (scp->match_text);
3537
4069
{
3538
4070
if (scp == NULL) return NULL;
3539
4071
scp->qual_choice = ValNodeFuncFree (scp->qual_choice, scp->free_vn_proc);
3540
scp->string_constraint = StringConstraintFree (scp->string_constraint);
4072
scp->qual_choice_match = ValNodeFuncFree (scp->qual_choice, scp->free_vn_proc);
4073
scp->string_constraint = StringConstraintXFree (scp->string_constraint);
3541
4074
scp->pseudo_constraint = MemFree (scp->pseudo_constraint);
3542
4075
scp = MemFree (scp);
3543
4076
return scp;
3569
4102
{
3570
4103
ccp_new->constraint_type = ccp->constraint_type;
3571
4104
ccp_new->qual_choice = QualChoiceCopy (ccp->qual_choice, ccp->copy_vn_proc);
4105
ccp_new->qual_choice_match = QualChoiceCopy (ccp->qual_choice_match, ccp->copy_vn_proc);
3572
4106
ccp_new->string_constraint = StringConstraintCopy (ccp->string_constraint);
3573
4107
ccp_new->copy_vn_proc = ccp->copy_vn_proc;
3574
4108
ccp_new->free_vn_proc = ccp->free_vn_proc;
3591
4125
{
3592
4126
StringConstraintClearText (fsp->scp);
3593
4127
ChoiceConstraintClearText (fsp->ccp);
3594
LocationConstraintClearText (fsp->lcp);
4128
LocationConstraintXClearText (fsp->lcp);
4129
StringConstraintClearText (fsp->id_list);
3595
4130
}
3596
4131
}
3597
4132
3605
4140
fsp_new->ccp = NULL;
3606
4141
fsp_new->lcp = NULL;
3607
4142
fsp_new->cgp = NULL;
4143
fsp_new->id_list = NULL;
3608
4144
}
3609
4145
return fsp_new;
3610
4146
}
3613
4149
{
3614
4150
if (fsp != NULL)
3615
4151
{
3616
fsp->scp = StringConstraintFree (fsp->scp);
4152
fsp->scp = StringConstraintXFree (fsp->scp);
3617
4153
fsp->ccp = ChoiceConstraintFree (fsp->ccp);
3618
fsp->lcp = LocationConstraintFree (fsp->lcp);
4154
fsp->lcp = LocationConstraintXFree (fsp->lcp);
3619
4155
fsp->cgp = ChoiceConstraintFree (fsp->cgp);
4156
fsp->id_list = StringConstraintXFree (fsp->id_list);
3620
4157
fsp = MemFree (fsp);
3621
4158
}
3622
4159
return fsp;
3635
4172
{
3636
4173
fsp_new->scp = StringConstraintCopy (fsp->scp);
3637
4174
fsp_new->ccp = ChoiceConstraintCopy (fsp->ccp);
3638
fsp_new->lcp = LocationConstraintCopy (fsp->lcp);
4175
fsp_new->lcp = LocationConstraintXCopy (fsp->lcp);
3639
4176
fsp_new->cgp = ChoiceConstraintCopy (fsp->cgp);
4177
fsp_new->id_list = StringConstraintCopy (fsp->id_list);
3640
4178
}
3641
4179
return fsp_new;
3642
4180
}
3706
4244
#define PARSE_FIELD_BIOSRC_STRING 2
3707
4245
#define PARSE_FIELD_SOURCE_QUAL 3
3708
4246
#define PARSE_FIELD_GENE_FIELD 4
3709
#define PARSE_FIELD_MRNA_FIELD 5
4247
#define PARSE_FIELD_RNA_FIELD 5
3710
4248
#define PARSE_FIELD_CDS_COMMENT 6
3711
4249
#define PARSE_FIELD_PROTEIN_FIELD 7
3712
4250
#define PARSE_FIELD_IMPORT_QUAL 8
3713
4251
#define PARSE_FIELD_FEATURE_NOTE 9
3714
4252
#define PARSE_FIELD_COMMENT_DESC 10
4253
#define PARSE_FIELD_DBXREF 11
3715
4254
3716
#define MAX_PARSE_FIELD_TYPE 10
4255
#define MAX_PARSE_FIELD_TYPE 11
4256
#define SEARCH_FIELD_PUBLICATION 12
3717
4257
3718
4258
#define PARSE_FIELD_FIRST_FEATURE 4
3719
4259
#define PARSE_FIELD_LAST_FEATURE 9
3720
4260
3721
extern Boolean DoesLocationMatchConstraint (SeqLocPtr slp, LocationConstraintPtr lcp);
4261
extern Boolean DoesLocationMatchConstraint (SeqLocPtr slp, LocationConstraintXPtr lcp);
3722
4262
3723
4263
typedef struct acceptpolicy
3724
4264
{
3972
4512
type_list[sfp->idx.subtype] = TRUE;
3973
4513
}
3974
4514
4515
4516
static void AddFeatureToList (ValNodePtr PNTR list, FeatDefPtr curr)
4517
{
4518
Char str [256];
4519
4520
if (list == NULL || curr == NULL) return;
4521
4522
if (curr->featdef_key == FEATDEF_PUB)
4523
{
4524
StringNCpy_0 (str, curr->typelabel, sizeof (str) - 15);
4525
StringCat (str, " (Publication)");
4526
ValNodeAddPointer (list, curr->featdef_key, StringSave (str));
4527
}
4528
else if (curr->featdef_key == FEATDEF_BIOSRC)
4529
{
4530
ValNodeAddPointer (list, FEATDEF_BIOSRC, StringSave ("BioSource"));
4531
}
4532
else if (curr->featdef_key == FEATDEF_otherRNA)
4533
{
4534
ValNodeAddPointer (list, FEATDEF_otherRNA, StringSave ("misc_RNA"));
4535
}
4536
else if (curr->featdef_key == FEATDEF_misc_RNA ||
4537
curr->featdef_key == FEATDEF_precursor_RNA ||
4538
curr->featdef_key == FEATDEF_mat_peptide ||
4539
curr->featdef_key == FEATDEF_sig_peptide ||
4540
curr->featdef_key == FEATDEF_transit_peptide ||
4541
curr->featdef_key == FEATDEF_Imp_CDS)
4542
{
4543
StringNCpy_0 (str, curr->typelabel, sizeof (str) - 10);
4544
StringCat (str, "_imp");
4545
ValNodeAddPointer (list, curr->featdef_key, StringSave (str));
4546
}
4547
else
4548
{
4549
ValNodeAddPointer (list, curr->featdef_key, StringSave (curr->typelabel));
4550
}
4551
}
4552
3975
4553
extern ValNodePtr BuildFeatureDialogList (Boolean list_most_used_first, SeqEntryPtr sep)
3976
4554
{
3977
4555
ValNodePtr feature_choice_list = NULL;
3978
4556
ValNodePtr import_feature_list = NULL;
3979
4557
ValNodePtr least_liked_feature_list = NULL;
3980
4558
ValNodePtr most_used_feature_list = NULL;
4559
ValNodePtr unused_list = NULL;
3981
4560
FeatDefPtr curr;
3982
4561
Uint1 key;
3983
4562
CharPtr label = NULL;
3984
Char str [256];
3985
4563
Boolean feature_type_list[256];
3986
4564
Boolean only_most_used = TRUE;
3987
4565
Int4 i;
4002
4580
if (key == FEATDEF_BAD
4003
4581
|| key == FEATDEF_Imp_CDS
4004
4582
|| key == FEATDEF_source
4005
|| key == FEATDEF_ORG
4006
|| !feature_type_list[key])
4007
{
4008
curr = FeatDefFindNext (curr, &key, &label, FEATDEF_ANY, TRUE);
4009
continue;
4010
}
4011
4012
if (curr->featdef_key == FEATDEF_PUB)
4013
{
4014
StringNCpy_0 (str, curr->typelabel, sizeof (str) - 15);
4015
StringCat (str, " (Publication)");
4016
ValNodeAddPointer (&feature_choice_list, curr->featdef_key, StringSave (str));
4017
}
4018
else if (curr->featdef_key == FEATDEF_BIOSRC)
4019
{
4020
ValNodeAddPointer (&feature_choice_list, FEATDEF_BIOSRC, StringSave ("BioSource"));
4021
}
4022
else if (curr->featdef_key == FEATDEF_otherRNA)
4023
{
4024
ValNodeAddPointer (&feature_choice_list, FEATDEF_otherRNA, StringSave ("misc_RNA"));
4025
if (list_most_used_first)
4026
{
4027
/* also add to most used list */
4028
ValNodeAddPointer (&most_used_feature_list, curr->featdef_key,
4029
StringSave ("misc_RNA"));
4583
|| key == FEATDEF_ORG)
4584
{
4585
curr = FeatDefFindNext (curr, &key, &label, FEATDEF_ANY, TRUE);
4586
continue;
4587
}
4588
else if (!feature_type_list[key])
4589
{
4590
AddFeatureToList (&unused_list, curr);
4591
curr = FeatDefFindNext (curr, &key, &label, FEATDEF_ANY, TRUE);
4592
continue;
4593
}
4594
4595
if (curr->featdef_key == FEATDEF_otherRNA) {
4596
AddFeatureToList (&feature_choice_list, curr);
4597
if (list_most_used_first) {
4598
AddFeatureToList (&most_used_feature_list, curr);
4030
4599
}
4031
4600
}
4032
4601
else if (curr->featdef_key == FEATDEF_misc_RNA ||
4036
4605
curr->featdef_key == FEATDEF_transit_peptide ||
4037
4606
curr->featdef_key == FEATDEF_Imp_CDS)
4038
4607
{
4039
StringNCpy_0 (str, curr->typelabel, sizeof (str) - 10);
4040
StringCat (str, "_imp");
4041
ValNodeAddPointer (&import_feature_list, curr->featdef_key, StringSave (str));
4608
AddFeatureToList (&import_feature_list, curr);
4042
4609
}
4043
4610
else if (curr->featdef_key == FEATDEF_TXINIT)
4044
4611
{
4045
ValNodeAddPointer (&least_liked_feature_list, FEATDEF_TXINIT, StringSave (curr->typelabel));
4612
AddFeatureToList (&least_liked_feature_list, curr);
4046
4613
}
4047
4614
else
4048
4615
{
4080
4647
CompareFeatureValNodeStrings);
4081
4648
least_liked_feature_list = SortValNode (least_liked_feature_list,
4082
4649
CompareFeatureValNodeStrings);
4650
unused_list = SortValNode (unused_list, CompareFeatureValNodeStrings);
4083
4651
4084
4652
if (most_used_feature_list != NULL && only_most_used) {
4085
4653
feature_choice_list = ValNodeFreeData (feature_choice_list);
4091
4659
feature_choice_list = ValNodeAppend (feature_choice_list, least_liked_feature_list);
4092
4660
feature_choice_list = ValNodeAppend (feature_choice_list, import_feature_list);
4093
4661
}
4662
feature_choice_list = ValNodeAppend (feature_choice_list, unused_list);
4094
4663
4095
4664
return feature_choice_list;
4096
4665
}
4257
4826
return FeatureSelectionDialogEx(h, allow_multi, NULL, change_notify, change_userdata);
4258
4827
}
4259
4828
4829
extern DialoG
4830
DescriptorSelectionDialog
4831
(GrouP h,
4832
Boolean allow_multi,
4833
Nlm_ChangeNotifyProc change_notify,
4834
Pointer change_userdata)
4835
{
4836
ValNodePtr descriptor_list = BuildDescriptorValNodeList ();
4837
return ValNodeSelectionDialogEx (h, descriptor_list, TALL_SELECTION_LIST,
4838
ValNodeStringName,
4839
ValNodeSimpleDataFree, ValNodeStringCopy,
4840
ValNodeChoiceMatch, "descriptor list",
4841
change_notify, change_userdata, allow_multi, FALSE,
4842
NULL);
4843
}
4844
4845
4260
4846
extern CharPtr SourceQualValNodeName (ValNodePtr vnp)
4261
4847
{
4262
4848
SourceQualDescPtr sqdp;
4351
4937
Nlm_ChangeNotifyProc change_notify,
4352
4938
Pointer change_userdata,
4353
4939
Int2 list_height,
4940
Boolean show_discouraged,
4354
4941
Boolean show_discontinued)
4355
4942
4356
4943
{
4362
4949
qual_choice_list = ValNodeNew (NULL);
4363
4950
qual_choice_list->choice = 1;
4364
4951
qual_choice_list->data.ptrvalue = StringSave ("All Notes");
4365
qual_choice_list->next = GetSourceQualDescList (TRUE, TRUE, show_discontinued);
4952
qual_choice_list->next = GetSourceQualDescList (TRUE, TRUE, show_discouraged, show_discontinued);
4366
4953
}
4367
4954
else
4368
4955
{
4369
qual_choice_list = GetSourceQualDescList (TRUE, TRUE, show_discontinued);
4956
qual_choice_list = GetSourceQualDescList (TRUE, TRUE, show_discouraged, show_discontinued);
4370
4957
}
4371
4958
/* note - the ValNodeSelectionDialog will free the qual_choice_list when done */
4372
4959
dlg = ValNodeSelectionDialog (h, qual_choice_list, list_height, SourceQualValNodeName,
4385
4972
4386
4973
{
4387
4974
return SourceQualTypeSelectionDialogEx (h, allow_multi, change_notify,
4388
change_userdata, 6, FALSE);
4975
change_userdata, 6, FALSE, FALSE);
4389
4976
}
4390
4977
4391
4978
static DialoG SourceQualTypeDiscSelectionDialog
4396
4983
4397
4984
{
4398
4985
return SourceQualTypeSelectionDialogEx (h, allow_multi, change_notify,
4399
change_userdata, 6, TRUE);
4986
change_userdata, 6, TRUE, TRUE);
4400
4987
}
4401
4988
4402
4989
static DialoG SourceQualTypeConstraintSelectionDialog
4407
4994
4408
4995
{
4409
4996
return SourceQualTypeSelectionDialogEx (h, allow_multi, change_notify,
4410
change_userdata, 4, TRUE);
4997
change_userdata, 4, TRUE, FALSE);
4411
4998
}
4412
4999
4413
5000
static DialoG SourceStringConstraintSelectionDialog
4424
5011
4425
5012
ValNodeAddPointer (&qual_choice_list, 1, StringSave ("Organism or Any Qual"));
4426
5013
ValNodeAddPointer (&qual_choice_list, 1, StringSave ("Organism"));
4427
qual_choice_list->next->next = GetSourceQualDescList (TRUE, TRUE, TRUE);
5014
qual_choice_list->next->next = GetSourceQualDescList (TRUE, TRUE, TRUE, FALSE);
4428
5015
ValNodeAddPointer (&qual_choice_list, 1, StringSave ("Lineage"));
5016
ValNodeAddPointer (&qual_choice_list, 1, StringSave ("Location"));
4429
5017
4430
5018
/* note - the ValNodeSelectionDialog will free the qual_choice_list when done */
4431
5019
dlg = ValNodeSelectionDialog (h, qual_choice_list, 4, SourceQualValNodeName,
4460
5048
return TRUE;
4461
5049
}
4462
5050
4463
if (DoesStringMatchConstraint (mod->subname, fsp->ccp->string_constraint))
5051
if (DoesStringMatchConstraintX (mod->subname, fsp->ccp->string_constraint))
4464
5052
{
4465
5053
if (fsp->ccp->string_constraint->not_present)
4466
5054
{
4507
5095
{
4508
5096
return TRUE;
4509
5097
}
4510
if (DoesStringMatchConstraint (ssp->name, fsp->ccp->string_constraint))
5098
if (DoesStringMatchConstraintX (ssp->name, fsp->ccp->string_constraint))
4511
5099
{
4512
5100
if (fsp->ccp->string_constraint->not_present)
4513
5101
{
4531
5119
}
4532
5120
}
4533
5121
5122
5123
static CharPtr GetSubfield (CharPtr str, Uint1 subfield)
5124
{
5125
CharPtr cp, cp2;
5126
Int4 num_colons = 0;
5127
CharPtr new_val = NULL;
5128
5129
if (StringHasNoText (str)) {
5130
return NULL;
5131
}
5132
5133
cp = StringChr (str, ':');
5134
while (cp != NULL) {
5135
num_colons ++;
5136
cp = StringChr (cp + 1, ':');
5137
}
5138
5139
if (subfield == 0) {
5140
new_val = StringSave (str);
5141
} else if (subfield == 1) {
5142
if (num_colons == 0) {
5143
return NULL;
5144
} else {
5145
cp = StringChr (str, ':');
5146
new_val = (CharPtr) MemNew (sizeof (Char) * (cp - str + 1));
5147
StringNCpy (new_val, str, cp - str);
5148
new_val[cp - str] = 0;
5149
}
5150
} else if (subfield == 2) {
5151
if (num_colons == 0 || num_colons == 1) {
5152
return NULL;
5153
} else {
5154
cp = StringChr (str, ':');
5155
cp2 = StringChr (cp + 1, ':');
5156
new_val = (CharPtr) MemNew (sizeof (Char) * (cp2 - cp));
5157
StringNCpy (new_val, cp + 1, cp2 - cp - 1);
5158
new_val[cp2 - cp - 1] = 0;
5159
}
5160
} else {
5161
if (num_colons == 0) {
5162
new_val = StringSave (str);
5163
} else {
5164
cp = StringRChr (str, ':');
5165
new_val = StringSave (cp + 1);
5166
}
5167
}
5168
return new_val;
5169
}
5170
5171
4534
5172
static CharPtr
4535
5173
GetSourceQualQualValueFromBiop
4536
5174
(BioSourcePtr biop,
4537
5175
SourceQualDescPtr sqdp,
4538
5176
FilterSetPtr fsp)
4539
5177
{
4540
CharPtr str = NULL, tmp_str;
5178
CharPtr str = NULL, field, tmp_str;
4541
5179
OrgModPtr mod;
4542
5180
SubSourcePtr ssp;
4543
5181
4557
5195
&& !StringHasNoText (mod->subname)
4558
5196
&& OrgModSpecialMatch (mod, fsp))
4559
5197
{
4560
if (str == NULL) {
4561
str = StringSave (mod->subname);
5198
field = GetSubfield (mod->subname, sqdp->subfield);
5199
if (!StringHasNoText (field)) {
5200
if (str == NULL) {
5201
str = field;
5202
} else {
5203
tmp_str = (CharPtr) MemNew ((StringLen (str) + StringLen (field) + 3) * sizeof (Char));
5204
StringCpy (tmp_str, str);
5205
StringCat (tmp_str, "; ");
5206
StringCat (tmp_str, field);
5207
field = MemFree (field);
5208
str = MemFree (str);
5209
str = tmp_str;
5210
}
4562
5211
} else {
4563
tmp_str = (CharPtr) MemNew ((StringLen (str) + StringLen (mod->subname) + 3) * sizeof (Char));
4564
StringCpy (tmp_str, str);
4565
StringCat (tmp_str, "; ");
4566
StringCat (tmp_str, mod->subname);
4567
str = MemFree (str);
4568
str = tmp_str;
5212
field = MemFree (field);
4569
5213
}
4570
5214
}
4571
5215
mod = mod->next;
4581
5225
&& !StringHasNoText (ssp->name)
4582
5226
&& SubSrcSpecialMatch (ssp, fsp))
4583
5227
{
5228
field = GetSubfield (ssp->name, sqdp->subfield);
5229
if (!StringHasNoText (field)) {
4584
5230
if (str == NULL) {
4585
str = StringSave (ssp->name);
5231
str = field;
4586
5232
} else {
4587
tmp_str = (CharPtr) MemNew ((StringLen (str) + StringLen (ssp->name) + 3) * sizeof (Char));
5233
tmp_str = (CharPtr) MemNew ((StringLen (str) + StringLen (field) + 3) * sizeof (Char));
4588
5234
StringCpy (tmp_str, str);
4589
5235
StringCat (tmp_str, "; ");
4590
StringCat (tmp_str, ssp->name);
5236
StringCat (tmp_str, field);
5237
field = MemFree (field);
4591
5238
str = MemFree (str);
4592
5239
str = tmp_str;
4593
5240
}
5241
} else {
5242
field = MemFree (field);
5243
}
4594
5244
}
4595
5245
ssp = ssp->next;
4596
5246
}
4896
5546
}
4897
5547
4898
5548
if (avp->etp == NULL
4899
|| avp->etp->existing_text_choice == EXISTING_TEXT_CHOICE_REPLACE_OLD
5549
|| avp->etp->existing_text_choice == eExistingTextChoiceReplaceOld
4900
5550
|| biop->genome == 0)
4901
5551
{
4902
5552
biop->genome = avp->field_list->choice;
4956
5606
}
4957
5607
4958
5608
if (avp->etp == NULL
4959
|| avp->etp->existing_text_choice == EXISTING_TEXT_CHOICE_REPLACE_OLD
5609
|| avp->etp->existing_text_choice == eExistingTextChoiceReplaceOld
4960
5610
|| biop->origin == 0)
4961
5611
{
4962
5612
biop->origin = avp->field_list->choice;
5011
5661
static void ApplyStringToSource (BioSourcePtr biop, Pointer userdata)
5012
5662
{
5013
5663
ApplyValuePtr avp;
5014
Boolean found = FALSE;
5015
5664
5016
5665
if (biop == NULL || userdata == NULL)
5017
5666
{
5030
5679
{
5031
5680
biop->org = OrgRefNew();
5032
5681
}
5033
if (avp->field_list->choice == 3
5034
|| avp->field_list->choice == 4)
5682
if (biop->org->orgname == NULL
5683
&& (avp->field_list->choice == 3
5684
|| avp->field_list->choice == 4))
5035
5685
{
5036
5686
biop->org->orgname = OrgNameNew ();
5037
5687
}
5126
5776
5127
5777
static void RemoveSourceQualFromBioSource (BioSourcePtr biop, Pointer userdata, FilterSetPtr fsp);
5128
5778
5779
static CharPtr RemoveSubfield (CharPtr orig, Uint1 subfield)
5780
{
5781
CharPtr cp, cp2;
5782
Int4 num_colons = 0;
5783
CharPtr new_val;
5784
5785
cp = StringChr (orig, ':');
5786
while (cp != NULL) {
5787
num_colons ++;
5788
cp = StringChr (cp + 1, ':');
5789
}
5790
new_val = orig;
5791
5792
if (subfield == 0) {
5793
new_val = MemFree (new_val);
5794
} else if (subfield == 1) {
5795
if (num_colons == 0) {
5796
/* no INST, just specID, nothing to remove */
5797
} else if (num_colons == 1) {
5798
cp = StringChr (orig, ':');
5799
new_val = StringSave (cp + 1);
5800
orig = MemFree (orig);
5801
} else {
5802
cp = StringChr (orig, ':');
5803
new_val = StringSave (cp);
5804
orig = MemFree (orig);
5805
}
5806
} else if (subfield == 2) {
5807
if (num_colons == 0 || num_colons == 1) {
5808
/* no COLL, nothing to remove */
5809
} else {
5810
cp = StringChr (orig, ':');
5811
cp2 = StringChr (cp + 1, ':');
5812
new_val = (CharPtr) MemNew (sizeof (Char) * (cp - orig + StringLen (cp2) + 1));
5813
StringNCpy (new_val, orig, cp - orig);
5814
StringCat (new_val, cp2);
5815
orig = MemFree (orig);
5816
if (StringCmp (new_val, ":") == 0) {
5817
new_val = MemFree (new_val);
5818
}
5819
}
5820
} else {
5821
/* specid */
5822
if (num_colons == 0) {
5823
new_val = MemFree (new_val);
5824
} else {
5825
cp = StringRChr (new_val, ':');
5826
*(cp + 1) = 0;
5827
}
5828
}
5829
return new_val;
5830
}
5831
5832
5833
static CharPtr ApplyToSubfield (CharPtr orig, ApplyValuePtr avp, Uint1 subfield)
5834
{
5835
CharPtr cp, cp2;
5836
Int4 num_colons = 0, len;
5837
CharPtr new_field, new_val;
5838
5839
cp = StringChr (orig, ':');
5840
while (cp != NULL) {
5841
num_colons ++;
5842
cp = StringChr (cp + 1, ':');
5843
}
5844
5845
new_val = orig;
5846
if (subfield == 0) {
5847
/* whole field */
5848
new_val = HandleApplyValue (orig, avp);
5849
} else if (subfield == 1) {
5850
/* INST */
5851
if (num_colons == 0) {
5852
/* all we have is the specID, we are adding INST */
5853
new_field = HandleApplyValue (NULL, avp);
5854
if (!StringHasNoText (new_field)) {
5855
new_val = (CharPtr) MemNew (sizeof (Char) * (StringLen (new_field) + StringLen (orig) + 2));
5856
sprintf (new_val, "%s:%s", new_field, orig == NULL ? "" : orig);
5857
orig = MemFree (orig);
5858
} else {
5859
new_val = orig;
5860
}
5861
new_field = MemFree (new_field);
5862
} else {
5863
cp = StringChr (orig, ':');
5864
len = cp - orig + 1;
5865
new_field = (CharPtr) MemNew (sizeof (Char) * len);
5866
StringNCpy (new_field, orig, len - 1);
5867
new_field[len - 1] = 0;
5868
new_field = HandleApplyValue (new_field, avp);
5869
new_val = (CharPtr) MemNew (sizeof (Char) * (StringLen (new_field) + StringLen (cp) + 1));
5870
sprintf (new_val, "%s%s", new_field == NULL ? "" : new_field, cp);
5871
orig = MemFree (orig);
5872
new_field = MemFree (new_field);
5873
}
5874
} else if (subfield == 2) {
5875
/* COLL */
5876
if (num_colons == 0) {
5877
/* add blank INST, then COLL, then existing specID */
5878
new_field = HandleApplyValue (NULL, avp);
5879
if (!StringHasNoText (new_field)) {
5880
new_val = (CharPtr) MemNew (sizeof (Char) * (3 + StringLen (new_field) + StringLen (orig)));
5881
sprintf (new_val, ":%s:%s", new_field, orig == NULL ? "" : orig);
5882
orig = MemFree (orig);
5883
} else {
5884
new_val = orig;
5885
}
5886
new_field = MemFree (new_field);
5887
} else if (num_colons == 1) {
5888
/* have INST and specID */
5889
new_field = HandleApplyValue (NULL, avp);
5890
if (!StringHasNoText (new_field)) {
5891
new_val = (CharPtr) MemNew (sizeof (Char) * (3 + StringLen (new_field) + StringLen (orig)));
5892
cp = StringChr (orig, ':');
5893
len = cp - orig;
5894
StringNCpy (new_val, orig, len);
5895
StringCat (new_val, ":");
5896
StringCat (new_val, new_field);
5897
StringCat (new_val, cp);
5898
orig = MemFree (orig);
5899
} else {
5900
new_val = orig;
5901
}
5902
new_field = MemFree (new_field);
5903
} else {
5904
cp = StringChr (orig, ':');
5905
cp2 = StringChr (cp + 1, ':');
5906
len = cp2 - cp;
5907
new_field = (CharPtr) MemNew (sizeof (Char) * len);
5908
StringNCpy (new_field, cp + 1, len - 1);
5909
new_field[len - 1] = 0;
5910
new_field = HandleApplyValue (new_field, avp);
5911
new_val = (CharPtr) MemNew (sizeof (Char) * (cp - orig + 1 + StringLen (new_field) + StringLen (cp2) + 1));
5912
StringNCpy (new_val, orig, cp - orig + 1);
5913
StringCat (new_val, new_field);
5914
StringCat (new_val, cp2);
5915
orig = MemFree (orig);
5916
new_field = MemFree (new_field);
5917
}
5918
} else {
5919
/* specid */
5920
if (num_colons == 0) {
5921
new_val = HandleApplyValue (orig, avp);
5922
} else {
5923
cp = StringRChr (orig, ':');
5924
new_field = StringSave (cp + 1);
5925
new_field = HandleApplyValue (new_field, avp);
5926
new_val = (CharPtr) MemNew (sizeof (Char) + (cp - orig + 1 + StringLen (new_field) + 1));
5927
StringNCpy (new_val, orig, cp - orig + 1);
5928
StringCat (new_val, new_field);
5929
orig = MemFree (orig);
5930
new_field = MemFree (new_field);
5931
}
5932
}
5933
return new_val;
5934
}
5935
5936
5129
5937
static void ApplySourceQualBioSourceCallback (BioSourcePtr biop, Pointer userdata, FilterSetPtr fsp)
5130
5938
{
5131
5939
ApplyValuePtr avp;
5185
5993
{
5186
5994
if (!is_nontext)
5187
5995
{
5188
mod->subname = HandleApplyValue (mod->subname, avp);
5996
mod->subname = ApplyToSubfield (mod->subname, avp, sqdp->subfield);
5189
5997
}
5190
5998
found = TRUE;
5191
5999
}
5202
6010
}
5203
6011
else
5204
6012
{
5205
mod->subname = StringSave (avp->new_text);
6013
mod->subname = ApplyToSubfield (mod->subname, avp, sqdp->subfield);
5206
6014
}
5207
6015
if (last_mod == NULL)
5208
6016
{
5224
6032
{
5225
6033
if (! is_nontext)
5226
6034
{
5227
ssp->name = HandleApplyValue (ssp->name, avp);
6035
ssp->name = ApplyToSubfield (ssp->name, avp, sqdp->subfield);
5228
6036
}
5229
6037
found = TRUE;
5230
6038
}
5241
6049
}
5242
6050
else
5243
6051
{
5244
ssp->name = StringSave (avp->new_text);
6052
ssp->name = ApplyToSubfield (ssp->name, avp, sqdp->subfield);
5245
6053
}
5246
6054
if (last_ssp == NULL)
5247
6055
{
5273
6081
ApplySourceQualBioSourceCallback (sdp->data.ptrvalue, userdata, fsp);
5274
6082
}
5275
6083
5276
static void RemoveOrgModFromBioSource (BioSourcePtr biop, Uint1 subtype, FilterSetPtr fsp)
6084
static void RemoveOrgModFromBioSource (BioSourcePtr biop, Uint1 subtype, Uint1 subfield, FilterSetPtr fsp)
5277
6085
{
5278
6086
OrgModPtr mod = NULL, prev_mod = NULL, next_mod;
5279
6087
5286
6094
if (mod->subtype == subtype
5287
6095
&& OrgModSpecialMatch (mod, fsp))
5288
6096
{
5289
if (prev_mod == NULL)
5290
{
5291
biop->org->orgname->mod = mod->next;
5292
}
5293
else
5294
{
5295
prev_mod->next = mod->next;
5296
}
5297
mod->next = NULL;
5298
OrgModFree (mod);
6097
mod->subname = RemoveSubfield (mod->subname, subfield);
6098
if (StringHasNoText (mod->subname)) {
6099
if (prev_mod == NULL)
6100
{
6101
biop->org->orgname->mod = mod->next;
6102
}
6103
else
6104
{
6105
prev_mod->next = mod->next;
6106
}
6107
mod->next = NULL;
6108
OrgModFree (mod);
6109
} else {
6110
prev_mod = mod;
6111
}
5299
6112
}
5300
6113
else
5301
6114
{
5306
6119
}
5307
6120
}
5308
6121
5309
static void RemoveSubSourceFromBioSource (BioSourcePtr biop, Uint2 subtype, FilterSetPtr fsp)
6122
static void RemoveSubSourceFromBioSource (BioSourcePtr biop, Uint2 subtype, Uint1 subfield, FilterSetPtr fsp)
5310
6123
{
5311
6124
SubSourcePtr ssp = NULL, prev_ssp = NULL, next_ssp;
5312
6125
5319
6132
if (ssp->subtype == subtype
5320
6133
&& SubSrcSpecialMatch (ssp, fsp))
5321
6134
{
5322
if (prev_ssp == NULL)
5323
{
5324
biop->subtype = ssp->next;
5325
}
5326
else
5327
{
5328
prev_ssp->next = ssp->next;
5329
}
5330
ssp->next = NULL;
5331
SubSourceFree (ssp);
6135
ssp->name = RemoveSubfield (ssp->name, subfield);
6136
if (StringHasNoText (ssp->name)) {
6137
if (prev_ssp == NULL)
6138
{
6139
biop->subtype = ssp->next;
6140
}
6141
else
6142
{
6143
prev_ssp->next = ssp->next;
6144
}
6145
ssp->next = NULL;
6146
SubSourceFree (ssp);
6147
} else {
6148
prev_ssp = ssp;
6149
}
5332
6150
}
5333
6151
else
5334
6152
{
5359
6177
sqdp = (SourceQualDescPtr) avp->field_list->data.ptrvalue;
5360
6178
if (sqdp->isOrgMod)
5361
6179
{
5362
RemoveOrgModFromBioSource (biop, sqdp->subtype, fsp);
6180
RemoveOrgModFromBioSource (biop, sqdp->subtype, sqdp->subfield, fsp);
5363
6181
}
5364
6182
else
5365
6183
{
5366
RemoveSubSourceFromBioSource (biop, sqdp->subtype, fsp);
6184
RemoveSubSourceFromBioSource (biop, sqdp->subtype, sqdp->subfield, fsp);
5367
6185
}
5368
6186
}
5369
6187
else if (avp->field_list->choice == 1
5370
6188
&& StringCmp (avp->field_list->data.ptrvalue, "All Notes") == 0)
5371
6189
{
5372
RemoveOrgModFromBioSource (biop, 255, fsp);
5373
RemoveSubSourceFromBioSource (biop, 255, fsp);
6190
RemoveOrgModFromBioSource (biop, 255, 0, fsp);
6191
RemoveSubSourceFromBioSource (biop, 255, 0, fsp);
5374
6192
}
5375
6193
}
5376
6194
5888
6706
/* this is an apply */
5889
6707
if (avp->etp != NULL)
5890
6708
{
5891
if (avp->etp->existing_text_choice == EXISTING_TEXT_CHOICE_LEAVE_OLD
6709
if (avp->etp->existing_text_choice == eExistingTextChoiceLeaveOld
5892
6710
&& sfp->dbxref != NULL)
5893
6711
{
5894
6712
return;
5895
6713
}
5896
else if (avp->etp->existing_text_choice == EXISTING_TEXT_CHOICE_REPLACE_OLD)
6714
else if (avp->etp->existing_text_choice == eExistingTextChoiceReplaceOld)
5897
6715
{
5898
6716
sfp->dbxref = RemoveDbxrefList (sfp->dbxref);
5899
6717
}
5912
6730
5913
6731
}
5914
6732
6733
static void SetRNAProduct (SeqFeatPtr sfp, ApplyValuePtr avp);
6734
5915
6735
static void SetGBQualString (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
5916
6736
{
5917
6737
GBQualPtr gbqual, gbqual_last = NULL;
5918
6738
ApplyValuePtr avp;
5919
6739
Boolean found = FALSE;
5920
RnaRefPtr rrp;
5921
6740
GeneRefPtr grp;
5922
6741
5923
6742
if (sfp == NULL || userdata == NULL)
5945
6764
else if (StringICmp (EditQualifierList[avp->field_list->data.intvalue - 1].name, "product") == 0
5946
6765
&& sfp->data.choice == SEQFEAT_RNA)
5947
6766
{
5948
rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
5949
if (rrp != NULL)
5950
{
5951
if (rrp->ext.choice == 0)
5952
{
5953
rrp->ext.choice = 1;
5954
rrp->ext.value.ptrvalue = NULL;
5955
}
5956
if (rrp->ext.choice == 1)
5957
{
5958
rrp->ext.value.ptrvalue = HandleApplyValue (rrp->ext.value.ptrvalue, avp);
5959
}
5960
}
6767
SetRNAProduct (sfp, avp);
5961
6768
return;
5962
6769
}
5963
6770
else if (StringICmp (EditQualifierList [avp->field_list->data.intvalue - 1].name, "map") == 0
6180
6987
GBQualPtr gbqual, gbqual_last = NULL, gbqual_next;
6181
6988
RnaRefPtr rrp;
6182
6989
GeneRefPtr grp;
6183
StringConstraintPtr scp;
6990
StringConstraintXPtr scp;
6184
6991
6185
6992
if (sfp == NULL || userdata == NULL)
6186
6993
{
6187
6994
return;
6188
6995
}
6189
scp = (StringConstraintPtr) userdata;
6996
scp = (StringConstraintXPtr) userdata;
6190
6997
if (scp == NULL)
6191
6998
{
6192
6999
return;
6193
7000
}
6194
7001
6195
if (DoesStringMatchConstraint ("note", scp))
7002
if (DoesStringMatchConstraintX ("note", scp))
6196
7003
{
6197
7004
sfp->comment = MemFree (sfp->comment);
6198
7005
}
6199
7006
6200
if (DoesStringMatchConstraint ("exception", scp))
7007
if (DoesStringMatchConstraintX ("exception", scp))
6201
7008
{
6202
7009
sfp->except_text = MemFree (sfp->except_text);
6203
7010
}
6204
7011
6205
if (DoesStringMatchConstraint ("product", scp) && sfp->data.choice == SEQFEAT_RNA)
7012
if (DoesStringMatchConstraintX ("product", scp) && sfp->data.choice == SEQFEAT_RNA)
6206
7013
{
6207
7014
rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
6208
7015
if (rrp != NULL && rrp->ext.choice == 1)
6212
7019
}
6213
7020
}
6214
7021
6215
if (DoesStringMatchConstraint ("map", scp) && sfp->data.choice == SEQFEAT_GENE)
7022
if (DoesStringMatchConstraintX ("map", scp) && sfp->data.choice == SEQFEAT_GENE)
6216
7023
{
6217
7024
grp = (GeneRefPtr) sfp->data.value.ptrvalue;
6218
7025
if (grp != NULL)
6221
7028
}
6222
7029
}
6223
7030
6224
if (DoesStringMatchConstraint ("db_xref", scp))
7031
if (DoesStringMatchConstraintX ("db_xref", scp))
6225
7032
{
6226
7033
sfp->dbxref = RemoveDbxrefList (sfp->dbxref);
6227
7034
}
6228
7035
6229
if (DoesStringMatchConstraint ("go_process", scp))
7036
if (DoesStringMatchConstraintX ("go_process", scp))
6230
7037
{
6231
7038
RemoveGoTerm (sfp, "process");
6232
7039
}
6233
7040
6234
if (DoesStringMatchConstraint ("go_function", scp))
7041
if (DoesStringMatchConstraintX ("go_function", scp))
6235
7042
{
6236
7043
RemoveGoTerm (sfp, "function");
6237
7044
}
6238
7045
6239
if (DoesStringMatchConstraint ("go_component", scp))
7046
if (DoesStringMatchConstraintX ("go_component", scp))
6240
7047
{
6241
7048
RemoveGoTerm (sfp, "component");
6242
7049
}
6245
7052
while (gbqual != NULL)
6246
7053
{
6247
7054
gbqual_next = gbqual->next;
6248
if (DoesStringMatchConstraint (gbqual->qual, scp))
7055
if (DoesStringMatchConstraintX (gbqual->qual, scp))
6249
7056
{
6250
7057
if (gbqual_last == NULL)
6251
7058
{
6338
7145
}
6339
7146
6340
7147
6341
static CharPtr ReplaceStringForParse(CharPtr src_text, TextPortionPtr text_portion)
7148
static CharPtr ReplaceStringForParse(CharPtr src_text, TextPortionXPtr text_portion)
6342
7149
{
6343
7150
CharPtr found_loc;
6344
7151
Int4 found_len;
6347
7154
if (src_text == NULL || text_portion == NULL) {
6348
7155
return NULL;
6349
7156
}
6350
// for parse, replace the source text with the portion we want
7157
/* for parse, replace the source text with the portion we want */
6351
7158
found_loc = NULL;
6352
7159
found_len = 0;
6353
FindTextPortionInString (src_text, text_portion, &found_loc, &found_len);
7160
FindTextPortionXInString (src_text, text_portion, &found_loc, &found_len);
6354
7161
if (found_loc != NULL)
6355
7162
{
6356
7163
dst_txt = (CharPtr)MemNew (found_len + 1);
6390
7197
}
6391
7198
6392
7199
avd.text_to_replace = NULL;
7200
avd.where_to_replace = EditApplyFindLocation_anywhere;
6393
7201
src_text = (cfp->get_str_func)(sfp, cfp->src_field_list, cfp->fsp);
6394
7202
6395
7203
if (cfp->strip_name_from_text)
6417
7225
}
6418
7226
else if (cfp->convert_type == CONVERT_TYPE_PARSE)
6419
7227
{
6420
// for parse, replace the source text with the portion we want
7228
/* for parse, replace the source text with the portion we want */
6421
7229
dst_text = src_text;
6422
7230
src_text = ReplaceStringForParse(src_text, cfp->text_portion);
6423
7231
if (src_text == NULL)
6481
7289
}
6482
7290
6483
7291
avd.text_to_replace = NULL;
7292
avd.where_to_replace = EditApplyFindLocation_anywhere;
6484
7293
src_text = (cfp->get_d_str_func)(sdp, cfp->src_field_list, cfp->fsp);
6485
7294
if (cfp->strip_name_from_text)
6486
7295
{
6508
7317
}
6509
7318
else if (cfp->convert_type == CONVERT_TYPE_PARSE)
6510
7319
{
6511
// for parse, replace the source text with the portion we want
7320
/* for parse, replace the source text with the portion we want */
6512
7321
dst_text = src_text;
6513
7322
src_text = ReplaceStringForParse(src_text, cfp->text_portion);
6514
7323
if (src_text == NULL)
6535
7344
|| (cfp->convert_type == CONVERT_TYPE_PARSE && cfp->remove_parsed))
6536
7345
{
6537
7346
/* put dst_text in the src_field */
7347
avd.etp = NULL;
6538
7348
avd.field_list = cfp->src_field_list;
6539
7349
avd.new_text = dst_text;
6540
7350
(cfp->set_d_str_func) (sdp, &avd, cfp->fsp);
6574
7384
src_val = (cfp->name_field_func)(cfp->src_field_list);
6575
7385
if (StringCmp (curr_val, src_val) == 0)
6576
7386
{
7387
avd.where_to_replace = EditApplyFindLocation_anywhere;
6577
7388
avd.field_list = cfp->dst_field_list;
6578
7389
avd.etp = NULL;
6579
7390
(cfp->set_str_func) (sfp, &avd, cfp->fsp);
6607
7418
src_val = (cfp->name_field_func)(cfp->src_field_list);
6608
7419
if (StringCmp (curr_val, src_val) == 0)
6609
7420
{
7421
avd.where_to_replace = EditApplyFindLocation_anywhere;
6610
7422
avd.field_list = cfp->dst_field_list;
6611
7423
avd.etp = NULL;
6612
7424
(cfp->set_d_str_func) (sdp, &avd, cfp->fsp);
7140
7952
grp->maploc = HandleApplyValue (grp->maploc, avp);
7141
7953
break;
7142
7954
case GENEFIELD_SYNONYM:
7143
grp->syn = ApplyValueToValNodeStringList (grp->syn, 0, avp);
7955
if (grp->syn == NULL || !StringHasNoText (avp->text_to_replace)) {
7956
grp->syn = ApplyValueToValNodeStringList (grp->syn, 0, avp);
7957
} else {
7958
grp->syn->data.ptrvalue = HandleApplyValue (grp->syn->data.ptrvalue, avp);
7959
}
7144
7960
break;
7145
7961
case GENEFIELD_LOCUS_TAG:
7146
7962
grp->locus_tag = HandleApplyValue (grp->locus_tag, avp);
7369
8185
sfp->comment = MemFree (sfp->comment);
7370
8186
}
7371
8187
8188
extern CharPtr
8189
GetCDSFieldString
8190
(SeqFeatPtr sfp,
8191
ValNodePtr cds_field,
8192
FilterSetPtr fsp)
8193
{
8194
ValNodePtr vnp;
8195
CharPtr str = NULL;
8196
BioseqPtr prot_bsp;
8197
SeqFeatPtr prot_sfp;
8198
SeqMgrFeatContext prot_context;
8199
ProtRefPtr prp;
8200
8201
if (sfp == NULL || cds_field == NULL || sfp->idx.subtype != FEATDEF_CDS)
8202
{
8203
return NULL;
8204
}
8205
8206
vnp = cds_field;
8207
8208
while (vnp != NULL && vnp->data.intvalue != FEATUREFIELD_NONE && StringHasNoText (str))
8209
{
8210
str = NULL;
8211
switch (vnp->data.intvalue)
8212
{
8213
case MRNAFIELD_PRODUCT:
8214
prot_bsp = BioseqFind (SeqLocId (sfp->product));
8215
prot_sfp = SeqMgrGetNextFeature (prot_bsp, NULL, SEQFEAT_PROT, 0, &prot_context);
8216
if (prot_sfp != NULL && prot_sfp->data.value.ptrvalue != NULL) {
8217
prp = (ProtRefPtr) prot_sfp->data.value.ptrvalue;
8218
if (prp->name != NULL && !StringHasNoText (prp->name->data.ptrvalue)) {
8219
str = prp->name->data.ptrvalue;
8220
}
8221
}
8222
break;
8223
case MRNAFIELD_COMMENT:
8224
str = sfp->comment;
8225
break;
8226
}
8227
vnp = vnp->next;
8228
}
8229
if (StringHasNoText (str))
8230
{
8231
str = NULL;
8232
}
8233
else
8234
{
8235
str = StringSave (str);
8236
}
8237
return str;
8238
}
8239
8240
extern void RemoveCDSFieldString (SeqFeatPtr sfp, ValNodePtr cds_field)
8241
{
8242
ValNodePtr vnp;
8243
Boolean found_nonempty = FALSE;
8244
BioseqPtr prot_bsp;
8245
SeqFeatPtr prot_sfp;
8246
SeqMgrFeatContext prot_context;
8247
ProtRefPtr prp;
8248
8249
if (sfp == NULL || cds_field == NULL || sfp->idx.subtype != FEATDEF_CDS)
8250
{
8251
return;
8252
}
8253
8254
vnp = cds_field;
8255
while (vnp != NULL && vnp->data.intvalue != FEATUREFIELD_NONE && !found_nonempty)
8256
{
8257
switch (vnp->data.intvalue)
8258
{
8259
case MRNAFIELD_PRODUCT:
8260
prot_bsp = BioseqFind (SeqLocId (sfp->product));
8261
prot_sfp = SeqMgrGetNextFeature (prot_bsp, NULL, SEQFEAT_PROT, 0, &prot_context);
8262
if (prot_sfp != NULL && prot_sfp->data.value.ptrvalue != NULL) {
8263
prp = (ProtRefPtr) prot_sfp->data.value.ptrvalue;
8264
if (prp->name != NULL && !StringHasNoText (prp->name->data.ptrvalue)) {
8265
found_nonempty = TRUE;
8266
if (vnp->choice != 0) {
8267
prp->name = ValNodeFreeData (prp->name);
8268
}
8269
}
8270
}
8271
break;
8272
case MRNAFIELD_COMMENT:
8273
if (!StringHasNoText (sfp->comment))
8274
{
8275
found_nonempty = TRUE;
8276
if (vnp->choice != 0)
8277
{
8278
sfp->comment = MemFree (sfp->comment);
8279
}
8280
}
8281
break;
8282
}
8283
vnp = vnp->next;
8284
}
8285
}
8286
7372
8287
#define PROTEINFIELD_NAME 1
7373
8288
#define PROTEINFIELD_DESC 2
7374
8289
#define PROTEINFIELD_EC_NUM 3
7375
8290
#define PROTEINFIELD_ACTIVITY 4
7376
8291
#define PROTEINFIELD_COMMENT 5
7377
8292
#define PROTEINFIELD_MATPEPTIDE_NAME 6
7378
#define PROTEINFIELD_MATPEPTIDE_COMMENT 7
8293
#define PROTEINFIELD_MATPEPTIDE_DESC 7
8294
#define PROTEINFIELD_MATPEPTIDE_COMMENT 8
7379
8295
7380
8296
static CharPtr protein_field_list [] =
7381
8297
{
7382
"name", "description", "E.C. number", "activity", "comment", "mat_peptide name", "mat_peptide comment"
8298
"name", "description", "E.C. number", "activity", "comment", "mat_peptide name", "mat_peptide description", "mat_peptide comment"
7383
8299
};
7384
8300
7385
8301
static int num_protein_fields = sizeof (protein_field_list) / sizeof (CharPtr);
7469
8385
str = val_vnp->data.ptrvalue;
7470
8386
}
7471
8387
break;
8388
case PROTEINFIELD_MATPEPTIDE_DESC:
8389
if (sfp->idx.subtype == FEATDEF_mat_peptide_aa && prp != NULL)
8390
{
8391
str = prp->desc;
8392
}
8393
break;
7472
8394
case PROTEINFIELD_MATPEPTIDE_COMMENT:
7473
8395
if (sfp->idx.subtype == FEATDEF_mat_peptide_aa)
7474
8396
{
7494
8416
ValNodePtr vnp;
7495
8417
ProtRefPtr prp = NULL;
7496
8418
Int4 field_choice;
7497
SeqFeatXrefPtr xref, prev;
8419
SeqFeatXrefPtr xref = NULL, prev;
7498
8420
7499
8421
if (sfp == NULL || protein_field == NULL)
7500
8422
{
7502
8424
}
7503
8425
7504
8426
vnp = protein_field;
7505
if (sfp->idx.subtype == FEATDEF_PROT) {
8427
if (sfp->idx.subtype == FEATDEF_PROT
8428
|| sfp->idx.subtype == FEATDEF_mat_peptide_aa) {
7506
8429
prp = (ProtRefPtr) sfp->data.value.ptrvalue;
7507
8430
} else if (sfp->idx.subtype == FEATDEF_CDS) {
7508
8431
xref = sfp->xref;
7520
8443
switch (field_choice)
7521
8444
{
7522
8445
case PROTEINFIELD_NAME:
7523
if (prp != NULL && prp->name != NULL)
8446
if (prp != NULL && prp->name != NULL && sfp->idx.subtype == FEATDEF_PROT)
7524
8447
{
7525
8448
prp->name = ValNodeFreeData (prp->name);
7526
8449
}
7555
8478
prp->name = ValNodeFreeData (prp->name);
7556
8479
}
7557
8480
break;
8481
case PROTEINFIELD_MATPEPTIDE_DESC:
8482
if (prp != NULL && sfp->idx.subtype == FEATDEF_mat_peptide_aa)
8483
{
8484
prp->desc = MemFree (prp->desc);
8485
}
8486
break;
7558
8487
case PROTEINFIELD_MATPEPTIDE_COMMENT:
7559
8488
if (sfp->idx.subtype == FEATDEF_mat_peptide_aa)
7560
8489
{
7589
8518
}
7590
8519
}
7591
8520
8521
extern ValNodePtr ApplyValueToValNodeStringListAsText (ValNodePtr list, Int2 choice, ApplyValuePtr avp);
8522
7592
8523
static void SetProteinFieldString (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
7593
8524
{
7594
8525
ProtRefPtr prp;
7598
8529
{
7599
8530
return;
7600
8531
}
8532
if (sfp->idx.subtype != FEATDEF_PROT && sfp->idx.subtype != FEATDEF_mat_peptide_aa)
8533
{
8534
return;
8535
}
7601
8536
7602
8537
avp = (ApplyValuePtr) userdata;
7603
8538
if (avp->field_list == NULL)
7608
8543
if (sfp->idx.subtype == FEATDEF_PROT)
7609
8544
{
7610
8545
if (avp->field_list->data.intvalue == PROTEINFIELD_MATPEPTIDE_NAME
8546
|| avp->field_list->data.intvalue == PROTEINFIELD_MATPEPTIDE_DESC
7611
8547
|| avp->field_list->data.intvalue == PROTEINFIELD_MATPEPTIDE_COMMENT)
7612
8548
{
7613
8549
return;
7616
8552
else if (sfp->idx.subtype == FEATDEF_mat_peptide_aa)
7617
8553
{
7618
8554
if (avp->field_list->data.intvalue != PROTEINFIELD_MATPEPTIDE_NAME
8555
&& avp->field_list->data.intvalue != PROTEINFIELD_MATPEPTIDE_DESC
7619
8556
&& avp->field_list->data.intvalue != PROTEINFIELD_MATPEPTIDE_COMMENT)
7620
8557
{
7621
8558
return;
7641
8578
{
7642
8579
case PROTEINFIELD_NAME:
7643
8580
case PROTEINFIELD_MATPEPTIDE_NAME:
7644
if (prp->name == NULL )
8581
if (prp->name == NULL || !StringHasNoText(avp->text_to_replace))
7645
8582
{
7646
8583
prp->name = ApplyValueToValNodeStringList (prp->name, 0, avp);
7647
8584
}
7651
8588
}
7652
8589
break;
7653
8590
case PROTEINFIELD_DESC:
7654
prp->desc = HandleExistingText (prp->desc, StringSave (avp->new_text), avp->etp);
8591
case PROTEINFIELD_MATPEPTIDE_DESC:
8592
prp->desc = HandleApplyValue (prp->desc, avp);
7655
8593
break;
7656
8594
case PROTEINFIELD_EC_NUM:
7657
if (prp->ec == NULL)
7658
{
7659
prp->ec = ApplyValueToValNodeStringList (prp->ec, 0, avp);
7660
}
7661
else
7662
{
7663
prp->ec->data.ptrvalue = HandleApplyValue (prp->ec->data.ptrvalue, avp);
7664
}
8595
prp->ec = ApplyValueToValNodeStringListAsText (prp->ec, 0, avp);
7665
8596
break;
7666
8597
case PROTEINFIELD_ACTIVITY:
7667
if (prp->activity == NULL)
8598
if (prp->activity == NULL || !StringHasNoText(avp->text_to_replace))
7668
8599
{
7669
8600
prp->activity = ApplyValueToValNodeStringList (prp->activity, 0, avp);
7670
8601
}
7675
8606
break;
7676
8607
case PROTEINFIELD_COMMENT:
7677
8608
case PROTEINFIELD_MATPEPTIDE_COMMENT:
7678
sfp->comment = HandleExistingText (sfp->comment, StringSave (avp->new_text), avp->etp);
8609
sfp->comment = HandleApplyValue (sfp->comment, avp);
7679
8610
break;
7680
8611
}
7681
8612
}
7781
8712
return d;
7782
8713
}
7783
8714
8715
8716
extern Boolean IsCDSetProteinProductChoice (ValNodePtr vnp)
8717
{
8718
if (vnp != NULL && vnp->data.intvalue == 2 + num_gene_fields + num_mrna_fields) {
8719
return TRUE;
8720
} else {
8721
return FALSE;
8722
}
8723
}
8724
8725
8726
static Boolean IsCDSetProteinQualChoice (ValNodePtr vnp)
8727
{
8728
if (vnp != NULL
8729
&& vnp->data.intvalue > 1 + num_gene_fields + num_mrna_fields
8730
&& vnp->data.intvalue <= 1 + num_gene_fields + num_mrna_fields + num_protein_fields)
8731
{
8732
return TRUE;
8733
}
8734
else
8735
{
8736
return FALSE;
8737
}
8738
}
8739
8740
static Boolean IsCDSetMatPeptideQualChoice (ValNodePtr vnp)
8741
{
8742
if (IsCDSetProteinQualChoice (vnp)
8743
&& StringNICmp (protein_field_list[vnp->data.intvalue - num_gene_fields - num_mrna_fields - 2],
8744
"mat_peptide", 11) == 0)
8745
{
8746
return TRUE;
8747
}
8748
else
8749
{
8750
return FALSE;
8751
}
8752
}
8753
8754
static Boolean IsCDSetMRNAQualChoice (ValNodePtr vnp)
8755
{
8756
if (vnp != NULL
8757
&& vnp->data.intvalue > 1 + num_gene_fields
8758
&& vnp->data.intvalue <= 1 + num_gene_fields + num_mrna_fields)
8759
{
8760
return TRUE;
8761
}
8762
else
8763
{
8764
return FALSE;
8765
}
8766
}
8767
8768
static Boolean IsCDSetGeneQualChoice (ValNodePtr vnp)
8769
{
8770
if (vnp != NULL
8771
&& vnp->data.intvalue > 1
8772
&& vnp->data.intvalue <= 1 + num_gene_fields)
8773
{
8774
return TRUE;
8775
}
8776
else
8777
{
8778
return FALSE;
8779
}
8780
}
8781
8782
static Boolean IsCDSetCDSQualChoice (ValNodePtr vnp)
8783
{
8784
if (vnp != NULL && vnp->data.intvalue == 1)
8785
{
8786
return TRUE;
8787
}
8788
else
8789
{
8790
return FALSE;
8791
}
8792
}
8793
7784
8794
extern CharPtr GetCDSGeneProtField (SeqFeatPtr sfp, ValNodePtr vnp, FilterSetPtr fsp)
7785
8795
{
7786
8796
CharPtr str = NULL;
7799
8809
7800
8810
field_choice = vnp->data.intvalue;
7801
8811
7802
if (vnp->data.intvalue == 1)
8812
if (IsCDSetCDSQualChoice(vnp))
7803
8813
{
7804
8814
/* CDS Comment */
7805
8815
str = GetCDSComment (sfp, NULL, NULL);
7806
8816
}
7807
else if (vnp->data.intvalue <= 1 + num_gene_fields)
8817
else if (IsCDSetGeneQualChoice (vnp))
7808
8818
{
7809
8819
vn.data.intvalue = vnp->data.intvalue - 1;
7810
8820
str = GetGeneFieldString (sfp, &vn, NULL);
7811
8821
}
7812
else if (vnp->data.intvalue <= 1 + num_gene_fields + num_mrna_fields)
8822
else if (IsCDSetMRNAQualChoice (vnp))
7813
8823
{
7814
8824
vn.data.intvalue = vnp->data.intvalue - num_gene_fields - 1;
7815
8825
str = GetmRNAFieldString (sfp, &vn, NULL);
7816
8826
}
7817
else if (vnp->data.intvalue <= 1 + num_gene_fields + num_mrna_fields + num_protein_fields)
8827
else if (IsCDSetProteinQualChoice (vnp))
7818
8828
{
7819
8829
vn.data.intvalue = vnp->data.intvalue - num_gene_fields - num_mrna_fields - 1;
7820
8830
str = GetProteinFieldString (sfp, &vn, NULL);
7824
8834
return str;
7825
8835
}
7826
8836
7827
static void RemoveCDSGeneProtField (SeqFeatPtr sfp, ValNodePtr vnp)
8837
/* we could have multiple mat_peptides in a CDSset, some that match the constraint and some that do not */
8838
static Boolean DoesConstraintDisqualifyFeature (SeqFeatPtr sfp, ChoiceConstraintPtr ccp)
8839
{
8840
Boolean is_disqualified = FALSE;
8841
Boolean does_match = FALSE;
8842
CharPtr str;
8843
8844
if (sfp == NULL || ccp == NULL
8845
|| ccp->constraint_type == CHOICE_CONSTRAINT_ANY
8846
|| sfp->idx.subtype != FEATDEF_mat_peptide_aa
8847
|| !IsCDSetMatPeptideQualChoice(ccp->qual_choice))
8848
{
8849
is_disqualified = FALSE;
8850
}
8851
else if (ccp->constraint_type == CHOICE_CONSTRAINT_QUAL_PRESENT && ccp->qual_choice != NULL)
8852
{
8853
str = GetCDSGeneProtField (sfp, ccp->qual_choice, NULL);
8854
if (str == NULL)
8855
{
8856
is_disqualified = TRUE;
8857
}
8858
MemFree (str);
8859
}
8860
else if (ccp->constraint_type == CHOICE_CONSTRAINT_STRING)
8861
{
8862
str = GetCDSGeneProtField (sfp, ccp->qual_choice, NULL);
8863
does_match = DoesStringMatchConstraintX (str, ccp->string_constraint);
8864
MemFree (str);
8865
if (ccp->string_constraint != NULL && ccp->string_constraint->not_present)
8866
{
8867
does_match = ! does_match;
8868
}
8869
if (!does_match)
8870
{
8871
is_disqualified = TRUE;
8872
}
8873
}
8874
return is_disqualified;
8875
8876
}
8877
8878
extern void RemoveCDSGeneProtField (SeqFeatPtr sfp, ValNodePtr vnp, FilterSetPtr fsp)
7828
8879
{
7829
8880
ValNode vn;
7830
8881
7832
8883
{
7833
8884
return;
7834
8885
}
8886
8887
if (fsp != NULL && fsp->cgp != NULL && DoesConstraintDisqualifyFeature (sfp, fsp->cgp))
8888
{
8889
return;
8890
}
7835
8891
7836
8892
while (vnp != NULL)
7837
8893
{
7862
8918
}
7863
8919
}
7864
8920
7865
static void
8921
8922
extern Uint2 FeatDefTypeFromFieldList (ValNodePtr vnp)
8923
{
8924
if (vnp == NULL)
8925
{
8926
return 0;
8927
}
8928
else if (IsCDSetCDSQualChoice(vnp))
8929
{
8930
return FEATDEF_CDS;
8931
}
8932
else if (IsCDSetGeneQualChoice (vnp))
8933
{
8934
return FEATDEF_GENE;
8935
}
8936
else if (IsCDSetMRNAQualChoice(vnp))
8937
{
8938
return FEATDEF_mRNA;
8939
}
8940
else if (IsCDSetProteinQualChoice (vnp))
8941
{
8942
if (IsCDSetMatPeptideQualChoice (vnp))
8943
{
8944
return FEATDEF_mat_peptide_aa;
8945
}
8946
else
8947
{
8948
return FEATDEF_PROT;
8949
}
8950
}
8951
else
8952
{
8953
return 0;
8954
}
8955
}
8956
8957
8958
/* return TRUE if actually set field, FALSE otherwise */
8959
extern Boolean
7866
8960
SetCDSGeneProtField
7867
8961
(SeqFeatPtr sfp,
7868
8962
ValNodePtr vnp,
7869
CharPtr new_text,
7870
ExistingTextPtr etp)
8963
ApplyValuePtr avp,
8964
FilterSetPtr fsp)
7871
8965
{
7872
ValNode vn;
7873
ApplyValueData avd;
8966
ValNode vn;
8967
ApplyValueData local_avd;
8968
Uint2 choice;
7874
8969
7875
if (sfp == NULL || vnp == NULL)
7876
{
7877
return;
8970
if (sfp == NULL || vnp == NULL || avp == NULL)
8971
{
8972
return FALSE;
8973
}
8974
8975
choice = FeatDefTypeFromFieldList (vnp);
8976
if (FindFeatFromFeatDefType(choice) != sfp->data.choice)
8977
{
8978
return FALSE;
8979
}
8980
8981
if (fsp != NULL && fsp->cgp != NULL && DoesConstraintDisqualifyFeature (sfp, fsp->cgp))
8982
{
8983
return FALSE;
7878
8984
}
7879
8985
7880
8986
vn.choice = vnp->choice;
7881
8987
vn.next = NULL;
7882
avd.field_list = &vn;
7883
avd.new_text = StringSave (new_text);
7884
avd.etp = etp;
7885
avd.text_to_replace = NULL;
8988
local_avd.field_list = &vn;
8989
local_avd.new_text = avp->new_text;
8990
local_avd.etp = avp->etp;
8991
local_avd.text_to_replace = avp->text_to_replace;
8992
local_avd.where_to_replace = avp->where_to_replace;
7886
8993
7887
8994
if (vnp->data.intvalue == 1)
7888
8995
{
7889
8996
/* CDS Comment */
7890
SetCDSComment (sfp, &avd, NULL);
8997
SetCDSComment (sfp, &local_avd, NULL);
7891
8998
}
7892
8999
else if (vnp->data.intvalue <= 1 + num_gene_fields)
7893
9000
{
7894
9001
vn.data.intvalue = vnp->data.intvalue - 1;
7895
SetGeneFieldString (sfp, &avd, NULL);
9002
SetGeneFieldString (sfp, &local_avd, NULL);
7896
9003
}
7897
9004
else if (vnp->data.intvalue <= 1 + num_gene_fields + num_mrna_fields)
7898
9005
{
7899
9006
vn.data.intvalue = vnp->data.intvalue - num_gene_fields - 1;
7900
SetmRNAFieldString (sfp, &avd, NULL);
9007
SetmRNAFieldString (sfp, &local_avd, NULL);
7901
9008
}
7902
9009
else if (vnp->data.intvalue <= 1 + num_gene_fields + num_mrna_fields + num_protein_fields)
7903
9010
{
7904
9011
vn.data.intvalue = vnp->data.intvalue - num_gene_fields - num_mrna_fields - 1;
7905
SetProteinFieldString (sfp, &avd, NULL);
9012
SetProteinFieldString (sfp, &local_avd, NULL);
7906
9013
}
7907
9014
7908
avd.new_text = MemFree (avd.new_text);
9015
/* no need to free any part of local_avd */
9016
9017
return TRUE;
7909
9018
}
7910
9019
7911
#define RNAFIELD_NAME 1
9020
#define RNAFIELD_PRODUCT 1
7912
9021
#define RNAFIELD_COMMENT 2
7913
#define RNAFIELD_PRODUCT 3
7914
#define RNAFIELD_CODONS_RECOGNIZED 4
9022
#define RNAFIELD_CODONS_RECOGNIZED 3
9023
#define RNAFIELD_NCRNA_CLASS 4
7915
9024
#define RNAFIELD_ANTICODON 5
7916
9025
#define RNAFIELD_TRANSCRIPT_ID 6
7917
9026
7918
9027
static CharPtr rna_field_list [] =
7919
9028
{
7920
"Name", "Comment", "Product GBQual", "Codons Recognized", "Anticodon", "Transcript ID"
9029
"Product", "Comment", "Codons Recognized", "ncRNA class", "Anticodon", "Transcript ID"
7921
9030
};
7922
9031
7923
9032
static Int4 num_rna_fields = sizeof (rna_field_list) / sizeof (CharPtr);
8013
9122
DialoG dlg;
8014
9123
Int4 i;
8015
9124
8016
for (i = 0; i < 3; i++)
9125
for (i = 0; i < 4; i++)
8017
9126
{
8018
9127
ValNodeAddInt (&choice_list, 0, i + 1);
8019
9128
}
8032
9141
}
8033
9142
8034
9143
static CharPtr rna_subtype_list [] = { "misc_RNA", "preRna", "mRNA", "tRNA",
8035
"rRNA", "snRNA", "scRNA", "snoRNA"};
9144
"rRNA", "ncRNA", "tmRNA"};
8036
9145
static Int2 num_rna_subtypes = sizeof (rna_subtype_list) / sizeof (CharPtr);
8037
9146
8038
9147
static CharPtr GetRNASubtypeName (ValNodePtr vnp)
8061
9170
ValNodeAddInt (&choice_list, 2, FEATDEF_mRNA);
8062
9171
ValNodeAddInt (&choice_list, 3, FEATDEF_tRNA);
8063
9172
ValNodeAddInt (&choice_list, 4, FEATDEF_rRNA);
8064
ValNodeAddInt (&choice_list, 5, FEATDEF_snRNA);
8065
ValNodeAddInt (&choice_list, 6, FEATDEF_scRNA);
8066
ValNodeAddInt (&choice_list, 7, FEATDEF_snoRNA);
9173
ValNodeAddInt (&choice_list, 5, FEATDEF_ncRNA);
9174
ValNodeAddInt (&choice_list, 6, FEATDEF_tmRNA);
8067
9175
8068
9176
dlg = ValNodeSelectionDialog (h, choice_list, TALL_SELECTION_LIST,
8069
9177
GetRNASubtypeName, NULL,
8074
9182
}
8075
9183
8076
9184
8077
static CharPtr GetRNANameString (SeqFeatPtr sfp)
9185
static CharPtr GetRNAProductString (SeqFeatPtr sfp)
8078
9186
{
8079
9187
RnaRefPtr rrp;
8080
9188
SeqMgrFeatContext context;
8081
9189
CharPtr str = NULL;
9190
GBQualPtr gbqual;
8082
9191
8083
9192
if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA || sfp->data.value.ptrvalue == NULL)
8084
9193
{
8085
9194
return NULL;
8086
9195
}
9196
8087
9197
rrp = sfp->data.value.ptrvalue;
8088
if (rrp->ext.choice == 1 && !StringHasNoText (rrp->ext.value.ptrvalue))
9198
if (rrp->ext.choice == 0
9199
|| (rrp->ext.choice == 1 && StringHasNoText (rrp->ext.value.ptrvalue))
9200
|| (rrp->ext.choice == 1
9201
&& (StringCmp (rrp->ext.value.ptrvalue, "ncRNA") == 0
9202
|| StringCmp (rrp->ext.value.ptrvalue, "tmRNA") == 0
9203
|| StringCmp (rrp->ext.value.ptrvalue, "misc_RNA") == 0)))
8089
9204
{
8090
str = StringSave (rrp->ext.value.ptrvalue);
9205
gbqual = sfp->qual;
9206
while (gbqual != NULL && str == NULL) {
9207
if (StringICmp (gbqual->qual, "product") == 0
9208
&& !StringHasNoText (gbqual->val))
9209
{
9210
str = StringSave (gbqual->val);
9211
}
9212
gbqual = gbqual->next;
9213
}
8091
9214
}
8092
else if (rrp->ext.choice == 2 && rrp->ext.value.ptrvalue != NULL)
9215
9216
if (str == NULL)
8093
9217
{
8094
if (SeqMgrGetDesiredFeature (sfp->idx.entityID, NULL, 0, 0, sfp, &context) != NULL
8095
&& !StringHasNoText (context.label))
8096
{
8097
str = (CharPtr) MemNew (sizeof (Char) + (StringLen (context.label) + 6));
8098
sprintf (str, "tRNA-%s", context.label);
9218
if (rrp->ext.choice == 1 && !StringHasNoText (rrp->ext.value.ptrvalue)
9219
&& StringCmp (rrp->ext.value.ptrvalue, "ncRNA") != 0
9220
&& StringCmp (rrp->ext.value.ptrvalue, "tmRNA") != 0
9221
&& StringCmp (rrp->ext.value.ptrvalue, "misc_RNA") != 0)
9222
{
9223
str = StringSave (rrp->ext.value.ptrvalue);
9224
}
9225
else if (rrp->ext.choice == 2 && rrp->ext.value.ptrvalue != NULL)
9226
{
9227
if (SeqMgrGetDesiredFeature (sfp->idx.entityID, NULL, 0, 0, sfp, &context) != NULL
9228
&& !StringHasNoText (context.label)
9229
&& StringCmp (context.label, "tRNA") != 0)
9230
{
9231
str = (CharPtr) MemNew (sizeof (Char) + (StringLen (context.label) + 6));
9232
sprintf (str, "tRNA-%s", context.label);
9233
}
8099
9234
}
8100
9235
}
8101
9236
return str;
8105
9240
{
8106
9241
RnaRefPtr rrp;
8107
9242
CharPtr str = NULL;
8108
GBQualPtr gbqual;
8109
9243
ValNode vn;
8110
9244
GeneRefPtr grp;
8111
9245
SeqFeatPtr gene;
8112
9246
SeqMgrFeatContext context;
8113
9247
Int4 field_choice;
9248
GBQualPtr qual;
8114
9249
8115
9250
if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA || vnp == NULL)
8116
9251
{
8124
9259
field_choice = vnp->data.intvalue;
8125
9260
switch (vnp->data.intvalue)
8126
9261
{
8127
case RNAFIELD_NAME :
8128
str = GetRNANameString (sfp);
9262
case RNAFIELD_PRODUCT :
9263
str = GetRNAProductString (sfp);
8129
9264
break;
8130
9265
case RNAFIELD_COMMENT :
8131
9266
if (!StringHasNoText (sfp->comment))
8133
9268
str = StringSave (sfp->comment);
8134
9269
}
8135
9270
break;
8136
case RNAFIELD_PRODUCT :
8137
gbqual = sfp->qual;
8138
while (gbqual != NULL && str == NULL) {
8139
if (StringICmp (gbqual->qual, "product") == 0
8140
&& !StringHasNoText (gbqual->val))
9271
case RNAFIELD_NCRNA_CLASS :
9272
for (qual = sfp->qual; qual != NULL && str == NULL; qual = qual->next)
9273
{
9274
if (StringCmp (qual->qual, "ncRNA_class") == 0
9275
&& !StringHasNoText (qual->val))
8141
9276
{
8142
str = StringSave (gbqual->val);
9277
str = StringSave (qual->val);
8143
9278
}
8144
gbqual = gbqual->next;
8145
9279
}
8146
9280
break;
8147
9281
default:
8206
9340
GBQualPtr gbqual, gbqual_last = NULL;
8207
9341
8208
9342
if (sfp == NULL || sfp->data.value.ptrvalue == NULL
8209
|| sfp->data.choice != SEQFEAT_RNA
9343
|| sfp->idx.subtype != FEATDEF_tRNA
8210
9344
|| avp == NULL)
8211
9345
{
8212
9346
return;
8213
9347
}
8214
9348
8215
9349
rrp = sfp->data.value.ptrvalue;
9350
if (rrp->ext.choice == 0)
9351
{
9352
trp = MemNew (sizeof (tRNA));
9353
trp->aatype = 0;
9354
MemSet (trp->codon, 255, sizeof (trp->codon));
9355
trp->anticodon = NULL;
9356
rrp->ext.value.ptrvalue = trp;
9357
rrp->ext.choice = 2;
9358
}
8216
9359
if (rrp->ext.choice != 2)
8217
9360
{
8218
9361
return;
8219
9362
}
8220
9363
trp = (tRNAPtr) rrp->ext.value.ptrvalue;
8221
9364
8222
name_string = GetRNANameString (sfp);
9365
name_string = GetRNAProductString (sfp);
8223
9366
name_string = HandleApplyValue (name_string, avp);
8224
9367
if (!IsParseabletRNAName(name_string))
8225
9368
{
8262
9405
{
8263
9406
new_aa = ParseTRnaString (name_string, &justTrnaText, codon, TRUE);
8264
9407
trp->aa = new_aa;
9408
trp->aatype = 2;
8265
9409
name_string = MemFree (name_string);
8266
9410
}
8267
9411
}
8268
9412
8269
9413
9414
static void SetRNAProduct (SeqFeatPtr sfp, ApplyValuePtr avp)
9415
{
9416
RnaRefPtr rrp;
9417
GBQualPtr gbq, prev_gbq = NULL;
9418
9419
if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA || sfp->data.value.ptrvalue == NULL || avp == NULL)
9420
{
9421
return;
9422
}
9423
9424
rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
9425
9426
gbq = sfp->qual;
9427
while (gbq != NULL && StringCmp (gbq->qual, "product") != 0)
9428
{
9429
prev_gbq = gbq;
9430
gbq = gbq->next;
9431
}
9432
if (gbq != NULL)
9433
{
9434
gbq->val = HandleApplyValue (gbq->val, avp);
9435
if (StringHasNoText (gbq->val))
9436
{
9437
if (prev_gbq == NULL)
9438
{
9439
sfp->qual = gbq->next;
9440
}
9441
else
9442
{
9443
prev_gbq->next = gbq->next;
9444
}
9445
gbq->next = NULL;
9446
gbq = GBQualFree (gbq);
9447
}
9448
}
9449
else if (sfp->idx.subtype == FEATDEF_tRNA || rrp->ext.choice == 2)
9450
{
9451
SettRNAName (sfp, avp);
9452
}
9453
else if (rrp->ext.choice == 1
9454
&& (StringCmp (rrp->ext.value.ptrvalue, "ncRNA") == 0
9455
|| StringCmp (rrp->ext.value.ptrvalue, "tmRNA") == 0
9456
|| StringCmp (rrp->ext.value.ptrvalue, "misc_RNA") == 0))
9457
{
9458
gbq = GBQualNew();
9459
gbq->qual = StringSave ("product");
9460
gbq->val = HandleApplyValue (gbq->val, avp);
9461
gbq->next = sfp->qual;
9462
sfp->qual = gbq;
9463
}
9464
else if (rrp->ext.choice == 1 || rrp->ext.choice == 0)
9465
{
9466
rrp->ext.value.ptrvalue = HandleApplyValue (rrp->ext.value.ptrvalue, avp);
9467
if (StringHasNoText (rrp->ext.value.ptrvalue))
9468
{
9469
rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
9470
rrp->ext.choice = 0;
9471
}
9472
else
9473
{
9474
rrp->ext.choice = 1;
9475
}
9476
}
9477
}
9478
9479
8270
9480
static void SetRNAFieldString (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
8271
9481
{
8272
9482
RnaRefPtr rrp;
8273
9483
ApplyValuePtr avp;
8274
GBQualPtr gbqual, gbqual_last = NULL;
8275
9484
SeqFeatPtr gene;
8276
9485
GeneRefPtr grp;
8277
9486
SeqMgrFeatContext context;
9487
GBQualPtr qual;
9488
Boolean found = FALSE;
8278
9489
8279
9490
if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA || userdata == NULL)
8280
9491
{
8291
9502
8292
9503
switch (avp->field_list->data.intvalue)
8293
9504
{
8294
case RNAFIELD_NAME :
8295
if (rrp != NULL)
8296
{
8297
if (rrp->ext.choice == 0)
8298
{
8299
rrp->ext.choice = 1;
8300
rrp->ext.value.ptrvalue = NULL;
8301
}
8302
if (rrp->ext.choice == 1)
8303
{
8304
rrp->ext.value.ptrvalue = HandleApplyValue (rrp->ext.value.ptrvalue, avp);
8305
}
8306
else if (rrp->ext.choice == 2)
8307
{
8308
SettRNAName (sfp, avp);
8309
}
8310
}
9505
case RNAFIELD_PRODUCT :
9506
SetRNAProduct (sfp, avp);
8311
9507
break;
8312
9508
case RNAFIELD_COMMENT :
8313
9509
sfp->comment = HandleApplyValue (sfp->comment, avp);
8314
9510
break;
8315
case RNAFIELD_PRODUCT :
8316
gbqual = sfp->qual;
8317
while (gbqual != NULL && StringICmp (gbqual->qual, "product") != 0)
8318
{
8319
gbqual_last = gbqual;
8320
gbqual = gbqual->next;
8321
}
8322
if (gbqual == NULL)
8323
{
8324
if (StringHasNoText (avp->text_to_replace))
8325
{
8326
gbqual = GBQualNew ();
8327
if (gbqual == NULL)
8328
{
8329
return;
8330
}
8331
gbqual->qual = StringSave ("product");
8332
gbqual->val = StringSave (avp->new_text);
8333
if (gbqual_last == NULL)
8334
{
8335
sfp->qual = gbqual;
8336
}
8337
else
8338
{
8339
gbqual->next = gbqual_last->next;
8340
gbqual_last->next = gbqual;
8341
}
8342
}
8343
else
8344
{
8345
/* don't create new product for edit/replace */
8346
}
8347
}
8348
else
8349
{
8350
gbqual->val = HandleApplyValue (gbqual->val, avp);
9511
case RNAFIELD_NCRNA_CLASS :
9512
for (qual = sfp->qual; qual != NULL; qual = qual->next)
9513
{
9514
if (StringCmp (qual->qual, "ncRNA_class") == 0)
9515
{
9516
qual->val = HandleApplyValue (qual->val, avp);
9517
found = TRUE;
9518
}
9519
}
9520
if (!found)
9521
{
9522
qual = GBQualNew ();
9523
qual->qual = StringSave ("ncRNA_class");
9524
qual->val = StringSave (avp->new_text);
9525
qual->next = sfp->qual;
9526
sfp->qual = qual;
8351
9527
}
8352
9528
break;
8353
9529
default:
8370
9546
}
8371
9547
}
8372
9548
9549
9550
static void RemoveRNAProduct (SeqFeatPtr sfp)
9551
{
9552
RnaRefPtr rrp;
9553
GBQualPtr gbq, prev_gbq = NULL;
9554
tRNAPtr trp;
9555
9556
if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA || sfp->data.value.ptrvalue == NULL)
9557
{
9558
return;
9559
}
9560
9561
rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
9562
9563
gbq = sfp->qual;
9564
while (gbq != NULL && StringCmp (gbq->qual, "product") != 0)
9565
{
9566
prev_gbq = gbq;
9567
gbq = gbq->next;
9568
}
9569
if (gbq != NULL)
9570
{
9571
if (prev_gbq == NULL)
9572
{
9573
sfp->qual = gbq->next;
9574
}
9575
else
9576
{
9577
prev_gbq->next = gbq->next;
9578
}
9579
gbq->next = NULL;
9580
gbq = GBQualFree (gbq);
9581
}
9582
else if (rrp->ext.choice == 1
9583
&& (StringCmp (rrp->ext.value.ptrvalue, "ncRNA") == 0
9584
|| StringCmp (rrp->ext.value.ptrvalue, "tmRNA") == 0
9585
|| StringCmp (rrp->ext.value.ptrvalue, "misc_RNA") == 0))
9586
{
9587
/* do nothing - already have no product */
9588
}
9589
else if (rrp->ext.choice == 0)
9590
{
9591
/* do nothing - already have no product */
9592
}
9593
else if (rrp->ext.choice == 1)
9594
{
9595
rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
9596
rrp->ext.choice = 0;
9597
}
9598
else if (rrp->ext.choice == 2)
9599
{
9600
trp = (tRNAPtr) rrp->ext.value.ptrvalue;
9601
if (trp != NULL)
9602
{
9603
trp->aatype = 0;
9604
}
9605
}
9606
}
9607
9608
8373
9609
static void RemoveRNAField (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
8374
9610
{
8375
9611
RnaRefPtr rrp;
8376
GBQualPtr gbqual, prev_qual = NULL, next_qual;
8377
9612
tRNAPtr trp;
8378
9613
ApplyValuePtr avp;
8379
9614
SeqFeatPtr gene;
8380
9615
GeneRefPtr grp;
8381
9616
ValNode vn;
8382
9617
SeqMgrFeatContext context;
9618
GBQualPtr qual, qual_prev = NULL, qual_next;
8383
9619
8384
9620
if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA || userdata == NULL)
8385
9621
{
8396
9632
8397
9633
switch (avp->field_list->data.intvalue)
8398
9634
{
8399
case RNAFIELD_NAME :
8400
if (rrp != NULL && rrp->ext.value.ptrvalue != NULL)
8401
{
8402
if (rrp->ext.choice == 1)
8403
{
8404
rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
8405
}
8406
else if (rrp->ext.choice == 2)
8407
{
8408
trp = (tRNAPtr) rrp->ext.value.ptrvalue;
8409
if (trp != NULL)
8410
{
8411
trp->aatype = 0;
8412
}
8413
}
8414
}
9635
case RNAFIELD_PRODUCT :
9636
RemoveRNAProduct (sfp);
8415
9637
break;
8416
9638
case RNAFIELD_COMMENT :
8417
9639
sfp->comment = MemFree (sfp->comment);
8418
9640
break;
8419
case RNAFIELD_PRODUCT :
8420
gbqual = sfp->qual;
8421
while (gbqual != NULL)
9641
case RNAFIELD_NCRNA_CLASS :
9642
qual = sfp->qual;
9643
while (qual != NULL)
8422
9644
{
8423
next_qual = gbqual->next;
8424
if (StringICmp (gbqual->qual, "product") == 0)
9645
qual_next = qual->next;
9646
if (StringCmp (qual->qual, "ncRNA_class") == 0)
8425
9647
{
8426
if (prev_qual == NULL)
9648
if (qual_prev == NULL)
8427
9649
{
8428
sfp->qual = sfp->qual->next;
9650
sfp->qual = qual_next;
8429
9651
}
8430
9652
else
8431
9653
{
8432
prev_qual->next = gbqual->next;
9654
qual_prev->next = qual_next;
8433
9655
}
8434
gbqual->next = NULL;
8435
GBQualFree (gbqual);
9656
qual->next = NULL;
9657
qual = GBQualFree (qual);
8436
9658
}
8437
9659
else
8438
9660
{
8439
prev_qual = gbqual;
9661
qual_prev = qual;
8440
9662
}
8441
gbqual = next_qual;
9663
qual = qual_next;
8442
9664
}
8443
break;
9665
break;
8444
9666
case RNAFIELD_ANTICODON :
8445
9667
if (rrp->ext.choice == 2) {
8446
9668
trp = (tRNAPtr) rrp->ext.value.ptrvalue;
8547
9769
gbqual = sfp->qual;
8548
9770
while (gbqual != NULL && StringHasNoText (str))
8549
9771
{
8550
if (vnp->data.intvalue < NUM_EXON_FIELDS + 2
8551
&& vnp->data.intvalue >= 2
8552
&& StringCmp (gbqual->qual, exon_field_list[vnp->data.intvalue - 2]) == 0)
9772
if (vnp->data.intvalue < NUM_EXON_FIELDS + 1
9773
&& vnp->data.intvalue >= 1
9774
&& StringCmp (gbqual->qual, exon_field_list[vnp->data.intvalue - 1]) == 0)
8553
9775
{
8554
9776
str = gbqual->val;
8555
9777
}
8600
9822
prev_qual = NULL;
8601
9823
while (gbqual != NULL)
8602
9824
{
8603
if (vnp->data.intvalue < NUM_EXON_FIELDS + 2
8604
&& vnp->data.intvalue >= 2
8605
&& StringCmp (gbqual->qual, exon_field_list[vnp->data.intvalue - 2]) == 0)
9825
if (vnp->data.intvalue <= NUM_EXON_FIELDS + 1
9826
&& vnp->data.intvalue >= 1
9827
&& StringCmp (gbqual->qual, exon_field_list[vnp->data.intvalue - 1]) == 0)
8606
9828
{
8607
9829
if (!StringHasNoText (gbqual->val))
8608
9830
{
8612
9834
if (prev_qual == NULL)
8613
9835
{
8614
9836
sfp->qual = gbqual->next;
8615
gbqual->next = NULL;
8616
GBQualFree (gbqual);
8617
return;
9837
} else {
9838
prev_qual->next = gbqual->next;
8618
9839
}
9840
gbqual->next = NULL;
9841
GBQualFree (gbqual);
9842
return;
8619
9843
}
8620
9844
}
8621
9845
}
9846
prev_qual = gbqual;
8622
9847
gbqual = gbqual->next;
8623
9848
}
8624
9849
}
8639
9864
8640
9865
avp = (ApplyValuePtr) userdata;
8641
9866
if (avp->field_list == NULL
8642
|| avp->field_list->data.intvalue >= NUM_EXON_FIELDS + 2
8643
|| avp->field_list->data.intvalue < 2)
9867
|| avp->field_list->data.intvalue >= NUM_EXON_FIELDS + 1
9868
|| avp->field_list->data.intvalue < 1)
8644
9869
{
8645
9870
return;
8646
9871
}
8654
9879
while (gbqual != NULL)
8655
9880
{
8656
9881
if (StringCmp (gbqual->qual,
8657
exon_field_list[avp->field_list->data.intvalue - 2]) == 0)
9882
exon_field_list[avp->field_list->data.intvalue - 1]) == 0)
8658
9883
{
8659
9884
gbqual->val = HandleApplyValue (gbqual->val, avp);
8660
9885
found = TRUE;
8665
9890
if (!found)
8666
9891
{
8667
9892
gbqual = GBQualNew ();
8668
gbqual->qual = StringSave (exon_field_list[avp->field_list->data.intvalue - 2]);
9893
gbqual->qual = StringSave (exon_field_list[avp->field_list->data.intvalue - 1]);
8669
9894
gbqual->val = StringSave (avp->new_text);
8670
9895
if (prev_qual == NULL)
8671
9896
{
8816
10041
}
8817
10042
8818
10043
10044
static CharPtr GetDbxrefFromBioSource (BioSourcePtr biop, ValNodePtr vnp)
10045
{
10046
ValNodePtr dbx;
10047
DbtagPtr dbtag;
10048
Char buf[20];
10049
10050
if (biop == NULL || vnp == NULL || vnp->data.ptrvalue == NULL || biop->org == NULL)
10051
{
10052
return NULL;
10053
}
10054
10055
dbx = biop->org->db;
10056
while (dbx != NULL)
10057
{
10058
dbtag = (DbtagPtr) dbx->data.ptrvalue;
10059
if (dbtag != NULL && dbtag->tag != NULL
10060
&& StringCmp (dbtag->db, vnp->data.ptrvalue) == 0)
10061
{
10062
if (dbtag->tag->str == NULL)
10063
{
10064
sprintf (buf, "%d", dbtag->tag->id);
10065
return StringSave (buf);
10066
}
10067
else
10068
{
10069
return StringSave (dbtag->tag->str);
10070
}
10071
}
10072
dbx = dbx->next;
10073
}
10074
return NULL;
10075
}
10076
10077
static CharPtr
10078
GetBioSourceFeatureDbxrefString
10079
(SeqFeatPtr sfp,
10080
ValNodePtr vnp,
10081
FilterSetPtr fsp)
10082
{
10083
if (sfp == NULL || sfp->data.choice != SEQFEAT_BIOSRC || vnp == NULL)
10084
{
10085
return NULL;
10086
}
10087
10088
return GetDbxrefFromBioSource (sfp->data.value.ptrvalue, vnp);
10089
}
10090
10091
static CharPtr
10092
GetBioSourceDescriptorDbxrefString
10093
(SeqDescrPtr sdp,
10094
ValNodePtr vnp,
10095
FilterSetPtr fsp)
10096
{
10097
if (sdp == NULL || sdp->choice != Seq_descr_source || vnp == NULL)
10098
{
10099
return NULL;
10100
}
10101
return GetDbxrefFromBioSource (sdp->data.ptrvalue, vnp);
10102
}
10103
10104
10105
static void ApplyBioSourceDbxrefBioSourceCallback (BioSourcePtr biop, Pointer userdata)
10106
{
10107
ApplyValuePtr avp;
10108
ValNodePtr dbx;
10109
DbtagPtr dbtag;
10110
Boolean found = FALSE;
10111
Char buf[20];
10112
10113
if (biop == NULL || userdata == NULL)
10114
{
10115
return;
10116
}
10117
10118
avp = (ApplyValuePtr) userdata;
10119
if (avp->field_list != NULL && !StringHasNoText (avp->new_text))
10120
{
10121
if (biop->org == NULL)
10122
{
10123
biop->org = OrgRefNew();
10124
}
10125
dbx = biop->org->db;
10126
while (dbx != NULL && !found)
10127
{
10128
dbtag = (DbtagPtr) dbx->data.ptrvalue;
10129
if (dbtag != NULL && dbtag->tag != NULL
10130
&& StringCmp (dbtag->db, avp->field_list->data.ptrvalue) == 0)
10131
{
10132
found = TRUE;
10133
}
10134
if (!found)
10135
{
10136
dbx = dbx->next;
10137
}
10138
}
10139
if (!found)
10140
{
10141
dbtag = DbtagNew();
10142
dbtag->db = StringSave (avp->field_list->data.ptrvalue);
10143
ValNodeAddPointer (&(biop->org->db), 0, dbtag);
10144
}
10145
if (dbtag->tag == NULL)
10146
{
10147
dbtag->tag = ObjectIdNew();
10148
}
10149
/* if it was a number before, make it a string now */
10150
if (dbtag->tag->id > 0 && dbtag->tag->str == NULL)
10151
{
10152
sprintf (buf, "%s", dbtag->tag->id);
10153
dbtag->tag->id = 0;
10154
dbtag->tag->str = StringSave (buf);
10155
}
10156
dbtag->tag->str = HandleApplyValue (dbtag->tag->str, avp);
10157
}
10158
10159
}
10160
10161
static void ApplyBioSourceDbxrefFeatureCallback (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
10162
{
10163
if (sfp == NULL || sfp->data.choice != SEQFEAT_BIOSRC || userdata == NULL)
10164
{
10165
return;
10166
}
10167
ApplyBioSourceDbxrefBioSourceCallback (sfp->data.value.ptrvalue, userdata);
10168
}
10169
10170
static void ApplyBioSourceDbxrefDescriptorCallback (SeqDescrPtr sdp, Pointer userdata, FilterSetPtr fsp)
10171
{
10172
if (sdp == NULL || sdp->choice != Seq_descr_source || userdata == NULL)
10173
{
10174
return;
10175
}
10176
ApplyBioSourceDbxrefBioSourceCallback (sdp->data.ptrvalue, userdata);
10177
}
10178
10179
10180
8819
10181
#define TEXT_PORTION_START_AFTER 1
8820
10182
#define TEXT_PORTION_START_WITH 2
8821
10183
#define TEXT_PORTION_END_AFTER 1
8829
10191
TexT start_text;
8830
10192
GrouP end_choice;
8831
10193
TexT end_text;
10194
ButtoN rem_before;
10195
ButtoN also_rem_before;
10196
ButtoN rem_after;
10197
ButtoN also_rem_after;
8832
10198
ButtoN insensitive;
8833
10199
ButtoN whole_word;
8834
} TextPortionDialogData, PNTR TextPortionDialogPtr;
8835
8836
static void ResetTextPortionDialog (TextPortionDialogPtr tp)
10200
10201
Boolean inside;
10202
10203
Nlm_ChangeNotifyProc change_notify;
10204
Pointer change_userdata;
10205
} TextPortionXDialogData, PNTR TextPortionXDialogPtr;
10206
10207
10208
static void OutsideEnableDisable (TextPortionXDialogPtr tp)
10209
{
10210
if (tp == NULL || tp->inside)
10211
{
10212
return;
10213
}
10214
if (GetStatus (tp->rem_before))
10215
{
10216
Enable (tp->start_text);
10217
Enable (tp->also_rem_before);
10218
}
10219
else
10220
{
10221
Disable (tp->start_text);
10222
Disable (tp->also_rem_before);
10223
}
10224
if (GetStatus (tp->rem_after))
10225
{
10226
Enable (tp->end_text);
10227
Enable (tp->also_rem_after);
10228
}
10229
else
10230
{
10231
Disable (tp->end_text);
10232
Disable (tp->also_rem_after);
10233
}
10234
}
10235
10236
static void ResetTextPortionXDialog (TextPortionXDialogPtr tp)
8837
10237
{
8838
10238
if (tp == NULL)
8839
10239
{
8840
10240
return;
8841
10241
}
8842
SetValue (tp->start_choice, TEXT_PORTION_START_AFTER);
10242
if (tp->inside)
10243
{
10244
SetValue (tp->start_choice, TEXT_PORTION_START_AFTER);
10245
SetValue (tp->end_choice, TEXT_PORTION_END_AFTER);
10246
}
10247
else
10248
{
10249
SetStatus (tp->rem_before, FALSE);
10250
SetStatus (tp->also_rem_before, FALSE);
10251
SetStatus (tp->rem_after, FALSE);
10252
SetStatus (tp->also_rem_after, FALSE);
10253
}
8843
10254
SetTitle (tp->start_text, "");
8844
SetValue (tp->end_choice, TEXT_PORTION_END_AFTER);
8845
10255
SetTitle (tp->end_text, "");
8846
10256
SetStatus (tp->insensitive, FALSE);
8847
10257
SetStatus (tp->whole_word, FALSE);
10258
OutsideEnableDisable (tp);
8848
10259
}
8849
10260
8850
static void TextPortionToDialog (DialoG d, Pointer data)
10261
static void TextPortionXToDialog (DialoG d, Pointer data)
8851
10262
{
8852
TextPortionDialogPtr tdlg;
8853
TextPortionPtr tdata;
10263
TextPortionXDialogPtr tdlg;
10264
TextPortionXPtr tdata;
8854
10265
Int4 start_choice, end_choice;
8855
10266
8856
tdlg = (TextPortionDialogPtr) GetObjectExtra (d);
10267
tdlg = (TextPortionXDialogPtr) GetObjectExtra (d);
8857
10268
if (tdlg == NULL)
8858
10269
{
8859
10270
return;
8860
10271
}
8861
tdata = (TextPortionPtr) data;
8862
ResetTextPortionDialog (tdlg);
10272
tdata = (TextPortionXPtr) data;
10273
ResetTextPortionXDialog (tdlg);
8863
10274
if (tdata != NULL)
8864
10275
{
8865
10276
start_choice = tdata->end_choice;
8872
10283
{
8873
10284
end_choice = TEXT_PORTION_END_AFTER;
8874
10285
}
8875
SetValue (tdlg->start_choice, start_choice);
8876
SetValue (tdlg->end_choice, end_choice);
10286
if (tdlg->inside)
10287
{
10288
SetValue (tdlg->start_choice, start_choice);
10289
SetValue (tdlg->end_choice, end_choice);
10290
}
10291
else
10292
{
10293
SetStatus (tdlg->rem_before, StringHasNoText (tdata->start_text));
10294
SetStatus (tdlg->rem_after, StringHasNoText (tdata->end_text));
10295
if (start_choice == TEXT_PORTION_START_AFTER)
10296
{
10297
SetStatus (tdlg->also_rem_before, TRUE);
10298
}
10299
else
10300
{
10301
SetStatus (tdlg->also_rem_before, FALSE);
10302
}
10303
if (end_choice == TEXT_PORTION_END_AFTER)
10304
{
10305
SetStatus (tdlg->also_rem_after, TRUE);
10306
}
10307
else
10308
{
10309
SetStatus (tdlg->also_rem_after, FALSE);
10310
}
10311
}
8877
10312
if (tdata->start_text != NULL)
8878
10313
{
8879
10314
SetTitle (tdlg->start_text, tdata->start_text);
8885
10320
SetStatus (tdlg->insensitive, tdata->insensitive);
8886
10321
SetStatus (tdlg->whole_word, tdata->whole_word);
8887
10322
}
10323
OutsideEnableDisable (tdlg);
8888
10324
}
8889
10325
8890
static Pointer DialogToTextPortion (DialoG d)
10326
static Pointer DialogToTextPortionX (DialoG d)
8891
10327
{
8892
TextPortionDialogPtr tdlg;
8893
TextPortionPtr tdata;
10328
TextPortionXDialogPtr tdlg;
10329
TextPortionXPtr tdata;
8894
10330
8895
tdlg = (TextPortionDialogPtr) GetObjectExtra (d);
10331
tdlg = (TextPortionXDialogPtr) GetObjectExtra (d);
8896
10332
if (tdlg == NULL)
8897
10333
{
8898
10334
return NULL;
8899
10335
}
8900
10336
8901
tdata = (TextPortionPtr) MemNew (sizeof (TextPortionData));
10337
tdata = (TextPortionXPtr) MemNew (sizeof (TextPortionXData));
8902
10338
if (tdata != NULL)
8903
10339
{
8904
tdata->start_choice = GetValue (tdlg->start_choice);
8905
tdata->end_choice = GetValue (tdlg->end_choice);
8906
tdata->start_text = JustSaveStringFromText (tdlg->start_text);
8907
tdata->end_text = JustSaveStringFromText (tdlg->end_text);
10340
if (tdlg->inside)
10341
{
10342
tdata->start_choice = GetValue (tdlg->start_choice);
10343
tdata->end_choice = GetValue (tdlg->end_choice);
10344
tdata->start_text = JustSaveStringFromText (tdlg->start_text);
10345
tdata->end_text = JustSaveStringFromText (tdlg->end_text);
10346
}
10347
else
10348
{
10349
if (GetStatus (tdlg->rem_before))
10350
{
10351
tdata->start_text = JustSaveStringFromText (tdlg->start_text);
10352
}
10353
else
10354
{
10355
tdata->start_text = NULL;
10356
}
10357
if (GetStatus (tdlg->rem_after))
10358
{
10359
tdata->end_text = JustSaveStringFromText (tdlg->end_text);
10360
}
10361
else
10362
{
10363
tdata->end_text = NULL;
10364
}
10365
10366
if (GetStatus (tdlg->also_rem_before))
10367
{
10368
tdata->start_choice = TEXT_PORTION_START_AFTER;
10369
}
10370
else
10371
{
10372
tdata->start_choice = TEXT_PORTION_START_WITH;
10373
}
10374
if (GetStatus (tdlg->also_rem_after))
10375
{
10376
tdata->end_choice = TEXT_PORTION_END_AFTER;
10377
}
10378
else
10379
{
10380
tdata->end_choice = TEXT_PORTION_END_WITH;
10381
}
10382
10383
}
10384
8908
10385
tdata->insensitive = GetStatus (tdlg->insensitive);
8909
10386
tdata->whole_word = GetStatus (tdlg->whole_word);
8910
10387
}
8911
10388
return tdata;
8912
10389
}
8913
10390
8914
static void TextPortionMessage (DialoG d, Int2 mssg)
10391
static void TextPortionXMessage (DialoG d, Int2 mssg)
8915
10392
8916
10393
{
8917
TextPortionDialogPtr tp;
10394
TextPortionXDialogPtr tp;
8918
10395
8919
tp = (TextPortionDialogPtr) GetObjectExtra (d);
10396
tp = (TextPortionXDialogPtr) GetObjectExtra (d);
8920
10397
if (tp != NULL) {
8921
10398
switch (mssg) {
8922
10399
case VIB_MSG_INIT :
8923
ResetTextPortionDialog (tp);
10400
ResetTextPortionXDialog (tp);
8924
10401
break;
8925
10402
case VIB_MSG_ENTER :
8926
10403
Select (tp->start_text);
8931
10408
}
8932
10409
}
8933
10410
8934
static ValNodePtr TestTextPortionDialog (DialoG d)
10411
static ValNodePtr TestTextPortionXDialog (DialoG d)
8935
10412
8936
10413
{
8937
10414
return NULL;
8938
10415
}
8939
10416
8940
extern DialoG TextPortionDialog (GrouP h)
8941
{
8942
TextPortionDialogPtr tp;
10417
static void ChangeTextPortionXGroup (GrouP g)
10418
{
10419
TextPortionXDialogPtr tp;
10420
10421
tp = (TextPortionXDialogPtr) GetObjectExtra (g);
10422
if (tp == NULL) return;
10423
10424
if (tp->change_notify != NULL)
10425
{
10426
(tp->change_notify) (tp->change_userdata);
10427
}
10428
}
10429
10430
static void ChangeTextPortionXText (TexT t)
10431
{
10432
TextPortionXDialogPtr tp;
10433
10434
tp = (TextPortionXDialogPtr) GetObjectExtra (t);
10435
if (tp == NULL) return;
10436
10437
if (tp->change_notify != NULL)
10438
{
10439
(tp->change_notify) (tp->change_userdata);
10440
}
10441
}
10442
10443
10444
static void ChangeTextPortionXBtn (ButtoN b)
10445
{
10446
TextPortionXDialogPtr tp;
10447
10448
tp = (TextPortionXDialogPtr) GetObjectExtra (b);
10449
if (tp == NULL) return;
10450
OutsideEnableDisable (tp);
10451
10452
if (tp->change_notify != NULL)
10453
{
10454
(tp->change_notify) (tp->change_userdata);
10455
}
10456
}
10457
10458
10459
10460
extern DialoG TextPortionXDialogEx (GrouP h, Boolean inside, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata)
10461
{
10462
TextPortionXDialogPtr tp;
8943
10463
GrouP p, g1, g2;
8944
10464
8945
tp = (TextPortionDialogPtr) MemNew (sizeof (TextPortionDialogData));
10465
tp = (TextPortionXDialogPtr) MemNew (sizeof (TextPortionXDialogData));
8946
10466
if (tp == NULL)
8947
10467
{
8948
10468
return NULL;
8952
10472
SetObjectExtra (p, tp, StdCleanupExtraProc);
8953
10473
8954
10474
tp->dialog = (DialoG) p;
8955
tp->todialog = TextPortionToDialog;
8956
tp->fromdialog = DialogToTextPortion;
8957
tp->dialogmessage = TextPortionMessage;
8958
tp->testdialog = TestTextPortionDialog;
8959
8960
g1 = HiddenGroup (p, 2, 0, NULL);
10475
tp->todialog = TextPortionXToDialog;
10476
tp->fromdialog = DialogToTextPortionX;
10477
tp->dialogmessage = TextPortionXMessage;
10478
tp->testdialog = TestTextPortionXDialog;
10479
10480
tp->change_notify = change_notify;
10481
tp->change_userdata = change_userdata;
10482
tp->inside = inside;
10483
10484
g1 = HiddenGroup (p, 3, 0, NULL);
8961
10485
SetGroupSpacing (g1, 10, 10);
8962
10486
8963
tp->start_choice = HiddenGroup (g1, 2, 0, NULL);
8964
RadioButton (tp->start_choice, "just after");
8965
RadioButton (tp->start_choice, "starting at");
8966
SetValue (tp->start_choice, TEXT_PORTION_START_AFTER);
10487
if (inside)
10488
{
10489
StaticPrompt (g1, "Between", 0, popupMenuHeight, programFont, 'r');
10490
tp->start_choice = HiddenGroup (g1, 2, 0, ChangeTextPortionXGroup);
10491
RadioButton (tp->start_choice, "just after");
10492
RadioButton (tp->start_choice, "starting at");
10493
SetValue (tp->start_choice, TEXT_PORTION_START_AFTER);
10494
SetObjectExtra (tp->start_choice, tp, NULL);
8967
10495
8968
tp->start_text = DialogText (g1, "", 10, NULL);
8969
8970
tp->end_choice = HiddenGroup (g1, 2, 0, NULL);
8971
RadioButton (tp->end_choice, "up to");
8972
RadioButton (tp->end_choice, "including");
8973
SetValue (tp->end_choice, TEXT_PORTION_END_AFTER);
10496
tp->start_text = DialogText (g1, "", 10, ChangeTextPortionXText);
10497
SetObjectExtra (tp->start_text, tp, NULL);
8974
10498
8975
tp->end_text = DialogText (g1, "", 10, NULL);
10499
StaticPrompt (g1, "And", 0, popupMenuHeight, programFont, 'r');
10500
tp->end_choice = HiddenGroup (g1, 2, 0, ChangeTextPortionXGroup);
10501
RadioButton (tp->end_choice, "up to");
10502
RadioButton (tp->end_choice, "including");
10503
SetValue (tp->end_choice, TEXT_PORTION_END_AFTER);
10504
SetObjectExtra (tp->start_choice, tp, NULL);
10505
10506
tp->end_text = DialogText (g1, "", 10, ChangeTextPortionXText);
10507
SetObjectExtra (tp->start_text, tp, NULL);
10508
}
10509
else
10510
{
10511
tp->rem_before = CheckBox (g1, "Before", ChangeTextPortionXBtn);
10512
SetObjectExtra (tp->rem_before, tp, NULL);
10513
tp->start_text = DialogText (g1, "", 10, ChangeTextPortionXText);
10514
SetObjectExtra (tp->start_text, tp, NULL);
10515
tp->also_rem_before = CheckBox (g1, "Also Remove Entered Text", ChangeTextPortionXBtn);
10516
10517
tp->rem_after = CheckBox (g1, "After", ChangeTextPortionXBtn);
10518
SetObjectExtra (tp->rem_after, tp, NULL);
10519
tp->end_text = DialogText (g1, "", 10, ChangeTextPortionXText);
10520
SetObjectExtra (tp->end_text, tp, NULL);
10521
tp->also_rem_after = CheckBox (g1, "Also Remove Entered Text", ChangeTextPortionXBtn);
10522
}
8976
10523
8977
10524
g2 = HiddenGroup (p, 2, 0, NULL);
8978
tp->insensitive = CheckBox (g2, "Case insensitive", NULL);
8979
tp->whole_word = CheckBox (g2, "Whole word", NULL);
10525
tp->insensitive = CheckBox (g2, "Case insensitive", ChangeTextPortionXBtn);
10526
SetObjectExtra (tp->insensitive, tp, NULL);
10527
tp->whole_word = CheckBox (g2, "Whole word", ChangeTextPortionXBtn);
10528
SetObjectExtra (tp->whole_word, tp, NULL);
8980
10529
8981
10530
AlignObjects (ALIGN_CENTER, (HANDLE) g1, (HANDLE) g2, NULL);
8982
10531
8983
ResetTextPortionDialog (tp);
10532
ResetTextPortionXDialog (tp);
8984
10533
return (DialoG) p;
8985
10534
}
8986
10535
8987
extern TextPortionPtr TextPortionFree (TextPortionPtr tp)
10536
extern DialoG TextPortionXDialog (GrouP h)
10537
{
10538
return TextPortionXDialogEx (h, TRUE, NULL, NULL);
10539
}
10540
10541
extern TextPortionXPtr TextPortionXFree (TextPortionXPtr tp)
8988
10542
{
8989
10543
if (tp == NULL) return NULL;
8990
10544
tp->start_text = MemFree (tp->start_text);
9027
10581
}
9028
10582
9029
10583
extern void
9030
FindTextPortionInString
10584
FindTextPortionXInString
9031
10585
(CharPtr str,
9032
TextPortionPtr tp,
10586
TextPortionXPtr tp,
9033
10587
CharPtr PNTR ploc,
9034
10588
Int4Ptr plen)
9035
10589
{
9130
10684
PointerToDialog (d, NULL);
9131
10685
}
9132
10686
10687
typedef struct changecasedlg {
10688
DIALOG_MESSAGE_BLOCK
10689
GrouP change_case;
10690
} ChangeCaseDlgData, PNTR ChangeCaseDlgPtr;
10691
10692
typedef enum {
10693
eChangeCaseNone = 1,
10694
eChangeCaseAllLower,
10695
eChangeCaseCapFirst
10696
} EChangeCaseRule;
10697
10698
typedef struct changecase {
10699
EChangeCaseRule change;
10700
} ChangeCaseData, PNTR ChangeCasePtr;
10701
10702
static void DataToChangeCaseDialog (DialoG d, Pointer data)
10703
{
10704
ChangeCasePtr ccp = (ChangeCasePtr) data;
10705
ChangeCaseDlgPtr dlg = (ChangeCaseDlgPtr) GetObjectExtra (d);
10706
if (dlg == NULL) return;
10707
10708
if (ccp == NULL || ccp->change == eChangeCaseNone) {
10709
SetValue (dlg->change_case, eChangeCaseNone);
10710
} else {
10711
SetValue (dlg->change_case, ccp->change);
10712
}
10713
}
10714
10715
static Pointer ChangeCaseDialogToData (DialoG d)
10716
{
10717
ChangeCaseDlgPtr dlg = (ChangeCaseDlgPtr) GetObjectExtra (d);
10718
ChangeCasePtr ccp = (ChangeCasePtr) MemNew (sizeof (ChangeCaseData));
10719
10720
if (dlg == NULL) {
10721
ccp->change = eChangeCaseNone;
10722
} else {
10723
ccp->change = GetValue (dlg->change_case);
10724
}
10725
return ccp;
10726
}
10727
10728
static DialoG ChangeCaseDialog (GrouP h)
10729
{
10730
ChangeCaseDlgPtr dlg;
10731
GrouP p;
10732
10733
dlg = (ChangeCaseDlgPtr) MemNew (sizeof (ChangeCaseDlgData));
10734
if (dlg == NULL)
10735
{
10736
return NULL;
10737
}
10738
10739
p = HiddenGroup (h, -1, 0, NULL);
10740
SetObjectExtra (p, dlg, StdCleanupExtraProc);
10741
SetGroupSpacing (p, 10, 10);
10742
10743
dlg->dialog = (DialoG) p;
10744
dlg->todialog = DataToChangeCaseDialog;
10745
dlg->fromdialog = ChangeCaseDialogToData;
10746
dlg->dialogmessage = NULL;
10747
dlg->testdialog = NULL;
10748
10749
dlg->change_case = NormalGroup (p, 3, 0, "Capitalization", programFont, NULL);
10750
SetGroupSpacing (dlg->change_case, 10, 10);
10751
10752
RadioButton (dlg->change_case, "No change");
10753
RadioButton (dlg->change_case, "To lower");
10754
RadioButton (dlg->change_case, "First cap, rest lower");
10755
SetValue (dlg->change_case, eChangeCaseNone);
10756
10757
return (DialoG) p;
10758
}
10759
10760
10761
static void ChangeCase (CharPtr PNTR pText, ChangeCasePtr ccp, ValNodePtr orgnames)
10762
{
10763
if (ccp != NULL) {
10764
switch (ccp->change) {
10765
case eChangeCaseNone:
10766
break;
10767
case eChangeCaseAllLower:
10768
FixCapitalizationInTitle (pText, FALSE, orgnames);
10769
break;
10770
case eChangeCaseCapFirst:
10771
FixCapitalizationInTitle (pText, TRUE, orgnames);
10772
break;
10773
}
10774
}
10775
}
10776
9133
10777
typedef struct stringconstraintdialog
9134
10778
{
9135
10779
DIALOG_MESSAGE_BLOCK
9137
10781
TexT match_text;
9138
10782
ButtoN insensitive;
9139
10783
ButtoN whole_word;
9140
} StringConstraintDialogData, PNTR StringConstraintDialogPtr;
10784
} StringConstraintDialogXData, PNTR StringConstraintDialogXPtr;
9141
10785
9142
static void ResetStringConstraintDialog (StringConstraintDialogPtr scdp)
10786
static void ResetStringConstraintDialogX (StringConstraintDialogXPtr scdp)
9143
10787
{
9144
10788
if (scdp == NULL) return;
9145
10789
9149
10793
SetStatus (scdp->whole_word, FALSE);
9150
10794
}
9151
10795
10796
10797
static Int4 GetPopupPosForStringConstraint (StringConstraintXPtr scp)
10798
{
10799
Int4 rval = 1;
10800
10801
if (scp == NULL) return 1;
10802
10803
switch (scp->match_location)
10804
{
10805
case eStringConstraintContains:
10806
if (scp->not_present)
10807
{
10808
rval = 2;
10809
} else {
10810
rval = 1;
10811
}
10812
break;
10813
case eStringConstraintEquals:
10814
if (scp->not_present) {
10815
rval = 4;
10816
} else {
10817
rval = 3;
10818
}
10819
break;
10820
case eStringConstraintStarts:
10821
if (scp->not_present) {
10822
rval = 9;
10823
} else {
10824
rval = 5;
10825
}
10826
break;
10827
case eStringConstraintEnds:
10828
if (scp->not_present) {
10829
rval = 10;
10830
} else {
10831
rval = 6;
10832
}
10833
break;
10834
case eStringConstraintInList:
10835
if (scp->not_present) {
10836
rval = 8;
10837
} else {
10838
rval = 7;
10839
}
10840
break;
10841
}
10842
return rval;
10843
}
10844
10845
9152
10846
static void StringConstraintToDialog (DialoG d, Pointer data)
9153
10847
9154
10848
{
9155
StringConstraintDialogPtr scdp;
9156
StringConstraintPtr scp;
9157
Int4 match_location;
10849
StringConstraintDialogXPtr scdp;
10850
StringConstraintXPtr scp;
9158
10851
9159
scdp = (StringConstraintDialogPtr) GetObjectExtra (d);
9160
scp = (StringConstraintPtr) data;
10852
scdp = (StringConstraintDialogXPtr) GetObjectExtra (d);
10853
scp = (StringConstraintXPtr) data;
9161
10854
if (scdp == NULL)
9162
10855
{
9163
10856
return;
9165
10858
9166
10859
if (scp == NULL)
9167
10860
{
9168
ResetStringConstraintDialog (scdp);
10861
ResetStringConstraintDialogX (scdp);
9169
10862
}
9170
10863
else
9171
10864
{
9172
match_location = scp->match_location;
9173
if (match_location < STRING_CONSTRAINT_CONTAINS || match_location > STRING_CONSTRAINT_ENDS)
9174
{
9175
match_location = STRING_CONSTRAINT_CONTAINS;
9176
}
9177
9178
if (scp->not_present)
9179
{
9180
match_location += STRING_CONSTRAINT_ENDS;
9181
}
9182
9183
SetValue (scdp->match_choice, match_location);
10865
SetValue (scdp->match_choice, GetPopupPosForStringConstraint (scp));
9184
10866
9185
10867
if (StringHasNoText (scp->match_text))
9186
10868
{
9199
10881
static Pointer DialogToStringConstraint (DialoG d)
9200
10882
9201
10883
{
9202
StringConstraintDialogPtr scdp;
9203
StringConstraintPtr scp;
10884
StringConstraintDialogXPtr scdp;
10885
StringConstraintXPtr scp;
9204
10886
Int4 match_choice;
9205
10887
9206
scdp = (StringConstraintDialogPtr) GetObjectExtra (d);
10888
scdp = (StringConstraintDialogXPtr) GetObjectExtra (d);
9207
10889
if (scdp == NULL)
9208
10890
{
9209
10891
return NULL;
9210
10892
}
9211
scp = (StringConstraintPtr) MemNew (sizeof (StringConstraintData));
10893
scp = (StringConstraintXPtr) MemNew (sizeof (StringConstraintData));
9212
10894
if (scp != NULL)
9213
10895
{
9214
10896
scp->match_text = SaveStringFromText (scdp->match_text);
9218
10900
switch (match_choice)
9219
10901
{
9220
10902
case 1:
9221
scp->match_location = STRING_CONSTRAINT_CONTAINS;
10903
scp->match_location = eStringConstraintContains;
9222
10904
scp->not_present = FALSE;
9223
10905
break;
9224
10906
case 2:
9225
scp->match_location = STRING_CONSTRAINT_CONTAINS;
10907
scp->match_location = eStringConstraintContains;
9226
10908
scp->not_present = TRUE;
9227
10909
break;
9228
10910
case 3:
9229
scp->match_location = STRING_CONSTRAINT_EQUALS;
10911
scp->match_location = eStringConstraintEquals;
9230
10912
scp->not_present = FALSE;
9231
10913
break;
9232
10914
case 4:
9233
scp->match_location = STRING_CONSTRAINT_EQUALS;
10915
scp->match_location = eStringConstraintEquals;
9234
10916
scp->not_present = TRUE;
9235
10917
break;
9236
10918
case 5:
9237
scp->match_location = STRING_CONSTRAINT_STARTS;
10919
scp->match_location = eStringConstraintStarts;
9238
10920
scp->not_present = FALSE;
9239
10921
break;
9240
10922
case 6:
9241
scp->match_location = STRING_CONSTRAINT_ENDS;
10923
scp->match_location = eStringConstraintEnds;
9242
10924
scp->not_present = FALSE;
9243
10925
break;
9244
10926
case 7:
9245
scp->match_location = STRING_CONSTRAINT_STARTS;
9246
scp->not_present = TRUE;
10927
scp->match_location = eStringConstraintInList;
10928
scp->not_present = FALSE;
9247
10929
break;
9248
10930
case 8:
9249
scp->match_location = STRING_CONSTRAINT_ENDS;
10931
scp->match_location = eStringConstraintInList;
10932
scp->not_present = TRUE;
10933
break;
10934
case 9:
10935
scp->match_location = eStringConstraintStarts;
10936
scp->not_present = TRUE;
10937
break;
10938
case 10:
10939
scp->match_location = eStringConstraintEnds;
9250
10940
scp->not_present = TRUE;
9251
10941
break;
9252
10942
default:
9253
scp->match_location = STRING_CONSTRAINT_CONTAINS;
10943
scp->match_location = eStringConstraintContains;
9254
10944
scp->not_present = FALSE;
9255
10945
break;
9256
10946
}
9261
10951
static void StringConstraintMessage (DialoG d, Int2 mssg)
9262
10952
9263
10953
{
9264
StringConstraintDialogPtr scdp;
10954
StringConstraintDialogXPtr scdp;
9265
10955
9266
scdp = (StringConstraintDialogPtr) GetObjectExtra (d);
10956
scdp = (StringConstraintDialogXPtr) GetObjectExtra (d);
9267
10957
if (scdp != NULL) {
9268
10958
switch (mssg) {
9269
10959
case VIB_MSG_INIT :
9270
ResetStringConstraintDialog (scdp);
10960
ResetStringConstraintDialogX (scdp);
9271
10961
break;
9272
10962
case VIB_MSG_ENTER :
9273
10963
Select (scdp->match_text);
9278
10968
}
9279
10969
}
9280
10970
9281
static ValNodePtr TestStringConstraintDialog (DialoG d)
10971
static ValNodePtr TestStringConstraintDialogX (DialoG d)
9282
10972
9283
10973
{
9284
10974
return NULL;
9285
10975
}
9286
10976
9287
extern DialoG StringConstraintDialog (GrouP h, CharPtr label, Boolean clear_btn)
10977
extern DialoG StringConstraintDialogX (GrouP h, CharPtr label, Boolean clear_btn)
9288
10978
9289
10979
{
9290
StringConstraintDialogPtr scdp;
10980
StringConstraintDialogXPtr scdp;
9291
10981
GrouP p, g, k;
9292
10982
ButtoN b = NULL;
9293
10983
9294
scdp = (StringConstraintDialogPtr) MemNew (sizeof (StringConstraintDialogData));
10984
scdp = (StringConstraintDialogXPtr) MemNew (sizeof (StringConstraintDialogXData));
9295
10985
if (scdp == NULL)
9296
10986
{
9297
10987
return NULL;
9304
10994
scdp->todialog = StringConstraintToDialog;
9305
10995
scdp->fromdialog = DialogToStringConstraint;
9306
10996
scdp->dialogmessage = StringConstraintMessage;
9307
scdp->testdialog = TestStringConstraintDialog;
10997
scdp->testdialog = TestStringConstraintDialogX;
9308
10998
9309
10999
g = HiddenGroup (p, 3, 0, NULL);
9310
11000
SetGroupSpacing (g, 10, 10);
9321
11011
PopupItem (scdp->match_choice, "Does not equal");
9322
11012
PopupItem (scdp->match_choice, "Starts with");
9323
11013
PopupItem (scdp->match_choice, "Ends with");
11014
PopupItem (scdp->match_choice, "Is one of");
11015
PopupItem (scdp->match_choice, "Is not one of");
9324
11016
PopupItem (scdp->match_choice, "Does not start with");
9325
11017
PopupItem (scdp->match_choice, "Does not end with");
9326
11018
SetValue (scdp->match_choice, 1);
9495
11187
DialoG string_qual_choice;
9496
11188
DialoG string_constraint;
9497
11189
DialoG pseudo_constraint;
11190
DialoG match_1;
11191
DialoG match_2;
9498
11192
FreeValNodeProc free_vn_proc;
9499
11193
CopyValNodeDataProc copy_vn_proc;
9500
11194
} ChoiceConstraintDialogData, PNTR ChoiceConstraintDialogPtr;
9516
11210
Enable (scdp->present_qual_choice);
9517
11211
Disable (scdp->string_qual_choice);
9518
11212
Disable (scdp->string_constraint);
11213
Disable (scdp->match_1);
11214
Disable (scdp->match_2);
9519
11215
SafeDisable (scdp->pseudo_constraint);
9520
11216
}
9521
11217
else if (constraint_type == CHOICE_CONSTRAINT_STRING)
9523
11219
Enable (scdp->string_qual_choice);
9524
11220
Enable (scdp->string_constraint);
9525
11221
Disable (scdp->present_qual_choice);
11222
Disable (scdp->match_1);
11223
Disable (scdp->match_2);
11224
SafeDisable (scdp->pseudo_constraint);
11225
}
11226
else if (constraint_type == CHOICE_CONSTRAINT_MATCH)
11227
{
11228
Enable (scdp->match_1);
11229
Enable (scdp->match_2);
11230
Disable (scdp->string_qual_choice);
11231
Disable (scdp->string_constraint);
11232
Disable (scdp->present_qual_choice);
9526
11233
SafeDisable (scdp->pseudo_constraint);
9527
11234
}
9528
11235
else if (constraint_type == CHOICE_CONSTRAINT_PSEUDO)
9530
11237
Disable (scdp->present_qual_choice);
9531
11238
Disable (scdp->string_qual_choice);
9532
11239
Disable (scdp->string_constraint);
11240
Disable (scdp->match_1);
11241
Disable (scdp->match_2);
9533
11242
Enable (scdp->pseudo_constraint);
9534
11243
}
9535
11244
else
9537
11246
Disable (scdp->present_qual_choice);
9538
11247
Disable (scdp->string_qual_choice);
9539
11248
Disable (scdp->string_constraint);
11249
Disable (scdp->match_1);
11250
Disable (scdp->match_2);
9540
11251
SafeDisable (scdp->pseudo_constraint);
9541
11252
}
9542
11253
}
9587
11298
PointerToDialog (src_dlg->string_qual_choice, src_data->qual_choice);
9588
11299
PointerToDialog (src_dlg->string_constraint, src_data->string_constraint);
9589
11300
}
11301
else if (constraint_type == CHOICE_CONSTRAINT_MATCH)
11302
{
11303
PointerToDialog (src_dlg->match_1, src_data->qual_choice);
11304
PointerToDialog (src_dlg->match_2, src_data->qual_choice_match);
11305
}
9590
11306
else if (constraint_type == CHOICE_CONSTRAINT_PSEUDO)
9591
11307
{
9592
11308
PointerToDialog (src_dlg->pseudo_constraint, src_data->pseudo_constraint);
9619
11335
src_data->qual_choice = DialogToPointer (src_dlg->string_qual_choice);
9620
11336
src_data->string_constraint = DialogToPointer (src_dlg->string_constraint);
9621
11337
}
11338
else if (src_data->constraint_type == CHOICE_CONSTRAINT_MATCH)
11339
{
11340
src_data->qual_choice = DialogToPointer (src_dlg->match_1);
11341
src_data->qual_choice_match = DialogToPointer (src_dlg->match_2);
11342
}
9622
11343
else if (src_data->constraint_type == CHOICE_CONSTRAINT_PSEUDO)
9623
11344
{
9624
11345
src_data->pseudo_constraint = DialogToPointer (src_dlg->pseudo_constraint);
9697
11418
RadioButton (scdp->constraint_type, "When");
9698
11419
q = HiddenGroup (scdp->constraint_type, 2, 0, NULL);
9699
11420
scdp->string_qual_choice = func_string (q, TRUE, NULL, NULL);
9700
scdp->string_constraint = StringConstraintDialog (q, NULL, FALSE);
11421
scdp->string_constraint = StringConstraintDialogX (q, NULL, FALSE);
9701
11422
11423
RadioButton (scdp->constraint_type, "When");
11424
q = HiddenGroup (scdp->constraint_type, 3, 0, NULL);
11425
scdp->match_1 = func_string (q, TRUE, NULL, NULL);
11426
StaticPrompt (q, "Equals", 0, dialogTextHeight, systemFont, 'l');
11427
scdp->match_2 = func_string (q, TRUE, NULL, NULL);
11428
9702
11429
if (use_pseudo)
9703
11430
{
9704
11431
RadioButton (scdp->constraint_type, "When");
9715
11442
Disable (scdp->present_qual_choice);
9716
11443
Disable (scdp->string_qual_choice);
9717
11444
Disable (scdp->string_constraint);
11445
Disable (scdp->match_1);
11446
Disable (scdp->match_2);
9718
11447
9719
11448
scdp->free_vn_proc = free_vn_proc;
9720
11449
scdp->copy_vn_proc = copy_vn_proc;
9730
11459
return (DialoG) p;
9731
11460
}
9732
11461
9733
extern DialoG SourceConstraintDialog (GrouP h, Boolean clear_btn)
11462
extern DialoG SourceConstraintDialogX (GrouP h, Boolean clear_btn)
9734
11463
{
9735
11464
return ConstraintChoiceDialog (h, SourceQualTypeConstraintSelectionDialog,
9736
11465
SourceStringConstraintSelectionDialog,
9762
11491
clear_btn, TRUE);
9763
11492
}
9764
11493
9765
typedef struct locationconstraintdialog
11494
typedef struct LocationConstraintXdialog
9766
11495
{
9767
11496
DIALOG_MESSAGE_BLOCK
9768
11497
PopuP interval_end_choice;
9775
11504
PopuP strand;
9776
11505
PopuP sequence_type;
9777
11506
Boolean show_interval_controls;
9778
} LocationConstraintDialogData, PNTR LocationConstraintDialogPtr;
11507
} LocationConstraintXDialogData, PNTR LocationConstraintXDialogPtr;
9779
11508
9780
11509
static void ShowLocationChoiceControls (PopuP p)
9781
11510
9782
11511
{
9783
LocationConstraintDialogPtr lcdp;
11512
LocationConstraintXDialogPtr lcdp;
9784
11513
Int4 match_choice;
9785
11514
9786
lcdp = (LocationConstraintDialogPtr) GetObjectExtra (p);
11515
lcdp = (LocationConstraintXDialogPtr) GetObjectExtra (p);
9787
11516
if (lcdp == NULL || lcdp->interval_end_choice == NULL) return;
9788
11517
9789
11518
if (GetValue (lcdp->interval_end_choice) == LOCATION_CONSTRAINT_WHOLE_INTERVAL)
9834
11563
}
9835
11564
}
9836
11565
9837
static void ResetLocationConstraintDialog (LocationConstraintDialogPtr lcdp)
11566
static void ResetLocationConstraintXDialog (LocationConstraintXDialogPtr lcdp)
9838
11567
{
9839
11568
if (lcdp == NULL) return;
9840
11569
9848
11577
ShowLocationChoiceControls (lcdp->interval_end_choice);
9849
11578
}
9850
11579
9851
static void LocationConstraintToDialog (DialoG d, Pointer data)
11580
static void LocationConstraintXToDialog (DialoG d, Pointer data)
9852
11581
9853
11582
{
9854
LocationConstraintDialogPtr lcdp;
9855
LocationConstraintPtr lcp;
11583
LocationConstraintXDialogPtr lcdp;
11584
LocationConstraintXPtr lcp;
9856
11585
Int4 interval_end_choice;
9857
11586
Int4 match_choice;
9858
11587
Char tmp [15];
9859
11588
Int4 strand;
9860
11589
Int4 sequence_type;
9861
11590
9862
lcdp = (LocationConstraintDialogPtr) GetObjectExtra (d);
11591
lcdp = (LocationConstraintXDialogPtr) GetObjectExtra (d);
9863
11592
if (lcdp == NULL)
9864
11593
{
9865
11594
return;
9866
11595
}
9867
lcp = (LocationConstraintPtr) data;
11596
lcp = (LocationConstraintXPtr) data;
9868
11597
9869
ResetLocationConstraintDialog (lcdp);
11598
ResetLocationConstraintXDialog (lcdp);
9870
11599
if (lcp != NULL)
9871
11600
{
9872
11601
interval_end_choice = lcp->interval_end_choice;
9942
11671
ShowLocationChoiceControls (lcdp->interval_match_choice);
9943
11672
}
9944
11673
9945
static Pointer DialogToLocationConstraint (DialoG d)
11674
static Pointer DialogToLocationConstraintX (DialoG d)
9946
11675
9947
11676
{
9948
LocationConstraintDialogPtr lcdp;
9949
LocationConstraintPtr lcp;
11677
LocationConstraintXDialogPtr lcdp;
11678
LocationConstraintXPtr lcp;
9950
11679
CharPtr tmp;
9951
11680
9952
lcdp = (LocationConstraintDialogPtr) GetObjectExtra (d);
11681
lcdp = (LocationConstraintXDialogPtr) GetObjectExtra (d);
9953
11682
if (lcdp == NULL)
9954
11683
{
9955
11684
return NULL;
9956
11685
}
9957
lcp = (LocationConstraintPtr) MemNew (sizeof (LocationConstraintData));
11686
lcp = (LocationConstraintXPtr) MemNew (sizeof (LocationConstraintXData));
9958
11687
if (lcp != NULL)
9959
11688
{
9960
11689
if (lcdp->show_interval_controls)
10024
11753
return lcp;
10025
11754
}
10026
11755
10027
static void LocationConstraintMessage (DialoG d, Int2 mssg)
11756
static void LocationConstraintXMessage (DialoG d, Int2 mssg)
10028
11757
10029
11758
{
10030
LocationConstraintDialogPtr lcdp;
11759
LocationConstraintXDialogPtr lcdp;
10031
11760
10032
lcdp = (LocationConstraintDialogPtr) GetObjectExtra (d);
11761
lcdp = (LocationConstraintXDialogPtr) GetObjectExtra (d);
10033
11762
if (lcdp != NULL) {
10034
11763
switch (mssg) {
10035
11764
case VIB_MSG_INIT :
10036
ResetLocationConstraintDialog (lcdp);
11765
ResetLocationConstraintXDialog (lcdp);
10037
11766
break;
10038
11767
case VIB_MSG_ENTER :
10039
11768
if (lcdp->show_interval_controls)
10051
11780
}
10052
11781
}
10053
11782
10054
static ValNodePtr TestLocationConstraintDialog (DialoG d)
11783
static ValNodePtr TestLocationConstraintXDialog (DialoG d)
10055
11784
10056
11785
{
10057
11786
return NULL;
10059
11788
10060
11789
10061
11790
extern DialoG
10062
LocationConstraintDialog
11791
LocationConstraintXDialog
10063
11792
(GrouP h,
10064
11793
Boolean show_interval_controls,
10065
11794
Boolean clear_btn)
10066
11795
10067
11796
{
10068
LocationConstraintDialogPtr lcdp;
11797
LocationConstraintXDialogPtr lcdp;
10069
11798
GrouP p, g, k, val_grp, strand_grp, g2, g3, g4;
10070
11799
ButtoN b = NULL;
10071
11800
10072
lcdp = (LocationConstraintDialogPtr) MemNew (sizeof (LocationConstraintDialogData));
11801
lcdp = (LocationConstraintXDialogPtr) MemNew (sizeof (LocationConstraintXDialogData));
10073
11802
if (lcdp == NULL)
10074
11803
{
10075
11804
return NULL;
10079
11808
SetObjectExtra (p, lcdp, StdCleanupExtraProc);
10080
11809
10081
11810
lcdp->dialog = (DialoG) p;
10082
lcdp->todialog = LocationConstraintToDialog;
10083
lcdp->fromdialog = DialogToLocationConstraint;
10084
lcdp->dialogmessage = LocationConstraintMessage;
10085
lcdp->testdialog = TestLocationConstraintDialog;
11811
lcdp->todialog = LocationConstraintXToDialog;
11812
lcdp->fromdialog = DialogToLocationConstraintX;
11813
lcdp->dialogmessage = LocationConstraintXMessage;
11814
lcdp->testdialog = TestLocationConstraintXDialog;
10086
11815
10087
11816
lcdp->show_interval_controls = show_interval_controls;
10088
11817
10164
11893
return (DialoG) p;
10165
11894
}
10166
11895
10167
static Boolean DoesStrandMatchConstraint (SeqLocPtr slp, LocationConstraintPtr lcp)
11896
static Boolean DoesStrandMatchConstraint (SeqLocPtr slp, LocationConstraintXPtr lcp)
10168
11897
{
10169
11898
Uint2 strand;
10170
11899
Boolean rval = FALSE;
10206
11935
return rval;
10207
11936
}
10208
11937
10209
static Boolean DoesSequenceTypeMatchContraint (SeqLocPtr slp, LocationConstraintPtr lcp)
11938
static Boolean DoesSequenceTypeMatchContraint (SeqLocPtr slp, LocationConstraintXPtr lcp)
10210
11939
{
10211
11940
Boolean rval = FALSE;
10212
11941
BioseqPtr bsp;
10237
11966
return rval;
10238
11967
}
10239
11968
10240
extern Boolean DoesLocationMatchConstraint (SeqLocPtr slp, LocationConstraintPtr lcp)
11969
extern Boolean DoesLocationMatchConstraint (SeqLocPtr slp, LocationConstraintXPtr lcp)
10241
11970
10242
11971
{
10243
11972
Boolean rval = FALSE;
10382
12111
DialoG source_constraint;
10383
12112
DialoG location_constraint;
10384
12113
DialoG cds_gene_prot_constraint;
12114
DialoG id_list_constraint;
10385
12115
10386
12116
DialoG tbs;
10387
DialoG pages[4];
12117
DialoG pages[6];
10388
12118
Int4 current_page;
10389
12119
10390
12120
} FilterFormData, PNTR FilterFormPtr;
10405
12135
PointerToDialog (dlg->source_constraint, NULL);
10406
12136
PointerToDialog (dlg->location_constraint, NULL);
10407
12137
PointerToDialog (dlg->cds_gene_prot_constraint, NULL);
12138
PointerToDialog (dlg->id_list_constraint, NULL);
10408
12139
10409
12140
if (dlg_data != NULL)
10410
12141
{
10412
12143
PointerToDialog (dlg->source_constraint, dlg_data->ccp);
10413
12144
PointerToDialog (dlg->location_constraint, dlg_data->lcp);
10414
12145
PointerToDialog (dlg->cds_gene_prot_constraint, dlg_data->cgp);
10415
}
10416
}
12146
PointerToDialog (dlg->id_list_constraint, dlg_data->id_list);
12147
}
12148
}
12149
12150
static void ApplyNthPage (FilterFormPtr dlg, FilterSetPtr dlg_data, Int4 page)
12151
{
12152
if (page < 0) return;
12153
12154
/* adjust page value to reflect missing pages */
12155
if (dlg->source_constraint == NULL)
12156
{
12157
page++;
12158
}
12159
if (dlg->string_constraint == NULL && page >= 1)
12160
{
12161
page++;
12162
}
12163
if (dlg->location_constraint == NULL && page >= 2)
12164
{
12165
page++;
12166
}
12167
if (dlg->cds_gene_prot_constraint == NULL && page >= 3)
12168
{
12169
page++;
12170
}
12171
if (dlg->id_list_constraint == NULL && page >= 4)
12172
{
12173
page++;
12174
}
12175
12176
switch (page)
12177
{
12178
case 0:
12179
dlg_data->ccp = DialogToPointer (dlg->source_constraint);
12180
break;
12181
case 1:
12182
dlg_data->scp = DialogToPointer (dlg->string_constraint);
12183
break;
12184
case 2:
12185
dlg_data->lcp = DialogToPointer (dlg->location_constraint);
12186
break;
12187
case 3:
12188
dlg_data->cgp = DialogToPointer (dlg->cds_gene_prot_constraint);
12189
break;
12190
case 4:
12191
dlg_data->id_list = DialogToPointer (dlg->id_list_constraint);
12192
break;
12193
}
12194
12195
}
12196
10417
12197
10418
12198
static Pointer DialogToFilter (DialoG d)
10419
12199
{
10430
12210
10431
12211
if (dlg_data != NULL)
10432
12212
{
10433
dlg_data->scp = DialogToPointer (dlg->string_constraint);
10434
dlg_data->ccp = DialogToPointer (dlg->source_constraint);
10435
dlg_data->lcp = DialogToPointer (dlg->location_constraint);
10436
dlg_data->cgp = DialogToPointer (dlg->cds_gene_prot_constraint);
12213
if (dlg->tbs == NULL)
12214
{
12215
dlg_data->scp = DialogToPointer (dlg->string_constraint);
12216
dlg_data->ccp = DialogToPointer (dlg->source_constraint);
12217
dlg_data->lcp = DialogToPointer (dlg->location_constraint);
12218
dlg_data->cgp = DialogToPointer (dlg->cds_gene_prot_constraint);
12219
dlg_data->id_list = DialogToPointer (dlg->id_list_constraint);
12220
}
12221
else
12222
{
12223
/* only take one value */
12224
ApplyNthPage (dlg, dlg_data, dlg->current_page);
12225
}
10437
12226
}
10438
12227
return dlg_data;
10439
12228
}
10482
12271
Boolean has_source_constraint,
10483
12272
Boolean has_location_constraint,
10484
12273
Boolean has_cds_gene_prot_constraint,
12274
Boolean has_id_list_constraint,
10485
12275
CharPtr string_constraint_label)
10486
12276
{
10487
12277
GrouP g, k;
10494
12284
if (! has_string_constraint
10495
12285
&& ! has_source_constraint
10496
12286
&& ! has_location_constraint
10497
&& ! has_cds_gene_prot_constraint)
12287
&& ! has_cds_gene_prot_constraint
12288
&& ! has_id_list_constraint)
10498
12289
{
10499
12290
return NULL;
10500
12291
}
10532
12323
{
10533
12324
filterTabs [num_pages++] = "CDS-Gene-Prot-mRNA Set Constraint";
10534
12325
}
12326
if (has_id_list_constraint)
12327
{
12328
filterTabs [num_pages++] = "Sequence ID Constraint";
12329
}
10535
12330
filterTabs [num_pages] = NULL;
10536
12331
10537
12332
if (num_pages > 1)
10544
12339
num_pages = 0;
10545
12340
if (has_source_constraint)
10546
12341
{
10547
ffp->source_constraint = SourceConstraintDialog (k, FALSE);
12342
ffp->source_constraint = SourceConstraintDialogX (k, FALSE);
10548
12343
ffp->pages [num_pages++] = ffp->source_constraint;
10549
12344
}
10550
12345
if (has_string_constraint)
10551
12346
{
10552
ffp->string_constraint = StringConstraintDialog (k, string_constraint_label, FALSE);
12347
ffp->string_constraint = StringConstraintDialogX (k, string_constraint_label, FALSE);
10553
12348
ffp->pages [num_pages++] = ffp->string_constraint;
10554
12349
}
10555
12350
if (has_location_constraint)
10556
12351
{
10557
ffp->location_constraint = LocationConstraintDialog (k, FALSE, FALSE);
12352
ffp->location_constraint = LocationConstraintXDialog (k, FALSE, FALSE);
10558
12353
ffp->pages [num_pages++] = ffp->location_constraint;
10559
12354
}
10560
12355
if (has_cds_gene_prot_constraint)
10562
12357
ffp->cds_gene_prot_constraint = CDSGeneProtConstraintDialog (k, FALSE);
10563
12358
ffp->pages [num_pages++] = ffp->cds_gene_prot_constraint;
10564
12359
}
12360
if (has_id_list_constraint)
12361
{
12362
ffp->id_list_constraint = StringConstraintDialogX (k, "Where sequence ID", FALSE);
12363
ffp->pages[num_pages++] = ffp->id_list_constraint;
12364
}
10565
12365
for (i = 1; i < num_pages; i++)
10566
12366
{
10567
12367
Hide (ffp->pages [i]);
10569
12369
AlignObjects (ALIGN_CENTER, (HANDLE) ffp->pages [0],
10570
12370
(HANDLE) ffp->pages [1],
10571
12371
(HANDLE) ffp->pages [2],
12372
(HANDLE) ffp->pages [3],
10572
12373
NULL);
10573
12374
clear_constraints = PushButton (g, "Clear Constraints", ClearAllConstraints);
10574
12375
SetObjectExtra (clear_constraints, ffp, NULL);
10578
12379
{
10579
12380
if (has_source_constraint)
10580
12381
{
10581
ffp->source_constraint = SourceConstraintDialog (g, TRUE);
12382
ffp->source_constraint = SourceConstraintDialogX (g, TRUE);
10582
12383
}
10583
12384
else if (has_string_constraint)
10584
12385
{
10585
ffp->string_constraint = StringConstraintDialog (g, string_constraint_label, TRUE);
12386
ffp->string_constraint = StringConstraintDialogX (g, string_constraint_label, TRUE);
10586
12387
}
10587
12388
else if (has_location_constraint)
10588
12389
{
10589
ffp->location_constraint = LocationConstraintDialog (g, FALSE, TRUE);
12390
ffp->location_constraint = LocationConstraintXDialog (g, FALSE, TRUE);
10590
12391
}
10591
12392
else if (has_cds_gene_prot_constraint)
10592
12393
{
10593
12394
ffp->cds_gene_prot_constraint = CDSGeneProtConstraintDialog (g, TRUE);
10594
12395
}
12396
else if (has_id_list_constraint)
12397
{
12398
ffp->id_list_constraint = StringConstraintDialogX (g, "Where sequence ID", TRUE);
12399
}
10595
12400
}
10596
12401
return (DialoG) g;
10597
12402
}
10599
12404
/* Operations on constrained features and descriptors */
10600
12405
typedef struct objecthasstring
10601
12406
{
10602
StringConstraintPtr scp;
12407
StringConstraintXPtr scp;
10603
12408
Boolean found;
10604
12409
} ObjectHasStringData, PNTR ObjectHasStringPtr;
10605
12410
10619
12424
Uint1 descriptorChoice;
10620
12425
} ConstraintOpData, PNTR ConstraintOpPtr;
10621
12426
10622
extern Boolean DoesStringMatchConstraint (CharPtr pchSource, StringConstraintPtr scp)
12427
extern Boolean DoesStringMatchConstraintX (CharPtr pchSource, StringConstraintXPtr scp)
10623
12428
{
10624
12429
CharPtr pFound;
10625
12430
Boolean rval = FALSE;
10626
Char char_after;
12431
Char char_after = 0;
10627
12432
10628
12433
if (pchSource == NULL) return FALSE;
10629
12434
10630
12435
if (scp == NULL || StringHasNoText (scp->match_text)) return TRUE;
10631
10632
if (scp->insensitive)
10633
{
10634
pFound = StringISearch (pchSource, scp->match_text);
10635
}
10636
else
10637
{
10638
pFound = StringSearch (pchSource, scp->match_text);
10639
}
10640
10641
if (pFound != NULL)
10642
{
10643
rval = TRUE;
10644
char_after = *(pFound + StringLen (scp->match_text));
10645
if (scp->match_location == STRING_CONSTRAINT_STARTS && pFound != pchSource)
10646
{
10647
rval = FALSE;
10648
}
10649
else if (scp->match_location == STRING_CONSTRAINT_ENDS && char_after != 0)
10650
{
10651
rval = FALSE;
10652
}
10653
else if (scp->match_location == STRING_CONSTRAINT_EQUALS
10654
&& (pFound != pchSource || char_after != 0))
10655
{
10656
rval = FALSE;
10657
}
10658
else if (scp->whole_word)
10659
{
10660
rval = IsWholeWordMatch (pchSource, pFound, StringLen (scp->match_text));
10661
}
12436
12437
switch (scp->match_location)
12438
{
12439
case eStringConstraintContains:
12440
if (scp->insensitive)
12441
{
12442
pFound = StringISearch (pchSource, scp->match_text);
12443
}
12444
else
12445
{
12446
pFound = StringSearch (pchSource, scp->match_text);
12447
}
12448
if (pFound == NULL)
12449
{
12450
rval = FALSE;
12451
}
12452
else if (scp->whole_word)
12453
{
12454
rval = IsWholeWordMatch (pchSource, pFound, StringLen (scp->match_text));
12455
while (!rval && pFound != NULL)
12456
{
12457
if (scp->insensitive)
12458
{
12459
pFound = StringISearch (pFound + 1, scp->match_text);
12460
}
12461
else
12462
{
12463
pFound = StringSearch (pFound + 1, scp->match_text);
12464
}
12465
if (pFound != NULL)
12466
{
12467
rval = IsWholeWordMatch (pchSource, pFound, StringLen (scp->match_text));
12468
}
12469
}
12470
}
12471
else
12472
{
12473
rval = TRUE;
12474
}
12475
break;
12476
case eStringConstraintStarts:
12477
if (scp->insensitive)
12478
{
12479
pFound = StringISearch (pchSource, scp->match_text);
12480
}
12481
else
12482
{
12483
pFound = StringSearch (pchSource, scp->match_text);
12484
}
12485
if (pFound == pchSource)
12486
{
12487
if (scp->whole_word)
12488
{
12489
rval = IsWholeWordMatch (pchSource, pFound, StringLen (scp->match_text));
12490
}
12491
else
12492
{
12493
rval = TRUE;
12494
}
12495
}
12496
break;
12497
case eStringConstraintEnds:
12498
if (scp->insensitive)
12499
{
12500
pFound = StringISearch (pchSource, scp->match_text);
12501
}
12502
else
12503
{
12504
pFound = StringSearch (pchSource, scp->match_text);
12505
}
12506
while (pFound != NULL && !rval) {
12507
char_after = *(pFound + StringLen (scp->match_text));
12508
if (char_after == 0)
12509
{
12510
if (scp->whole_word)
12511
{
12512
rval = IsWholeWordMatch (pchSource, pFound, StringLen (scp->match_text));
12513
}
12514
else
12515
{
12516
rval = TRUE;
12517
}
12518
/* stop the search, we're at the end of the string */
12519
pFound = NULL;
12520
}
12521
else
12522
{
12523
if (scp->insensitive)
12524
{
12525
pFound = StringISearch (pFound + 1, scp->match_text);
12526
}
12527
else
12528
{
12529
pFound = StringSearch (pFound + 1, scp->match_text);
12530
}
12531
}
12532
}
12533
break;
12534
case eStringConstraintEquals:
12535
if (scp->insensitive)
12536
{
12537
if (StringICmp (pchSource, scp->match_text) == 0)
12538
{
12539
rval = TRUE;
12540
}
12541
}
12542
else
12543
{
12544
if (StringCmp (pchSource, scp->match_text) == 0)
12545
{
12546
rval = TRUE;
12547
}
12548
}
12549
break;
12550
case eStringConstraintInList:
12551
if (scp->insensitive)
12552
{
12553
pFound = StringISearch (scp->match_text, pchSource);
12554
}
12555
else
12556
{
12557
pFound = StringSearch (scp->match_text, pchSource);
12558
}
12559
if (pFound == NULL)
12560
{
12561
rval = FALSE;
12562
}
12563
else
12564
{
12565
rval = IsWholeWordMatch (scp->match_text, pFound, StringLen (pchSource));
12566
while (!rval && pFound != NULL)
12567
{
12568
if (scp->insensitive)
12569
{
12570
pFound = StringISearch (pFound + 1, pchSource);
12571
}
12572
else
12573
{
12574
pFound = StringSearch (pFound + 1, pchSource);
12575
}
12576
if (pFound != NULL)
12577
{
12578
rval = IsWholeWordMatch (scp->match_text, pFound, StringLen (pchSource));
12579
}
12580
}
12581
}
12582
if (!rval) {
12583
/* look for spans */
12584
rval = IsStringInSpanInList (pchSource, scp->match_text);
12585
}
12586
break;
10662
12587
}
10663
12588
return rval;
10664
12589
}
10673
12598
if (ISA_STRINGTYPE (AsnFindBaseIsa (pAEOS->atp)))
10674
12599
{
10675
12600
pchSource = (CharPtr) pAEOS->dvp->ptrvalue;
10676
ohsp->found |= DoesStringMatchConstraint (pchSource, ohsp->scp);
12601
ohsp->found |= DoesStringMatchConstraintX (pchSource, ohsp->scp);
10677
12602
}
10678
12603
}
10679
12604
10699
12624
if (!ohsp->found && omtp->datatype == OBJ_SEQFEAT)
10700
12625
{
10701
12626
sfp = (SeqFeatPtr) ptr;
10702
sfp = SeqMgrGetDesiredFeature (sfp->idx.entityID, NULL, 0, 0, sfp, &fcontext);
10703
ohsp->found = DoesStringMatchConstraint (fcontext.label, ohsp->scp);
10704
if (!ohsp->found && sfp->idx.subtype == FEATDEF_tRNA)
12627
if (SeqMgrFeaturesAreIndexed(sfp->idx.entityID) == 0) {
12628
SeqMgrIndexFeatures (sfp->idx.entityID, NULL);
12629
}
12630
12631
sfp = SeqMgrGetDesiredFeature (sfp->idx.entityID, NULL, sfp->idx.itemID, 0, sfp, &fcontext);
12632
ohsp->found = DoesStringMatchConstraintX (fcontext.label, ohsp->scp);
12633
if (!ohsp->found && sfp != NULL && sfp->idx.subtype == FEATDEF_tRNA)
10705
12634
{
10706
12635
search_txt = (CharPtr) MemNew ((StringLen (fcontext.label) + 6) * sizeof (Char));
10707
12636
if (search_txt != NULL)
10708
12637
{
10709
12638
sprintf (search_txt, "tRNA-%s", fcontext.label);
10710
ohsp->found = DoesStringMatchConstraint (search_txt, ohsp->scp);
12639
ohsp->found = DoesStringMatchConstraintX (search_txt, ohsp->scp);
10711
12640
search_txt = MemFree (search_txt);
10712
12641
}
10713
12642
}
10715
12644
return ohsp->found;
10716
12645
}
10717
12646
10718
static Boolean DoesDbtagMatchStringConstraint (DbtagPtr db_tag, StringConstraintPtr scp)
12647
static Boolean DoesDbtagMatchStringConstraint (DbtagPtr db_tag, StringConstraintXPtr scp)
10719
12648
{
10720
12649
Boolean rval = FALSE;
10721
12650
Char tmp_str [15];
10728
12657
{
10729
12658
rval = TRUE;
10730
12659
}
10731
else if (DoesStringMatchConstraint (db_tag->db, scp))
12660
else if (DoesStringMatchConstraintX (db_tag->db, scp))
10732
12661
{
10733
12662
rval = TRUE;
10734
12663
}
10735
12664
else if (db_tag->tag != NULL)
10736
12665
{
10737
if (DoesStringMatchConstraint (db_tag->tag->str, scp))
12666
if (DoesStringMatchConstraintX (db_tag->tag->str, scp))
10738
12667
{
10739
12668
rval = TRUE;
10740
12669
}
10741
12670
else if (db_tag->tag->str == NULL)
10742
12671
{
10743
12672
sprintf (tmp_str, "%d", db_tag->tag->id);
10744
if (DoesStringMatchConstraint (tmp_str, scp))
12673
if (DoesStringMatchConstraintX (tmp_str, scp))
10745
12674
{
10746
12675
rval = TRUE;
10747
12676
}
10763
12692
10764
12693
if (sqdp->isOrgMod)
10765
12694
{
10766
if (biop->org != NULL || biop->org->orgname != NULL)
12695
if (biop->org != NULL && biop->org->orgname != NULL)
10767
12696
{
10768
12697
mod = biop->org->orgname->mod;
10769
12698
while (mod != NULL && mod->subtype != sqdp->subtype)
10813
12742
return qual_found;
10814
12743
}
10815
12744
12745
static Boolean IsMatchAny (ValNodePtr vnp)
12746
{
12747
if (vnp == NULL
12748
|| vnp->data.ptrvalue == NULL
12749
|| (vnp->choice > 0 && StringICmp (vnp->data.ptrvalue, "Organism or Any Qual") == 0))
12750
{
12751
return TRUE;
12752
} else {
12753
return FALSE;
12754
}
12755
}
12756
12757
static Boolean DoFieldsMatch (BioSourcePtr biop, ChoiceConstraintPtr ccp)
12758
{
12759
ValNodePtr swap, swap2;
12760
ValNodePtr qual_choice_list = NULL, vnp1, vnp2;
12761
Boolean rval = FALSE;
12762
ChoiceConstraintData tmp_const;
12763
StringConstraintData scd;
12764
SourceQualDescPtr sqdp;
12765
CharPtr location;
12766
OrgModPtr mod = NULL;
12767
SubSourcePtr ssp;
12768
12769
if (biop == NULL) return FALSE;
12770
if (ccp == NULL) return TRUE;
12771
12772
/* Init temporary choice constraint */
12773
MemSet (&tmp_const, 0, sizeof (ChoiceConstraintData));
12774
MemSet (&scd, 0, sizeof (StringConstraintData));
12775
scd.match_location = eStringConstraintEquals;
12776
tmp_const.string_constraint = &scd;
12777
tmp_const.constraint_type = CHOICE_CONSTRAINT_STRING;
12778
12779
if (IsMatchAny (ccp->qual_choice) && IsMatchAny (ccp->qual_choice_match)) {
12780
/* both are wildcards */
12781
ValNodeAddPointer (&qual_choice_list, 1, StringSave ("Organism"));
12782
qual_choice_list->next = GetSourceQualDescList (TRUE, TRUE, TRUE, FALSE);
12783
ValNodeAddPointer (&qual_choice_list, 1, StringSave ("Lineage"));
12784
ValNodeAddPointer (&qual_choice_list, 1, StringSave ("Location"));
12785
12786
/* save original wildcards */
12787
swap = ccp->qual_choice;
12788
swap2 = ccp->qual_choice_match;
12789
for (vnp1 = qual_choice_list; vnp1 != NULL && vnp1->next != NULL && !rval; vnp1 = vnp1->next) {
12790
ccp->qual_choice = vnp1;
12791
for (vnp2 = vnp1->next; vnp2 != NULL && !rval; vnp2 = vnp2->next) {
12792
ccp->qual_choice_match = vnp2;
12793
if (DoFieldsMatch (biop, ccp)) {
12794
rval = TRUE;
12795
}
12796
}
12797
}
12798
/* put original wildcards back */
12799
ccp->qual_choice = swap;
12800
ccp->qual_choice_match = swap2;
12801
qual_choice_list = ValNodeFreeData (qual_choice_list);
12802
} else if (IsMatchAny (ccp->qual_choice) || IsMatchAny (ccp->qual_choice_match)) {
12803
/* one is a wild card */
12804
ValNodeAddPointer (&qual_choice_list, 1, StringSave ("Organism"));
12805
qual_choice_list->next = GetSourceQualDescList (TRUE, TRUE, TRUE, FALSE);
12806
ValNodeAddPointer (&qual_choice_list, 1, StringSave ("Lineage"));
12807
ValNodeAddPointer (&qual_choice_list, 1, StringSave ("Location"));
12808
12809
/* if one wild card, make it the first one */
12810
if (IsMatchAny (ccp->qual_choice_match)) {
12811
swap = ccp->qual_choice;
12812
ccp->qual_choice = ccp->qual_choice_match;
12813
ccp->qual_choice_match = swap;
12814
}
12815
/* save original wildcard */
12816
swap = ccp->qual_choice;
12817
for (vnp1 = qual_choice_list; vnp1 != NULL && !rval; vnp1 = vnp1->next) {
12818
if (SourceQualValNodeMatch (vnp1, ccp->qual_choice_match)) {
12819
/* don't compare something to itself */
12820
continue;
12821
} else {
12822
ccp->qual_choice = vnp1;
12823
rval = DoFieldsMatch (biop, ccp);
12824
}
12825
}
12826
/* put original wildcard back */
12827
ccp->qual_choice = swap;
12828
qual_choice_list = ValNodeFreeData (qual_choice_list);
12829
}
12830
else if (ccp->qual_choice->choice > 0)
12831
{
12832
tmp_const.qual_choice = ccp->qual_choice_match;
12833
if (StringICmp (ccp->qual_choice->data.ptrvalue, "Organism") == 0)
12834
{
12835
if (biop->org != NULL && !StringHasNoText (biop->org->taxname))
12836
{
12837
tmp_const.string_constraint->match_text = biop->org->taxname;
12838
rval = DoesOneSourceMatchConstraint (biop, &tmp_const);
12839
}
12840
}
12841
else if (StringICmp (ccp->qual_choice->data.ptrvalue, "Lineage") == 0)
12842
{
12843
if (biop->org != NULL && biop->org->orgname != NULL && !StringHasNoText (biop->org->orgname->lineage))
12844
{
12845
tmp_const.string_constraint->match_text = biop->org->orgname->lineage;
12846
rval = DoesOneSourceMatchConstraint (biop, &tmp_const);
12847
}
12848
}
12849
else if (StringICmp (ccp->qual_choice->data.ptrvalue, "Location") == 0)
12850
{
12851
location = GetLocationFromSource (biop, NULL);
12852
tmp_const.string_constraint->match_text = location;
12853
if (!StringHasNoText (location)) {
12854
rval = DoesOneSourceMatchConstraint (biop, &tmp_const);
12855
}
12856
location = MemFree (location);
12857
}
12858
}
12859
else
12860
{
12861
tmp_const.qual_choice = ccp->qual_choice_match;
12862
sqdp = (SourceQualDescPtr) ccp->qual_choice->data.ptrvalue;
12863
if (sqdp->isOrgMod)
12864
{
12865
if (biop->org != NULL && biop->org->orgname != NULL)
12866
{
12867
mod = biop->org->orgname->mod;
12868
}
12869
while (! rval && mod != NULL)
12870
{
12871
if (mod->subtype == sqdp->subtype && !StringHasNoText (mod->subname))
12872
{
12873
tmp_const.string_constraint->match_text = mod->subname;
12874
rval = DoesOneSourceMatchConstraint (biop, &tmp_const);
12875
}
12876
mod = mod->next;
12877
}
12878
}
12879
else
12880
{
12881
ssp = biop->subtype;
12882
while (!rval && ssp != NULL)
12883
{
12884
if (ssp->subtype == sqdp->subtype && !StringHasNoText (ssp->name))
12885
{
12886
tmp_const.string_constraint->match_text = ssp->name;
12887
rval = DoesOneSourceMatchConstraint (biop, &tmp_const);
12888
}
12889
ssp = ssp->next;
12890
}
12891
}
12892
}
12893
return rval;
12894
}
12895
10816
12896
extern Boolean
10817
12897
DoesOneSourceMatchConstraint
10818
12898
(BioSourcePtr biop, ChoiceConstraintPtr scp)
10821
12901
OrgModPtr mod = NULL;
10822
12902
SubSourcePtr ssp;
10823
12903
SourceQualDescPtr sqdp;
12904
CharPtr location;
10824
12905
10825
12906
if (scp == NULL || scp->constraint_type == CHOICE_CONSTRAINT_ANY)
10826
12907
{
10833
12914
10834
12915
if (scp->constraint_type == CHOICE_CONSTRAINT_STRING)
10835
12916
{
10836
if (scp->qual_choice == NULL
10837
|| scp->qual_choice->data.ptrvalue == NULL
10838
|| StringICmp (scp->qual_choice->data.ptrvalue, "Organism or Any Qual") == 0)
12917
if (IsMatchAny (scp->qual_choice))
10839
12918
{
10840
12919
if (biop->org != NULL)
10841
12920
{
10842
does_match = DoesStringMatchConstraint (biop->org->taxname, scp->string_constraint);
12921
does_match = DoesStringMatchConstraintX (biop->org->taxname, scp->string_constraint);
10843
12922
if (biop->org->orgname != NULL)
10844
12923
{
10845
12924
mod = biop->org->orgname->mod;
10846
12925
}
10847
12926
while (! does_match && mod != NULL)
10848
12927
{
10849
does_match = DoesStringMatchConstraint (mod->subname, scp->string_constraint);
12928
does_match = DoesStringMatchConstraintX (mod->subname, scp->string_constraint);
10850
12929
mod = mod->next;
10851
12930
}
10852
12931
}
10853
12932
ssp = biop->subtype;
10854
12933
while (!does_match && ssp != NULL)
10855
12934
{
10856
does_match = DoesStringMatchConstraint (ssp->name, scp->string_constraint);
12935
does_match = DoesStringMatchConstraintX (ssp->name, scp->string_constraint);
10857
12936
ssp = ssp->next;
10858
12937
}
10859
12938
}
10860
else if (StringICmp (scp->qual_choice->data.ptrvalue, "Organism") == 0)
12939
else if (scp->qual_choice->choice > 0 && StringICmp (scp->qual_choice->data.ptrvalue, "Organism") == 0)
10861
12940
{
10862
12941
if (biop->org != NULL)
10863
12942
{
10864
does_match = DoesStringMatchConstraint (biop->org->taxname, scp->string_constraint);
12943
does_match = DoesStringMatchConstraintX (biop->org->taxname, scp->string_constraint);
10865
12944
}
10866
12945
}
10867
else if (StringICmp (scp->qual_choice->data.ptrvalue, "Lineage") == 0)
12946
else if (scp->qual_choice->choice > 0 && StringICmp (scp->qual_choice->data.ptrvalue, "Lineage") == 0)
10868
12947
{
10869
12948
if (biop->org != NULL && biop->org->orgname != NULL)
10870
12949
{
10871
does_match = DoesStringMatchConstraint (biop->org->orgname->lineage,
12950
does_match = DoesStringMatchConstraintX (biop->org->orgname->lineage,
10872
12951
scp->string_constraint);
10873
12952
}
10874
12953
}
12954
else if (scp->qual_choice->choice > 0 && StringICmp (scp->qual_choice->data.ptrvalue, "Location") == 0)
12955
{
12956
location = GetLocationFromSource (biop, NULL);
12957
does_match = DoesStringMatchConstraintX (location, scp->string_constraint);
12958
location = MemFree (location);
12959
}
10875
12960
else
10876
12961
{
10877
12962
sqdp = (SourceQualDescPtr) scp->qual_choice->data.ptrvalue;
10885
12970
{
10886
12971
if (mod->subtype == sqdp->subtype)
10887
12972
{
10888
does_match = DoesStringMatchConstraint (mod->subname, scp->string_constraint);
12973
does_match = DoesStringMatchConstraintX (mod->subname, scp->string_constraint);
10889
12974
}
10890
12975
mod = mod->next;
10891
12976
}
10897
12982
{
10898
12983
if (ssp->subtype == sqdp->subtype)
10899
12984
{
10900
does_match = DoesStringMatchConstraint (ssp->name, scp->string_constraint);
12985
does_match = DoesStringMatchConstraintX (ssp->name, scp->string_constraint);
10901
12986
}
10902
12987
ssp = ssp->next;
10903
12988
}
10908
12993
does_match = ! does_match;
10909
12994
}
10910
12995
}
12996
else if (scp->constraint_type == CHOICE_CONSTRAINT_MATCH)
12997
{
12998
does_match = DoFieldsMatch (biop, scp);
12999
}
10911
13000
else
10912
13001
{
10913
13002
does_match = DoesSourceHaveQualPresent (biop, scp->qual_choice);
10934
13023
if (cop->fsp->scp->not_present)
10935
13024
{
10936
13025
if (DoesObjectMatchStringConstraint (cop->omtp, cop->aip, (Pointer) sfp, &(cop->ohsd))
10937
|| DoesStringMatchConstraint (fcontext.label, cop->fsp->scp))
13026
|| DoesStringMatchConstraintX (fcontext.label, cop->fsp->scp))
10938
13027
{
10939
13028
feature_matches = FALSE;
10940
13029
}
10942
13031
else
10943
13032
{
10944
13033
if (! DoesObjectMatchStringConstraint (cop->omtp, cop->aip, (Pointer) sfp, &(cop->ohsd))
10945
&& ! DoesStringMatchConstraint (fcontext.label, cop->fsp->scp))
13034
&& ! DoesStringMatchConstraintX (fcontext.label, cop->fsp->scp))
10946
13035
{
10947
13036
feature_matches = FALSE;
10948
13037
}
10962
13051
}
10963
13052
}
10964
13053
13054
13055
static void BioseqConstrainedFeaturesCallback (BioseqPtr bsp, Pointer userdata)
13056
{
13057
ConstraintOpPtr cop;
13058
SeqFeatPtr sfp;
13059
ObjMgrDataPtr omdp;
13060
BioseqExtraPtr bspextra;
13061
Int4 index;
13062
13063
if (bsp == NULL || userdata == NULL) return;
13064
cop = (ConstraintOpPtr) userdata;
13065
13066
omdp = SeqMgrGetOmdpForBioseq (bsp);
13067
if (omdp == NULL || omdp->datatype != OBJ_BIOSEQ) return;
13068
13069
bspextra = (BioseqExtraPtr) omdp->extradata;
13070
if (bspextra == NULL) {
13071
SeqMgrIndexFeatures (bsp->idx.entityID, NULL);
13072
omdp = SeqMgrGetOmdpForBioseq (bsp);
13073
if (omdp == NULL || omdp->datatype != OBJ_BIOSEQ) return;
13074
13075
bspextra = (BioseqExtraPtr) omdp->extradata;
13076
}
13077
if (bspextra == NULL) return;
13078
13079
for (index = 0; index < bspextra->numfeats; index++)
13080
{
13081
sfp = bspextra->featsByPos[index]->sfp;
13082
SeqEntryConstrainedFeaturesCallback (sfp, userdata);
13083
}
13084
}
13085
13086
10965
13087
static void SeqEntryConstrainedDescriptorsCallback (SeqDescrPtr sdp, Pointer userdata)
10966
13088
{
10967
13089
ConstraintOpPtr cop;
11059
13181
cop->omtp = ObjMgrTypeFind (cop->omp, OBJ_SEQFEAT, NULL, NULL);
11060
13182
if (cop->omtp != NULL)
11061
13183
{
11062
VisitFeaturesInSep (sep, cop, SeqEntryConstrainedFeaturesCallback);
13184
VisitBioseqsInSep (sep, cop, BioseqConstrainedFeaturesCallback);
11063
13185
}
11064
13186
}
11065
13187
11079
13201
ConstrainedSourceCallback (sep->next, cop);
11080
13202
}
11081
13203
13204
13205
static void ConstrainedBioseqCallback (SeqEntryPtr sep, ConstraintOpPtr cop)
13206
{
13207
BioseqPtr bsp = NULL;
13208
BioseqSetPtr bssp = NULL;
13209
SeqFeatPtr sfp;
13210
SeqDescPtr sdp;
13211
SeqMgrFeatContext fcontext;
13212
SeqMgrDescContext dcontext;
13213
13214
if (sep == NULL || sep->data.ptrvalue == NULL || cop == NULL || cop->fsp == NULL)
13215
{
13216
return;
13217
}
13218
13219
if (IS_Bioseq (sep))
13220
{
13221
bsp = (BioseqPtr) sep->data.ptrvalue;
13222
}
13223
else if (IS_Bioseq_set (sep))
13224
{
13225
bssp = (BioseqSetPtr) sep->data.ptrvalue;
13226
}
13227
13228
if (bsp != NULL && DoesIDListMeetStringConstraint (bsp->id, cop->fsp->id_list))
13229
{
13230
if (cop->feature_action != NULL)
13231
{
13232
cop->omtp = ObjMgrTypeFind (cop->omp, OBJ_SEQFEAT, NULL, NULL);
13233
if (cop->omtp != NULL)
13234
{
13235
for (sfp = SeqMgrGetNextFeature (bsp, NULL, 0, 0, &fcontext);
13236
sfp != NULL;
13237
sfp = SeqMgrGetNextFeature (bsp, sfp, 0, 0, &fcontext))
13238
{
13239
SeqEntryConstrainedFeaturesCallback (sfp, cop);
13240
}
13241
}
13242
}
13243
13244
if (cop->descriptor_action != NULL)
13245
{
13246
cop->omtp = ObjMgrTypeFind (cop->omp, OBJ_SEQDESC, NULL, NULL);
13247
if (cop->omtp != NULL)
13248
{
13249
for (sdp = SeqMgrGetNextDescriptor (bsp, NULL, 0, &dcontext);
13250
sdp != NULL;
13251
sdp = SeqMgrGetNextDescriptor (bsp, sdp, 0, &dcontext))
13252
{
13253
SeqEntryConstrainedDescriptorsCallback (sdp, cop);
13254
}
13255
}
13256
}
13257
}
13258
else if (bssp != NULL)
13259
{
13260
ConstrainedBioseqCallback (bssp->seq_set, cop);
13261
}
13262
ConstrainedBioseqCallback (sep->next, cop);
13263
}
13264
13265
11082
13266
extern void
11083
13267
OperateOnSeqEntryConstrainedObjects
11084
13268
(SeqEntryPtr sep,
11136
13320
bsp = (BioseqPtr) sep->data.ptrvalue;
11137
13321
}
11138
13322
11139
if (fsp == NULL || fsp->ccp == NULL || fsp->ccp->constraint_type == CHOICE_CONSTRAINT_ANY)
13323
if (fsp == NULL || (fsp->ccp == NULL && fsp->id_list == NULL)
13324
|| (fsp->ccp != NULL && fsp->ccp->constraint_type == CHOICE_CONSTRAINT_ANY)
13325
|| (fsp->id_list != NULL && bsp != NULL && DoesIDListMeetStringConstraint (bsp->id, fsp->id_list)))
11140
13326
{
11141
13327
if (feature_action != NULL)
11142
13328
{
11145
13331
{
11146
13332
if (bsp == NULL)
11147
13333
{
11148
VisitFeaturesInSep (sep, &cod, SeqEntryConstrainedFeaturesCallback);
13334
VisitBioseqsInSep (sep, &cod, BioseqConstrainedFeaturesCallback);
11149
13335
}
11150
13336
else
11151
13337
{
11180
13366
}
11181
13367
}
11182
13368
}
13369
else if (fsp->id_list != NULL)
13370
{
13371
ConstrainedBioseqCallback (sep, &cod);
13372
}
11183
13373
else
11184
13374
{
11185
13375
ConstrainedSourceCallback (sep, &cod);
11530
13720
seqfeat_choice, featdef_choice, descr_choice);
11531
13721
}
11532
13722
11533
typedef struct existingtextdlg
11534
{
11535
GrouP pre_app_grp;
11536
GrouP delim_grp;
11537
} ExistingTextDlgData, PNTR ExistingTextDlgPtr;
11538
11539
static void ChangePreAppIgnoreChoice (GrouP g)
11540
{
11541
ExistingTextDlgPtr etdp;
11542
Int4 handle_choice;
11543
11544
etdp = (ExistingTextDlgPtr) GetObjectExtra (g);
11545
if (etdp == NULL)
11546
{
11547
return;
11548
}
11549
11550
handle_choice = GetValue (etdp->pre_app_grp);
11551
if (handle_choice == 1 || handle_choice == 2)
11552
{
11553
Enable (etdp->delim_grp);
11554
}
11555
else
11556
{
11557
Disable (etdp->delim_grp);
11558
}
11559
}
11560
11561
extern ExistingTextPtr GetExistingTextHandlerInfo (GetSamplePtr gsp, Boolean non_text)
11562
{
11563
WindoW w;
11564
GrouP h, c;
11565
ExistingTextDlgData etdd;
11566
ButtoN b;
11567
ModalAcceptCancelData acd;
11568
ExistingTextPtr etp;
11569
Char txt [128];
11570
MsgAnswer ans;
11571
PrompT ppt;
11572
Int4 handle_choice;
11573
11574
if (gsp == NULL || gsp->num_found == 0)
11575
{
11576
return NULL;
11577
}
11578
11579
sprintf (txt, "%d affected fields already contain a value. Do you wish to overwrite existing text?",
11580
gsp->num_found);
11581
ans = Message (MSG_YNC, txt, 0, dialogTextHeight, systemFont, 'l');
11582
if (ans == ANS_CANCEL)
11583
{
11584
etp = (ExistingTextPtr) MemNew (sizeof (ExistingTextData));
11585
etp->existing_text_choice = EXISTING_TEXT_CHOICE_CANCEL;
11586
return etp;
11587
}
11588
else if (ans == ANS_YES)
11589
{
11590
etp = (ExistingTextPtr) MemNew (sizeof (ExistingTextData));
11591
etp->existing_text_choice = EXISTING_TEXT_CHOICE_REPLACE_OLD;
11592
return etp;
11593
}
11594
11595
w = MovableModalWindow(-20, -13, -10, -10, "How to Add New Text", NULL);
11596
h = HiddenGroup (w, -1, 0, NULL);
11597
SetGroupSpacing (h, 10, 10);
11598
etdd.pre_app_grp = HiddenGroup (h, 0, 3, ChangePreAppIgnoreChoice);
11599
SetGroupSpacing (etdd.pre_app_grp, 10, 10);
11600
RadioButton (etdd.pre_app_grp, "Append");
11601
RadioButton (etdd.pre_app_grp, "Prefix");
11602
RadioButton (etdd.pre_app_grp, "Ignore new text");
11603
SetValue (etdd.pre_app_grp, 1);
11604
SetObjectExtra (etdd.pre_app_grp, &etdd, NULL);
11605
11606
ppt = StaticPrompt (h, "Separate new text and old text with",
11607
0, dialogTextHeight, programFont, 'c');
11608
etdd.delim_grp = HiddenGroup (h, 0, 3, NULL);
11609
SetGroupSpacing (etdd.delim_grp, 10, 10);
11610
RadioButton (etdd.delim_grp, "Semicolon");
11611
RadioButton (etdd.delim_grp, "Space");
11612
RadioButton (etdd.delim_grp, "Do not separate");
11613
SetValue (etdd.delim_grp, 1);
11614
11615
c = HiddenGroup (h, 2, 0, NULL);
11616
SetGroupSpacing (c, 10, 10);
11617
b = PushButton (c, "Accept", ModalAcceptButton);
11618
SetObjectExtra (b, &acd, NULL);
11619
b = PushButton (c, "Cancel", ModalCancelButton);
11620
SetObjectExtra (b, &acd, NULL);
11621
AlignObjects (ALIGN_CENTER, (HANDLE) etdd.pre_app_grp,
11622
(HANDLE) ppt,
11623
(HANDLE) etdd.delim_grp,
11624
(HANDLE) c,
11625
NULL);
11626
Show (w);
11627
Select (w);
11628
acd.accepted = FALSE;
11629
acd.cancelled = FALSE;
11630
while (!acd.accepted && ! acd.cancelled)
11631
{
11632
ProcessExternalEvent ();
11633
Update ();
11634
}
11635
ProcessAnEvent ();
11636
etp = (ExistingTextPtr) MemNew (sizeof (ExistingTextData));
11637
if (acd.cancelled)
11638
{
11639
etp->existing_text_choice = EXISTING_TEXT_CHOICE_CANCEL;
11640
}
11641
else
11642
{
11643
handle_choice = GetValue (etdd.pre_app_grp);
11644
if (handle_choice == 1)
11645
{
11646
switch (GetValue (etdd.delim_grp))
11647
{
11648
case 1:
11649
etp->existing_text_choice = EXISTING_TEXT_CHOICE_APPEND_SEMI;
11650
break;
11651
case 2:
11652
etp->existing_text_choice = EXISTING_TEXT_CHOICE_APPEND_SPACE;
11653
break;
11654
case 3:
11655
etp->existing_text_choice = EXISTING_TEXT_CHOICE_APPEND_NONE;
11656
break;
11657
}
11658
}
11659
else if (handle_choice == 2)
11660
{
11661
switch (GetValue (etdd.delim_grp))
11662
{
11663
case 1:
11664
etp->existing_text_choice = EXISTING_TEXT_CHOICE_PREFIX_SEMI;
11665
break;
11666
case 2:
11667
etp->existing_text_choice = EXISTING_TEXT_CHOICE_PREFIX_SPACE;
11668
break;
11669
case 3:
11670
etp->existing_text_choice = EXISTING_TEXT_CHOICE_PREFIX_NONE;
11671
break;
11672
}
11673
}
11674
else
11675
{
11676
etp->existing_text_choice = EXISTING_TEXT_CHOICE_LEAVE_OLD;
11677
}
11678
}
11679
Remove (w);
11680
return etp;
11681
}
11682
11683
extern CharPtr HandleExistingText (CharPtr existing_text, CharPtr new_text, ExistingTextPtr etp)
11684
{
11685
CharPtr rstring = NULL;
11686
Int4 len;
11687
11688
if (StringHasNoText (existing_text) || etp == NULL)
11689
{
11690
MemFree (existing_text);
11691
return new_text;
11692
}
11693
switch (etp->existing_text_choice)
11694
{
11695
case EXISTING_TEXT_CHOICE_REPLACE_OLD:
11696
/* replace current text with new text */
11697
MemFree (existing_text);
11698
rstring = new_text;
11699
break;
11700
case EXISTING_TEXT_CHOICE_LEAVE_OLD:
11701
/* do not change current text */
11702
MemFree (new_text);
11703
rstring = existing_text;
11704
break;
11705
case EXISTING_TEXT_CHOICE_APPEND_SEMI:
11706
/* Append new text to current text, separated by semicolon */
11707
len = StringLen (new_text) + StringLen (existing_text) + 4;
11708
rstring = MemNew (len);
11709
if (rstring != NULL) {
11710
StringCpy (rstring, existing_text);
11711
StringCat (rstring, "; ");
11712
StringCat (rstring, new_text);
11713
MemFree (new_text);
11714
MemFree (existing_text);
11715
}
11716
break;
11717
case EXISTING_TEXT_CHOICE_APPEND_SPACE:
11718
/* Append new text to current text, separated by space */
11719
len = StringLen (new_text) + StringLen (existing_text) + 3;
11720
rstring = MemNew (len);
11721
if (rstring != NULL) {
11722
StringCpy (rstring, existing_text);
11723
StringCat (rstring, " ");
11724
StringCat (rstring, new_text);
11725
MemFree (new_text);
11726
MemFree (existing_text);
11727
}
11728
break;
11729
case EXISTING_TEXT_CHOICE_APPEND_NONE:
11730
/* Append new text to current text, no delimiter */
11731
len = StringLen (new_text) + StringLen (existing_text) + 1;
11732
rstring = MemNew (len);
11733
if (rstring != NULL) {
11734
StringCpy (rstring, existing_text);
11735
StringCat (rstring, new_text);
11736
MemFree (new_text);
11737
MemFree (existing_text);
11738
}
11739
break;
11740
case EXISTING_TEXT_CHOICE_PREFIX_SEMI:
11741
/* Prepend new text to current text, separated by semicolon */
11742
len = StringLen (new_text) + StringLen (existing_text) + 4;
11743
rstring = MemNew (len);
11744
if (rstring != NULL) {
11745
StringCpy (rstring, new_text);
11746
StringCat (rstring, "; ");
11747
StringCat (rstring, existing_text);
11748
MemFree (new_text);
11749
MemFree (existing_text);
11750
}
11751
break;
11752
case EXISTING_TEXT_CHOICE_PREFIX_SPACE:
11753
/* Prepend new text to current text, separated by semicolon */
11754
len = StringLen (new_text) + StringLen (existing_text) + 3;
11755
rstring = MemNew (len);
11756
if (rstring != NULL) {
11757
StringCpy (rstring, new_text);
11758
StringCat (rstring, " ");
11759
StringCat (rstring, existing_text);
11760
MemFree (new_text);
11761
MemFree (existing_text);
11762
}
11763
break;
11764
case EXISTING_TEXT_CHOICE_PREFIX_NONE:
11765
/* prefix current text with new text */
11766
len = StringLen (new_text) + StringLen (existing_text) + 1;
11767
rstring = MemNew (len);
11768
if (rstring != NULL) {
11769
StringCpy (rstring, new_text);
11770
StringCat (rstring, existing_text);
11771
MemFree (new_text);
11772
MemFree (existing_text);
11773
}
11774
break;
11775
}
11776
return rstring;
11777
}
11778
11779
13723
extern CharPtr HandleApplyValue (CharPtr orig_text, ApplyValuePtr avp)
11780
13724
{
11781
13725
CharPtr new_str, cp_found;
11806
13750
found_len = StringLen (avp->text_to_replace);
11807
13751
replace_len = StringLen (avp->new_text);
11808
13752
cp_found = StringISearch (orig_text, avp->text_to_replace);
13753
if (avp->where_to_replace == EditApplyFindLocation_beginning
13754
&& cp_found != orig_text) {
13755
cp_found = NULL;
13756
}
11809
13757
while (cp_found != NULL)
11810
13758
{
11811
new_len = StringLen (orig_text) + 1 - found_len + replace_len;
11812
new_str = (CharPtr) MemNew (new_len * sizeof (Char));
11813
if (new_str != NULL)
11814
{
11815
if (cp_found != orig_text)
13759
if (avp->where_to_replace == EditApplyFindLocation_end
13760
&& cp_found != orig_text + StringLen (orig_text) - found_len) {
13761
cp_found = StringISearch (cp_found + found_len, avp->text_to_replace);
13762
} else {
13763
new_len = StringLen (orig_text) + 1 - found_len + replace_len;
13764
new_str = (CharPtr) MemNew (new_len * sizeof (Char));
13765
if (new_str != NULL)
11816
13766
{
11817
StringNCpy (new_str, orig_text, cp_found - orig_text);
13767
if (cp_found != orig_text)
13768
{
13769
StringNCpy (new_str, orig_text, cp_found - orig_text);
13770
}
13771
StringCat (new_str, avp->new_text);
13772
StringCat (new_str, cp_found + found_len);
13773
cp_found = new_str + (cp_found - orig_text) + replace_len;
13774
orig_text = MemFree (orig_text);
13775
orig_text = new_str;
11818
13776
}
11819
StringCat (new_str, avp->new_text);
11820
StringCat (new_str, cp_found + found_len);
11821
cp_found = new_str + (cp_found - orig_text) + replace_len;
11822
orig_text = MemFree (orig_text);
11823
orig_text = new_str;
13777
cp_found = StringISearch (cp_found, avp->text_to_replace);
11824
13778
}
11825
cp_found = StringISearch (cp_found, avp->text_to_replace);
11826
13779
}
11827
13780
return orig_text;
11828
13781
}
11851
13804
return list;
11852
13805
}
11853
13806
13807
13808
13809
static void MakeSemicolonStringsIntoSeparateItems (ValNodePtr PNTR list)
13810
{
13811
ValNodePtr prev = NULL, vnp_next, vnp, vnp_new;
13812
CharPtr cp;
13813
13814
if (list == NULL || *list == NULL) return;
13815
13816
vnp = *list;
13817
while (vnp != NULL)
13818
{
13819
vnp_next = vnp->next;
13820
if (StringHasNoText (vnp->data.ptrvalue))
13821
{
13822
if (prev == NULL)
13823
{
13824
*list = vnp_next;
13825
}
13826
else
13827
{
13828
prev->next = vnp_next;
13829
}
13830
vnp->next = NULL;
13831
vnp = ValNodeFreeData (vnp);
13832
}
13833
else if ((cp = StringChr (vnp->data.ptrvalue, ';')) != NULL)
13834
{
13835
vnp_new = ValNodeNew (NULL);
13836
vnp_new->choice = vnp->choice;
13837
vnp_new->data.ptrvalue = StringSave (cp + 1);
13838
vnp_new->next = vnp_next;
13839
*cp = 0;
13840
vnp->next = vnp_new;
13841
vnp_next = vnp_new;
13842
prev = vnp;
13843
}
13844
else
13845
{
13846
prev = vnp;
13847
}
13848
vnp = vnp_next;
13849
}
13850
}
13851
13852
13853
extern ValNodePtr ApplyValueToValNodeStringListAsText (ValNodePtr list, Int2 choice, ApplyValuePtr avp)
13854
{
13855
ValNodePtr vnp;
13856
13857
if (avp == NULL)
13858
{
13859
return NULL;
13860
}
13861
13862
if (!StringHasNoText (avp->text_to_replace))
13863
{
13864
for (vnp = list; vnp != NULL; vnp = vnp->next)
13865
{
13866
vnp->data.ptrvalue = HandleApplyValue (vnp->data.ptrvalue, avp);
13867
}
13868
}
13869
else
13870
{
13871
if (avp->etp == NULL
13872
|| avp->etp->existing_text_choice == eExistingTextChoiceReplaceOld)
13873
{
13874
list = ValNodeFree (list);
13875
ValNodeAddPointer (&list, choice, StringSave (avp->new_text));
13876
}
13877
else if (avp->etp->existing_text_choice == eExistingTextChoiceAppendSemi)
13878
{
13879
ValNodeAddPointer (&list, choice, StringSave (avp->new_text));
13880
}
13881
else if (avp->etp->existing_text_choice == eExistingTextChoicePrefixSemi)
13882
{
13883
vnp = ValNodeNew(NULL);
13884
vnp->choice = (Uint1) choice;
13885
vnp->data.ptrvalue = StringSave (avp->new_text);
13886
vnp->next = list;
13887
list = vnp;
13888
}
13889
else if (avp->etp->existing_text_choice == eExistingTextChoiceLeaveOld)
13890
{
13891
if (list == NULL)
13892
{
13893
ValNodeAddPointer (&list, choice, StringSave (avp->new_text));
13894
}
13895
} else {
13896
for (vnp = list; vnp != NULL; vnp = vnp->next)
13897
{
13898
vnp->data.ptrvalue = HandleApplyValue (vnp->data.ptrvalue, avp);
13899
}
13900
}
13901
}
13902
13903
if (avp->etp == NULL || avp->etp->existing_text_choice != eExistingTextChoiceLeaveOld)
13904
{
13905
MakeSemicolonStringsIntoSeparateItems (&list);
13906
}
13907
return list;
13908
}
13909
13910
11854
13911
typedef struct parsefielddialog
11855
13912
{
11856
13913
DIALOG_MESSAGE_BLOCK
11857
PopuP parse_field_type;
13914
DialoG parse_field_type;
11858
13915
DialoG biosrc_string_choice;
11859
13916
DialoG source_qual_choice;
11860
13917
DialoG gene_field;
11861
DialoG mrna_field;
13918
DialoG rna_subtype;
13919
DialoG rna_field;
11862
13920
DialoG protein_field;
11863
13921
DialoG import_feature;
11864
13922
DialoG import_qual;
11865
13923
DialoG feature;
13924
GrouP dbxref_grp;
13925
TexT dbxref_db;
13926
GrouP feat_or_desc;
11866
13927
Nlm_ChangeNotifyProc change_notify;
11867
13928
Pointer change_userdata;
13929
Boolean is_search_field;
11868
13930
} ParseFieldDialogData, PNTR ParseFieldDialogPtr;
11869
13931
11870
static void ChangeParseFieldType (PopuP p)
13932
static void ChangeParseFieldType (Pointer data)
11871
13933
{
11872
13934
ParseFieldDialogPtr dlg;
11873
Int4 parse_field_type;
13935
ValNodePtr vnp;
11874
13936
11875
dlg = (ParseFieldDialogPtr) GetObjectExtra (p);
13937
dlg = (ParseFieldDialogPtr) data;
11876
13938
if (dlg == NULL)
11877
13939
{
11878
13940
return;
11879
13941
}
11880
parse_field_type = GetValue (dlg->parse_field_type);
13942
vnp = DialogToPointer (dlg->parse_field_type);
11881
13943
Hide (dlg->biosrc_string_choice);
13944
Hide (dlg->feat_or_desc);
11882
13945
Hide (dlg->source_qual_choice);
11883
13946
Hide (dlg->gene_field);
11884
Hide (dlg->mrna_field);
13947
Hide (dlg->rna_subtype);
13948
Hide (dlg->rna_field);
11885
13949
Hide (dlg->protein_field);
11886
13950
Hide (dlg->import_feature);
11887
13951
Hide (dlg->import_qual);
11888
13952
Hide (dlg->feature);
11889
switch (parse_field_type)
13953
Hide (dlg->dbxref_grp);
13954
if (vnp != NULL)
11890
13955
{
11891
case PARSE_FIELD_BIOSRC_STRING:
11892
Show (dlg->biosrc_string_choice);
11893
break;
11894
case PARSE_FIELD_SOURCE_QUAL:
11895
Show (dlg->source_qual_choice);
11896
break;
11897
case PARSE_FIELD_GENE_FIELD:
11898
Show (dlg->gene_field);
11899
break;
11900
case PARSE_FIELD_MRNA_FIELD:
11901
Show (dlg->mrna_field);
11902
break;
11903
case PARSE_FIELD_PROTEIN_FIELD:
11904
Show (dlg->protein_field);
11905
break;
11906
case PARSE_FIELD_IMPORT_QUAL:
11907
Show (dlg->import_feature);
11908
Show (dlg->import_qual);
11909
break;
11910
case PARSE_FIELD_FEATURE_NOTE:
11911
Show (dlg->feature);
11912
break;
13956
switch (vnp->choice)
13957
{
13958
case PARSE_FIELD_BIOSRC_STRING:
13959
Show (dlg->biosrc_string_choice);
13960
Show (dlg->feat_or_desc);
13961
break;
13962
case PARSE_FIELD_SOURCE_QUAL:
13963
Show (dlg->source_qual_choice);
13964
Show (dlg->feat_or_desc);
13965
break;
13966
case PARSE_FIELD_GENE_FIELD:
13967
Show (dlg->gene_field);
13968
break;
13969
case PARSE_FIELD_RNA_FIELD:
13970
Show (dlg->rna_subtype);
13971
Show (dlg->rna_field);
13972
break;
13973
case PARSE_FIELD_PROTEIN_FIELD:
13974
Show (dlg->protein_field);
13975
break;
13976
case PARSE_FIELD_IMPORT_QUAL:
13977
Show (dlg->import_feature);
13978
Show (dlg->import_qual);
13979
break;
13980
case PARSE_FIELD_FEATURE_NOTE:
13981
Show (dlg->feature);
13982
break;
13983
case PARSE_FIELD_DBXREF:
13984
Show (dlg->dbxref_grp);
13985
break;
13986
}
11913
13987
}
11914
13988
if (dlg->change_notify != NULL)
11915
13989
{
11919
13993
11920
13994
static void ResetParseFieldDialog (ParseFieldDialogPtr dlg)
11921
13995
{
13996
ValNode vn;
13997
11922
13998
if (dlg == NULL)
11923
13999
{
11924
14000
return;
11925
14001
}
11926
SetValue (dlg->parse_field_type, PARSE_FIELD_DEFLINE);
11927
ChangeParseFieldType (dlg->parse_field_type);
14002
vn.choice = PARSE_FIELD_DEFLINE;
14003
vn.data.ptrvalue = NULL;
14004
vn.next = NULL;
14005
PointerToDialog (dlg->parse_field_type, &vn);
14006
ChangeParseFieldType (dlg);
11928
14007
}
11929
14008
11930
14009
static void ParseFieldToDialog (DialoG d, Pointer data)
11932
14011
ParseFieldDialogPtr dlg;
11933
14012
ParseFieldPtr parse_field;
11934
14013
Int4 parse_field_type;
14014
ValNode vn;
11935
14015
11936
14016
dlg = (ParseFieldDialogPtr) GetObjectExtra (d);
11937
14017
if (dlg == NULL)
11943
14023
if (parse_field != NULL)
11944
14024
{
11945
14025
parse_field_type = parse_field->parse_field_type;
11946
if (parse_field_type < PARSE_FIELD_DEFLINE || parse_field_type > MAX_PARSE_FIELD_TYPE)
14026
if (parse_field_type < PARSE_FIELD_DEFLINE
14027
|| (dlg->is_search_field && parse_field_type > SEARCH_FIELD_PUBLICATION)
14028
|| (!dlg->is_search_field && parse_field_type > MAX_PARSE_FIELD_TYPE))
11947
14029
{
11948
14030
parse_field_type = PARSE_FIELD_DEFLINE;
11949
14031
}
11950
SetValue (dlg->parse_field_type, parse_field_type);
14032
vn.choice = parse_field_type;
14033
vn.data.ptrvalue = NULL;
14034
vn.next = NULL;
14035
PointerToDialog (dlg->parse_field_type, &vn);
11951
14036
switch (parse_field_type)
11952
14037
{
11953
14038
case PARSE_FIELD_BIOSRC_STRING:
11954
14039
PointerToDialog (dlg->biosrc_string_choice, parse_field->feature_field);
14040
if (parse_field->do_desc && parse_field->do_feat)
14041
{
14042
SetValue (dlg->feat_or_desc, 1);
14043
}
14044
else if (parse_field->do_desc)
14045
{
14046
SetValue (dlg->feat_or_desc, 2);
14047
}
14048
else if (parse_field->do_feat)
14049
{
14050
SetValue (dlg->feat_or_desc, 3);
14051
}
14052
else
14053
{
14054
SetValue (dlg->feat_or_desc, 1);
14055
}
11955
14056
break;
11956
14057
case PARSE_FIELD_SOURCE_QUAL:
11957
14058
PointerToDialog (dlg->source_qual_choice, parse_field->feature_field);
14059
if (parse_field->do_desc && parse_field->do_feat)
14060
{
14061
SetValue (dlg->feat_or_desc, 1);
14062
}
14063
else if (parse_field->do_desc)
14064
{
14065
SetValue (dlg->feat_or_desc, 2);
14066
}
14067
else if (parse_field->do_feat)
14068
{
14069
SetValue (dlg->feat_or_desc, 3);
14070
}
14071
else
14072
{
14073
SetValue (dlg->feat_or_desc, 1);
14074
}
14075
break;
14076
case PARSE_FIELD_DBXREF:
14077
if (parse_field->feature_field == NULL || parse_field->feature_field->data.ptrvalue == NULL)
14078
{
14079
SetTitle (dlg->dbxref_db, "");
14080
}
14081
else
14082
{
14083
SetTitle (dlg->dbxref_db, parse_field->feature_field->data.ptrvalue);
14084
}
14085
if (parse_field->do_desc && parse_field->do_feat)
14086
{
14087
SetValue (dlg->feat_or_desc, 1);
14088
}
14089
else if (parse_field->do_desc)
14090
{
14091
SetValue (dlg->feat_or_desc, 2);
14092
}
14093
else if (parse_field->do_feat)
14094
{
14095
SetValue (dlg->feat_or_desc, 3);
14096
}
14097
else
14098
{
14099
SetValue (dlg->feat_or_desc, 1);
14100
}
11958
14101
break;
11959
14102
case PARSE_FIELD_GENE_FIELD:
11960
14103
PointerToDialog (dlg->gene_field, parse_field->feature_field);
11961
14104
break;
11962
case PARSE_FIELD_MRNA_FIELD:
11963
PointerToDialog (dlg->mrna_field, parse_field->feature_field);
14105
case PARSE_FIELD_RNA_FIELD:
14106
PointerToDialog (dlg->rna_subtype, parse_field->feature_subtype);
14107
PointerToDialog (dlg->rna_field, parse_field->feature_field);
11964
14108
break;
11965
14109
case PARSE_FIELD_PROTEIN_FIELD:
11966
14110
PointerToDialog (dlg->protein_field, parse_field->feature_field);
11972
14116
case PARSE_FIELD_FEATURE_NOTE:
11973
14117
PointerToDialog (dlg->feature, parse_field->feature_field);
11974
14118
break;
14119
case SEARCH_FIELD_PUBLICATION:
14120
/* nothing to do here */
14121
break;
11975
14122
}
11976
14123
}
11977
ChangeParseFieldType (dlg->parse_field_type);
14124
ChangeParseFieldType (dlg);
11978
14125
}
11979
14126
11980
14127
static Pointer DialogToParseField (DialoG d)
11981
14128
{
11982
14129
ParseFieldDialogPtr dlg;
11983
14130
ParseFieldPtr parse_field;
14131
Int4 val;
14132
ValNodePtr vnp;
11984
14133
11985
14134
dlg = (ParseFieldDialogPtr) GetObjectExtra (d);
11986
14135
if (dlg == NULL)
11987
14136
{
11988
14137
return NULL;
11989
14138
}
14139
vnp = DialogToPointer (dlg->parse_field_type);
14140
if (vnp == NULL)
14141
{
14142
return NULL;
14143
}
14144
11990
14145
parse_field = (ParseFieldPtr) MemNew (sizeof (ParseFieldData));
11991
14146
if (parse_field != NULL)
11992
14147
{
11993
parse_field->parse_field_type = GetValue (dlg->parse_field_type);
14148
parse_field->parse_field_type = vnp->choice;
11994
14149
parse_field->feature_field = NULL;
11995
14150
switch (parse_field->parse_field_type)
11996
14151
{
11997
14152
case PARSE_FIELD_BIOSRC_STRING:
11998
14153
parse_field->feature_field = DialogToPointer (dlg->biosrc_string_choice);
14154
val = GetValue (dlg->feat_or_desc);
14155
switch (val)
14156
{
14157
case 2:
14158
parse_field->do_desc = TRUE;
14159
parse_field->do_feat = FALSE;
14160
break;
14161
case 3:
14162
parse_field->do_desc = FALSE;
14163
parse_field->do_feat = TRUE;
14164
break;
14165
case 1:
14166
default:
14167
parse_field->do_desc = TRUE;
14168
parse_field->do_feat = TRUE;
14169
break;
14170
}
11999
14171
break;
12000
14172
case PARSE_FIELD_SOURCE_QUAL:
12001
14173
parse_field->feature_field = DialogToPointer (dlg->source_qual_choice);
14174
val = GetValue (dlg->feat_or_desc);
14175
switch (val)
14176
{
14177
case 2:
14178
parse_field->do_desc = TRUE;
14179
parse_field->do_feat = FALSE;
14180
break;
14181
case 3:
14182
parse_field->do_desc = FALSE;
14183
parse_field->do_feat = TRUE;
14184
break;
14185
case 1:
14186
default:
14187
parse_field->do_desc = TRUE;
14188
parse_field->do_feat = TRUE;
14189
break;
14190
}
14191
break;
14192
case PARSE_FIELD_DBXREF:
14193
if (!TextHasNoText (dlg->dbxref_db))
14194
{
14195
ValNodeAddPointer (&(parse_field->feature_field), 0, SaveStringFromText (dlg->dbxref_db));
14196
}
14197
val = GetValue (dlg->feat_or_desc);
14198
switch (val)
14199
{
14200
case 2:
14201
parse_field->do_desc = TRUE;
14202
parse_field->do_feat = FALSE;
14203
break;
14204
case 3:
14205
parse_field->do_desc = FALSE;
14206
parse_field->do_feat = TRUE;
14207
break;
14208
case 1:
14209
default:
14210
parse_field->do_desc = TRUE;
14211
parse_field->do_feat = TRUE;
14212
break;
14213
}
12002
14214
break;
12003
14215
case PARSE_FIELD_GENE_FIELD:
12004
14216
parse_field->feature_field = DialogToPointer (dlg->gene_field);
12005
14217
break;
12006
case PARSE_FIELD_MRNA_FIELD:
12007
parse_field->feature_field = DialogToPointer (dlg->mrna_field);
14218
case PARSE_FIELD_RNA_FIELD:
14219
parse_field->feature_subtype = DialogToPointer (dlg->rna_subtype);
14220
parse_field->feature_field = DialogToPointer (dlg->rna_field);
12008
14221
break;
12009
14222
case PARSE_FIELD_PROTEIN_FIELD:
12010
14223
parse_field->feature_field = DialogToPointer (dlg->protein_field);
12016
14229
case PARSE_FIELD_FEATURE_NOTE:
12017
14230
parse_field->feature_field = DialogToPointer (dlg->feature);
12018
14231
break;
14232
case SEARCH_FIELD_PUBLICATION:
14233
/* nothing to do here */
14234
break;
12019
14235
}
12020
14236
}
14237
vnp = ValNodeFreeData (vnp);
12021
14238
return parse_field;
12022
14239
}
12023
14240
12053
14270
12054
14271
if (dlg != NULL)
12055
14272
{
12056
parse_field_type = GetValue (dlg->parse_field_type);
12057
switch (parse_field_type)
12058
{
12059
case PARSE_FIELD_DEFLINE:
12060
case PARSE_FIELD_CDS_COMMENT:
12061
case PARSE_FIELD_COMMENT_DESC:
12062
/* don't need any extra information */
12063
break;
12064
case PARSE_FIELD_BIOSRC_STRING:
12065
vnp = DialogToPointer (dlg->biosrc_string_choice);
12066
if (vnp == NULL)
12067
{
12068
head = AddStringToValNodeChain (head, "biosrc string type", 1);
12069
}
12070
ValNodeFree (vnp);
12071
break;
12072
case PARSE_FIELD_SOURCE_QUAL:
12073
vnp = DialogToPointer (dlg->source_qual_choice);
12074
if (vnp == NULL)
12075
{
12076
head = AddStringToValNodeChain (head, "source qual type", 1);
12077
}
12078
ValNodeFree (vnp);
12079
break;
12080
case PARSE_FIELD_GENE_FIELD:
12081
vnp = DialogToPointer (dlg->gene_field);
12082
if (vnp == NULL || vnp->data.intvalue == FEATUREFIELD_NONE)
12083
{
12084
head = AddStringToValNodeChain (head, "gene field", 1);
12085
}
12086
ValNodeFree (vnp);
12087
break;
12088
case PARSE_FIELD_MRNA_FIELD:
12089
vnp = DialogToPointer (dlg->mrna_field);
12090
if (vnp == NULL || vnp->data.intvalue == FEATUREFIELD_NONE)
12091
{
12092
head = AddStringToValNodeChain (head, "mRNA field", 1);
12093
}
12094
ValNodeFree (vnp);
12095
break;
12096
case PARSE_FIELD_PROTEIN_FIELD:
12097
vnp = DialogToPointer (dlg->protein_field);
12098
if (vnp == NULL || vnp->data.intvalue == FEATUREFIELD_NONE)
12099
{
12100
head = AddStringToValNodeChain (head, "protein field", 1);
12101
}
12102
ValNodeFree (vnp);
12103
break;
12104
case PARSE_FIELD_IMPORT_QUAL:
12105
vnp = DialogToPointer (dlg->import_qual);
12106
if (vnp == NULL)
12107
{
12108
ValNodeAddPointer (&head, 1, "import qualifier");
12109
}
12110
ValNodeFree (vnp);
12111
vnp = DialogToPointer (dlg->import_feature);
12112
if (vnp == NULL)
12113
{
12114
ValNodeAddPointer (&head, 1, "import feature");
12115
}
12116
ValNodeFree (vnp);
12117
break;
12118
case PARSE_FIELD_FEATURE_NOTE:
12119
vnp = DialogToPointer (dlg->feature);
12120
if (vnp == NULL)
12121
{
12122
ValNodeAddPointer (&head, 1, "feature");
12123
ValNodeFree (vnp);
12124
}
12125
break;
12126
default:
12127
head = AddStringToValNodeChain (head, "field type", 1);
12128
break;
14273
vnp = DialogToPointer (dlg->parse_field_type);
14274
if (vnp == NULL)
14275
{
14276
head = AddStringToValNodeChain (head, "destination type", 1);
14277
}
14278
else
14279
{
14280
parse_field_type = vnp->choice;
14281
vnp = ValNodeFreeData (vnp);
14282
switch (parse_field_type)
14283
{
14284
case PARSE_FIELD_DEFLINE:
14285
case PARSE_FIELD_CDS_COMMENT:
14286
case PARSE_FIELD_COMMENT_DESC:
14287
/* don't need any extra information */
14288
break;
14289
case PARSE_FIELD_BIOSRC_STRING:
14290
vnp = DialogToPointer (dlg->biosrc_string_choice);
14291
if (vnp == NULL)
14292
{
14293
head = AddStringToValNodeChain (head, "biosrc string type", 1);
14294
}
14295
ValNodeFree (vnp);
14296
break;
14297
case PARSE_FIELD_SOURCE_QUAL:
14298
vnp = DialogToPointer (dlg->source_qual_choice);
14299
if (vnp == NULL)
14300
{
14301
head = AddStringToValNodeChain (head, "source qual type", 1);
14302
}
14303
ValNodeFree (vnp);
14304
break;
14305
case PARSE_FIELD_GENE_FIELD:
14306
vnp = DialogToPointer (dlg->gene_field);
14307
if (vnp == NULL || vnp->data.intvalue == FEATUREFIELD_NONE)
14308
{
14309
head = AddStringToValNodeChain (head, "gene field", 1);
14310
}
14311
ValNodeFree (vnp);
14312
break;
14313
case PARSE_FIELD_RNA_FIELD:
14314
vnp = DialogToPointer (dlg->rna_subtype);
14315
if (vnp == NULL)
14316
{
14317
head = AddStringToValNodeChain (head, "RNA subtype", 1);
14318
}
14319
ValNodeFree (vnp);
14320
vnp = DialogToPointer (dlg->rna_field);
14321
if (vnp == NULL || vnp->data.intvalue == FEATUREFIELD_NONE)
14322
{
14323
head = AddStringToValNodeChain (head, "RNA field", 1);
14324
}
14325
ValNodeFree (vnp);
14326
break;
14327
case PARSE_FIELD_PROTEIN_FIELD:
14328
vnp = DialogToPointer (dlg->protein_field);
14329
if (vnp == NULL || vnp->data.intvalue == FEATUREFIELD_NONE)
14330
{
14331
head = AddStringToValNodeChain (head, "protein field", 1);
14332
}
14333
ValNodeFree (vnp);
14334
break;
14335
case PARSE_FIELD_IMPORT_QUAL:
14336
vnp = DialogToPointer (dlg->import_qual);
14337
if (vnp == NULL)
14338
{
14339
ValNodeAddPointer (&head, 1, "import qualifier");
14340
}
14341
ValNodeFree (vnp);
14342
vnp = DialogToPointer (dlg->import_feature);
14343
if (vnp == NULL)
14344
{
14345
ValNodeAddPointer (&head, 1, "import feature");
14346
}
14347
ValNodeFree (vnp);
14348
break;
14349
case PARSE_FIELD_FEATURE_NOTE:
14350
vnp = DialogToPointer (dlg->feature);
14351
if (vnp == NULL)
14352
{
14353
ValNodeAddPointer (&head, 1, "feature");
14354
ValNodeFree (vnp);
14355
}
14356
break;
14357
case PARSE_FIELD_DBXREF:
14358
if (TextHasNoText (dlg->dbxref_db))
14359
{
14360
ValNodeAddPointer (&head, 1, "specify database");
14361
}
14362
break;
14363
case SEARCH_FIELD_PUBLICATION:
14364
if (!dlg->is_search_field)
14365
{
14366
head = AddStringToValNodeChain (head, "field type", 1);
14367
}
14368
break;
14369
default:
14370
head = AddStringToValNodeChain (head, "field type", 1);
14371
break;
14372
}
12129
14373
}
12130
14374
}
12131
14375
12132
14376
return head;
12133
14377
}
12134
14378
12135
extern DialoG ParseFieldDestDialog
14379
14380
static ValNodePtr GetParseFieldDestList (Boolean include_pub, Boolean include_dbxref)
14381
{
14382
ValNodePtr list = NULL;
14383
14384
ValNodeAddPointer (&list, PARSE_FIELD_DEFLINE, StringSave ("Definition Line"));
14385
ValNodeAddPointer (&list, PARSE_FIELD_BIOSRC_STRING, StringSave ("Biosource"));
14386
ValNodeAddPointer (&list, PARSE_FIELD_SOURCE_QUAL, StringSave ("Source Qualifier"));
14387
ValNodeAddPointer (&list, PARSE_FIELD_GENE_FIELD, StringSave ("Gene Field"));
14388
ValNodeAddPointer (&list, PARSE_FIELD_RNA_FIELD, StringSave ("RNA Field"));
14389
ValNodeAddPointer (&list, PARSE_FIELD_CDS_COMMENT, StringSave ("CDS Comment"));
14390
ValNodeAddPointer (&list, PARSE_FIELD_PROTEIN_FIELD, StringSave ("Protein Field"));
14391
ValNodeAddPointer (&list, PARSE_FIELD_IMPORT_QUAL, StringSave ("Import Feature"));
14392
ValNodeAddPointer (&list, PARSE_FIELD_FEATURE_NOTE, StringSave ("Feature Note"));
14393
ValNodeAddPointer (&list, PARSE_FIELD_COMMENT_DESC, StringSave ("Comment Descriptor"));
14394
if (include_dbxref)
14395
{
14396
ValNodeAddPointer (&list, PARSE_FIELD_DBXREF, StringSave ("Dbxref"));
14397
}
14398
if (include_pub)
14399
{
14400
ValNodeAddPointer (&list, SEARCH_FIELD_PUBLICATION, StringSave ("Publication"));
14401
}
14402
return list;
14403
}
14404
14405
14406
static void ChangeParseFieldDestText (TexT t)
14407
{
14408
ParseFieldDialogPtr dlg;
14409
14410
dlg = (ParseFieldDialogPtr) GetObjectExtra (t);
14411
if (dlg != NULL && dlg->change_notify != NULL)
14412
{
14413
(dlg->change_notify) (dlg->change_userdata);
14414
}
14415
}
14416
14417
14418
extern DialoG ParseFieldDestDialogEx
12136
14419
(GrouP h,
12137
14420
Nlm_ChangeNotifyProc change_notify,
12138
Pointer change_userdata)
14421
Pointer change_userdata,
14422
Boolean is_search_field,
14423
Boolean include_dbxref)
12139
14424
{
12140
14425
ParseFieldDialogPtr dlg;
12141
GrouP p, g;
14426
GrouP p, m, g;
12142
14427
GrouP subgrp;
14428
ValNodePtr choice_list;
14429
ValNode vn;
12143
14430
12144
14431
dlg = (ParseFieldDialogPtr) MemNew (sizeof (ParseFieldDialogData));
12145
14432
if (dlg == NULL)
12147
14434
return NULL;
12148
14435
}
12149
14436
12150
p = HiddenGroup (h, 2, 0, NULL);
14437
p = HiddenGroup (h, -1, 0, NULL);
12151
14438
SetObjectExtra (p, dlg, StdCleanupExtraProc);
12152
14439
12153
14440
dlg->dialog = (DialoG) p;
12157
14444
dlg->testdialog = TestParseFieldDialog;
12158
14445
dlg->change_notify = change_notify;
12159
14446
dlg->change_userdata = change_userdata;
12160
12161
dlg->parse_field_type = PopupList (p, TRUE, ChangeParseFieldType);
12162
PopupItem (dlg->parse_field_type, "Definition Line");
12163
PopupItem (dlg->parse_field_type, "Biosource");
12164
PopupItem (dlg->parse_field_type, "Source Qualifier");
12165
PopupItem (dlg->parse_field_type, "Gene Field");
12166
PopupItem (dlg->parse_field_type, "mRNA Field");
12167
PopupItem (dlg->parse_field_type, "CDS Comment");
12168
PopupItem (dlg->parse_field_type, "Protein Field");
12169
PopupItem (dlg->parse_field_type, "Import Feature");
12170
PopupItem (dlg->parse_field_type, "Feature Note");
12171
PopupItem (dlg->parse_field_type, "Comment Descriptor");
12172
SetValue (dlg->parse_field_type, PARSE_FIELD_DEFLINE);
12173
SetObjectExtra (dlg->parse_field_type, dlg, NULL);
12174
12175
subgrp = HiddenGroup (p, 0, 0, NULL);
14447
dlg->is_search_field = is_search_field;
14448
14449
m = HiddenGroup (p, 2, 0, NULL);
14450
14451
choice_list = GetParseFieldDestList (is_search_field, include_dbxref);
14452
dlg->parse_field_type = ValNodeSelectionDialog (m, choice_list, TALL_SELECTION_LIST, ValNodeStringName,
14453
ValNodeSimpleDataFree, ValNodeStringCopy,
14454
ValNodeChoiceMatch, "parse destination",
14455
ChangeParseFieldType, dlg, FALSE);
14456
14457
subgrp = HiddenGroup (m, 0, 0, NULL);
12176
14458
dlg->biosrc_string_choice = BioSourceStringDialog (subgrp, FALSE, change_notify, change_userdata);
12177
14459
Hide (dlg->biosrc_string_choice);
12178
14460
dlg->source_qual_choice = SourceQualTypeSelectionDialog (subgrp, FALSE, change_notify, change_userdata);
12179
14461
Hide (dlg->source_qual_choice);
12180
14462
dlg->gene_field = GeneFieldSelectionDialog (subgrp, FALSE, change_notify, change_userdata);
12181
14463
Hide (dlg->gene_field);
12182
dlg->mrna_field = MRNAFieldSelectionDialog (subgrp, FALSE, change_notify, change_userdata);
12183
Hide (dlg->mrna_field);
14464
g = HiddenGroup (subgrp, 2, 0, NULL);
14465
dlg->rna_subtype = RNASubtypeSelectionDialog (g, FALSE, NULL, change_notify, change_userdata);
14466
Hide (dlg->rna_subtype);
14467
dlg->rna_field = RNAFieldSelectionDialog (g, FALSE,
14468
change_notify,
14469
change_userdata);
14470
Hide (dlg->rna_field);
12184
14471
dlg->protein_field = ProteinFieldSelectionDialog (subgrp, FALSE, change_notify, change_userdata);
12185
14472
Hide (dlg->protein_field);
12186
14473
g = HiddenGroup (subgrp, 2, 0, NULL);
12190
14477
Hide (dlg->import_qual);
12191
14478
dlg->feature = FeatureSelectionDialog (subgrp, TRUE, change_notify, change_userdata);
12192
14479
Hide (dlg->feature);
14480
if (include_dbxref)
14481
{
14482
dlg->dbxref_grp = HiddenGroup (subgrp, 2, 0, NULL);
14483
StaticPrompt (dlg->dbxref_grp, "Database:", 0, 0, programFont, 'r');
14484
dlg->dbxref_db = DialogText (dlg->dbxref_grp, "", 5, ChangeParseFieldDestText);
14485
SetObjectExtra (dlg->dbxref_db, dlg, NULL);
14486
Hide (dlg->dbxref_grp);
14487
}
14488
else
14489
{
14490
dlg->dbxref_db = NULL;
14491
}
14492
14493
vn.choice = PARSE_FIELD_DEFLINE;
14494
vn.data.ptrvalue = NULL;
14495
vn.next = NULL;
14496
PointerToDialog (dlg->parse_field_type, &vn);
14497
14498
dlg->feat_or_desc = HiddenGroup (p, 3, 0, NULL);
14499
RadioButton (dlg->feat_or_desc, "Descriptors and Features");
14500
RadioButton (dlg->feat_or_desc, "Descriptors Only");
14501
RadioButton (dlg->feat_or_desc, "Features Only");
14502
SetValue (dlg->feat_or_desc, 1);
14503
Hide (dlg->feat_or_desc);
14504
14505
AlignObjects (ALIGN_CENTER, (HANDLE) m, (HANDLE) dlg->feat_or_desc, NULL);
12193
14506
12194
14507
return (DialoG) p;
12195
14508
}
12196
14509
12197
#define PARSE_FIELD_SRC_DEFLINE 1
12198
#define PARSE_FIELD_SRC_GENBANK_FLATFILE 2
12199
#define PARSE_FIELD_SRC_LOCAL_ID 3
12200
#define PARSE_FIELD_SRC_TAXNAME 4
12201
#define PARSE_FIELD_SRC_COMMENT 5
12202
#define PARSE_FIELD_BANKIT_COMMENT 6
12203
#define PARSE_FIELD_STRUCTURED_COMMENT 7
12204
#define MAX_PARSE_FIELD 7
14510
extern DialoG ParseFieldDestDialog
14511
(GrouP h,
14512
Nlm_ChangeNotifyProc change_notify,
14513
Pointer change_userdata)
14514
{
14515
return ParseFieldDestDialogEx (h, change_notify, change_userdata, FALSE, FALSE);
14516
}
14517
/* Search Field dialog is identical to ParseFieldDestDialog except that it allows
14518
* an additional option, Publication.
14519
*/
14520
extern DialoG SearchFieldDialog
14521
(GrouP h,
14522
Nlm_ChangeNotifyProc change_notify,
14523
Pointer change_userdata)
14524
{
14525
return ParseFieldDestDialogEx (h, change_notify, change_userdata, TRUE, FALSE);
14526
}
14527
14528
14529
typedef enum
14530
{
14531
eParseFieldSrcDefLine = 1,
14532
eParseFieldSrcGenBankFlatFile,
14533
eParseFieldSrcLocalID,
14534
eParseFieldSrcTaxName,
14535
eParseFieldSrcSourceQual,
14536
eParseFieldSrcComment,
14537
eParseFieldSrcBankitComment,
14538
eParseFieldSrcStructuredComment,
14539
eParseFieldSrcTaxNameAfterNomial,
14540
eParseFieldSrcFileID
14541
} EParseFieldSrc;
14542
14543
const Int4 MAX_PARSE_FIELD = eParseFieldSrcFileID;
12205
14544
12206
14545
static CharPtr parse_src_field_list [] =
12207
14546
{
12208
"Definition Line", "GenBank Flatfile", "Local ID", "Organism Name", "Comment", "Bankit Comment", "Structured Comment"
14547
"Definition Line", "GenBank Flatfile", "Local ID", "Organism Name", "Source Qualifier", "Comment", "Bankit Comment",
14548
"Structured Comment", "Taxname after Binomial/Trinomial", "File ID"
12209
14549
};
12210
14550
12211
14551
static int num_parse_src_fields = sizeof (parse_src_field_list) / sizeof (CharPtr);
12212
14552
12213
14553
typedef struct parsefieldsrc
12214
14554
{
12215
Int4 parse_field;
12216
CharPtr comment_field;
14555
Int4 parse_field;
14556
SourceQualDescPtr sqdp;
14557
CharPtr comment_field;
12217
14558
} ParseFieldSrcData, PNTR ParseFieldSrcPtr;
12218
14559
12219
14560
static ParseFieldSrcPtr ParseFieldSrcFree (ParseFieldSrcPtr pfsp)
12220
14561
{
12221
14562
if (pfsp != NULL) {
12222
14563
pfsp->comment_field = MemFree (pfsp->comment_field);
14564
pfsp->sqdp = MemFree (pfsp->sqdp);
12223
14565
pfsp = MemFree (pfsp);
12224
14566
}
12225
14567
return pfsp;
12231
14573
DialoG parse_field;
12232
14574
PopuP comment_field;
12233
14575
ValNodePtr comment_field_list;
14576
DialoG src_qual;
12234
14577
Nlm_ChangeNotifyProc change_notify;
12235
14578
Pointer change_userdata;
12236
14579
} ParseFieldSrcDlgData, PNTR ParseFieldSrcDlgPtr;
12283
14626
if (dlg == NULL) return;
12284
14627
12285
14628
vnp = DialogToPointer (dlg->parse_field);
12286
if (vnp == NULL || vnp->data.intvalue != PARSE_FIELD_STRUCTURED_COMMENT) {
14629
if (vnp == NULL || vnp->data.intvalue != eParseFieldSrcStructuredComment) {
12287
14630
Hide (dlg->comment_field);
12288
14631
} else {
12289
14632
Show (dlg->comment_field);
12290
14633
}
14634
if (vnp == NULL || vnp->data.intvalue != eParseFieldSrcSourceQual) {
14635
Hide (dlg->src_qual);
14636
} else {
14637
Show (dlg->src_qual);
14638
}
12291
14639
12292
14640
if (dlg->change_notify != NULL) {
12293
14641
(dlg->change_notify)(dlg->change_userdata);
12331
14679
vn.choice = 0;
12332
14680
PointerToDialog (dlg->parse_field, &vn);
12333
14681
SetValue (dlg->comment_field, FindCommentFieldPosition (pfsp->comment_field, dlg->comment_field_list));
14682
vn.data.ptrvalue = pfsp->sqdp;
14683
PointerToDialog (dlg->src_qual, &vn);
12334
14684
}
12335
14685
}
12336
14686
ParseFieldChange (dlg);
12355
14705
vnp = ValNodeFree (vnp);
12356
14706
}
12357
14707
pfsp->comment_field = NULL;
12358
if (pfsp->parse_field == PARSE_FIELD_STRUCTURED_COMMENT) {
14708
pfsp->sqdp = NULL;
14709
if (pfsp->parse_field == eParseFieldSrcStructuredComment) {
12359
14710
field_pos = GetValue (dlg->comment_field);
12360
14711
if (field_pos > 0) {
12361
14712
vnp = dlg->comment_field_list;
12368
14719
pfsp->comment_field = StringSave (vnp->data.ptrvalue);
12369
14720
}
12370
14721
}
14722
} else if (pfsp->parse_field == eParseFieldSrcSourceQual) {
14723
vnp = DialogToPointer (dlg->src_qual);
14724
if (vnp != NULL) {
14725
pfsp->sqdp = vnp->data.ptrvalue;
14726
vnp->data.ptrvalue = NULL;
14727
vnp = ValNodeFreeData (vnp);
14728
}
12371
14729
}
14730
12372
14731
return pfsp;
12373
14732
}
12374
14733
12413
14772
}
12414
14773
}
12415
14774
14775
14776
static ValNodePtr TestParseFieldSource (DialoG d)
14777
14778
{
14779
ParseFieldSrcDlgPtr dlg;
14780
ValNodePtr head = NULL, vnp, vnp2;
14781
14782
dlg = (ParseFieldSrcDlgPtr) GetObjectExtra (d);
14783
14784
vnp = DialogToPointer (dlg->parse_field);
14785
if (vnp == NULL)
14786
{
14787
head = AddStringToValNodeChain (head, "field choice", 1);
14788
}
14789
else if (vnp->data.intvalue == eParseFieldSrcSourceQual)
14790
{
14791
vnp2 = DialogToPointer (dlg->src_qual);
14792
if (vnp2 == NULL)
14793
{
14794
head = AddStringToValNodeChain (head, "source qual", 1);
14795
}
14796
vnp2 = ValNodeFree (vnp2);
14797
}
14798
14799
vnp = ValNodeFree (vnp);
14800
14801
return head;
14802
}
14803
14804
12416
14805
extern DialoG ParseFieldSourceDialog
12417
14806
(GrouP h,
12418
14807
SeqEntryPtr sep,
12420
14809
Pointer change_userdata)
12421
14810
{
12422
14811
ParseFieldSrcDlgPtr dlg;
12423
GrouP p;
14812
GrouP p, k;
12424
14813
ValNodePtr vnp;
12425
14814
12426
14815
dlg = (ParseFieldSrcDlgPtr) MemNew (sizeof (ParseFieldSrcDlgData));
12437
14826
dlg->todialog = DataToParseFieldSrcDialog;
12438
14827
dlg->fromdialog = ParseFieldSrcDialogToData;
12439
14828
dlg->dialogmessage = ParseFieldSourceDialogMessage;
12440
dlg->testdialog = NULL;
14829
dlg->testdialog = TestParseFieldSource;
12441
14830
dlg->change_notify = change_notify;
12442
14831
dlg->change_userdata = change_userdata;
12443
14832
12445
14834
num_parse_src_fields, parse_src_field_list,
12446
14835
ParseFieldChange, dlg);
12447
14836
12448
dlg->comment_field = PopupList (p, TRUE, NULL);
14837
k = HiddenGroup (p, 0, 0, NULL);
14838
dlg->comment_field = PopupList (k, TRUE, NULL);
14839
dlg->src_qual = SourceQualTypeSelectionDialogEx (k, FALSE, change_notify,
14840
change_userdata, 6, FALSE, FALSE);
14841
AlignObjects (ALIGN_CENTER, (HANDLE) dlg->comment_field, (HANDLE) dlg->src_qual, NULL);
12449
14842
12450
// Add to comment_field list all user fields found in SeqEntry sep
14843
/* Add to comment_field list all user fields found in SeqEntry sep */
12451
14844
VisitDescriptorsInSep (sep, &(dlg->comment_field_list), AddCommentFieldName);
12452
14845
for (vnp = dlg->comment_field_list; vnp != NULL; vnp = vnp->next) {
12453
14846
PopupItem (dlg->comment_field, vnp->data.ptrvalue);
12523
14916
Char tmp[128];
12524
14917
CharPtr val_str = NULL, new_val_str, tmp_val_str;
12525
14918
ValNodePtr sample_field, sample_field_next;
12526
Boolean found_text = FALSE;
12527
14919
ValNodePtr new_row = NULL;
12528
14920
SeqIdPtr sip;
12529
14921
12744
15136
ValNodePtr sample_field, sample_field_next;
12745
15137
CharPtr sample_label = NULL;
12746
15138
Int4 max_char_per_line;
12747
FonT currentFont=NULL;
12748
15139
12749
15140
if (dlg == NULL)
12750
15141
{
12836
15227
ssp = (SetSamplePtr) userdata;
12837
15228
dlg->ssp = SetSampleFree (dlg->ssp);
12838
15229
dlg->ssp = SetSampleCopy (ssp);
12839
// RefreshSampleDialog (dlg);
12840
15230
}
12841
15231
12842
15232
static void
13533
15923
13534
15924
typedef struct parseaction
13535
15925
{
13536
TextPortionPtr tp;
15926
TextPortionXPtr tp;
13537
15927
FilterSetPtr fsp;
13538
15928
Int4 src_field;
13539
15929
CharPtr comment_field;
13573
15963
}
13574
15964
}
13575
15965
13576
static void DoParseAction (CharPtr src_str, ParseActionOpPtr paop)
13577
{
13578
CharPtr found_loc = NULL;
13579
Int4 found_len = 0;
13580
13581
if (StringHasNoText (src_str) || paop == NULL
13582
|| paop->parse_action_data == NULL
13583
|| paop->parse_action == NULL)
13584
{
13585
return;
13586
}
13587
13588
FindTextPortionInString (src_str, paop->parse_action_data->tp, &found_loc, &found_len);
13589
13590
if (found_loc != NULL)
13591
{
13592
(paop->parse_action) (paop->parse_action_data, paop->parse_userdata, found_loc, found_len);
13593
paop->parse_complete = TRUE;
13594
}
13595
13596
}
13597
13598
static void ParseActionDeflineText (SeqDescrPtr sdp, Pointer userdata)
13599
{
13600
ParseActionOpPtr paop;
13601
CharPtr tmp_string;
13602
Int4 last_pos;
13603
13604
paop = (ParseActionOpPtr) userdata;
13605
if (paop == NULL || paop->parse_action_data == NULL || paop->parse_action == NULL
13606
|| sdp == NULL || sdp->choice != Seq_descr_title)
13607
{
13608
return;
13609
}
13610
13611
tmp_string = StringSave (sdp->data.ptrvalue);
13612
if (tmp_string != NULL)
13613
{
13614
last_pos = StringLen (tmp_string) - 1;
13615
if (tmp_string [last_pos] == '.')
13616
{
13617
tmp_string [last_pos] = 0;
13618
}
13619
}
13620
DoParseAction (tmp_string, paop);
13621
tmp_string = MemFree (tmp_string);
13622
}
13623
13624
static void ParseActionTaxnameText (BioSourcePtr biop, Pointer userdata)
13625
{
13626
ParseActionOpPtr paop;
13627
13628
paop = (ParseActionOpPtr) userdata;
13629
if (paop == NULL || paop->parse_action_data == NULL || paop->parse_action == NULL
13630
|| biop == NULL || biop->org == NULL)
13631
{
13632
return;
13633
}
13634
13635
if (paop->parse_action_data->fsp != NULL
13636
&& ! DoesOneSourceMatchConstraint (biop, paop->parse_action_data->fsp->ccp))
13637
{
13638
return;
13639
}
13640
13641
DoParseAction (biop->org->taxname, paop);
13642
}
13643
13644
static void ParseActionLocalIDText (BioseqPtr bsp, Pointer userdata)
13645
{
13646
ParseActionOpPtr paop;
13647
SeqIdPtr sip;
13648
ObjectIdPtr oip;
13649
Char tmp_str [128];
13650
13651
paop = (ParseActionOpPtr) userdata;
13652
if (paop == NULL || paop->parse_action_data == NULL || paop->parse_action == NULL
13653
|| bsp == NULL || ISA_aa (bsp->mol))
13654
{
13655
return;
13656
}
13657
13658
for (sip = bsp->id; sip != NULL; sip = sip->next)
13659
{
13660
if (sip->choice == SEQID_LOCAL && sip->data.ptrvalue != NULL)
13661
{
13662
oip = (ObjectIdPtr) sip->data.ptrvalue;
13663
if (oip->str == NULL)
13664
{
13665
sprintf (tmp_str, "%d", oip->id);
13666
DoParseAction (tmp_str, paop);
13667
}
13668
else
13669
{
13670
DoParseAction (oip->str, paop);
13671
}
13672
}
13673
}
13674
}
13675
13676
static void ParseActionBankitComment (SeqDescrPtr sdp, Pointer userdata)
13677
{
13678
ParseActionOpPtr paop;
13679
UserObjectPtr uop;
13680
ObjectIdPtr oip;
13681
UserFieldPtr ufp;
13682
13683
if (sdp == NULL || userdata == NULL || sdp->data.ptrvalue == NULL)
13684
{
13685
return;
13686
}
13687
13688
paop = (ParseActionOpPtr) userdata;
13689
if (paop == NULL || paop->parse_action_data == NULL || paop->parse_action == NULL)
13690
{
13691
return;
13692
}
13693
13694
if (sdp->choice == Seq_descr_user && sdp->extended != 0)
13695
{
13696
/* Bankit Comments */
13697
uop = (UserObjectPtr) sdp->data.ptrvalue;
13698
oip = uop->type;
13699
if (oip != NULL && StringCmp (oip->str, "Submission") == 0)
13700
{
13701
for (ufp = uop->data; ufp != NULL; ufp = ufp->next)
13702
{
13703
oip = ufp->label;
13704
if (oip != NULL && StringCmp (oip->str, "AdditionalComment") == 0)
13705
{
13706
DoParseAction (ufp->data.ptrvalue, paop);
13707
}
13708
}
13709
}
13710
}
13711
}
13712
13713
static void ParseActionCommentDescriptor (SeqDescrPtr sdp, Pointer userdata)
13714
{
13715
ParseActionOpPtr paop;
13716
UserObjectPtr uop;
13717
ObjectIdPtr oip;
13718
UserFieldPtr ufp;
13719
13720
if (sdp == NULL || userdata == NULL || sdp->data.ptrvalue == NULL)
13721
{
13722
return;
13723
}
13724
13725
paop = (ParseActionOpPtr) userdata;
13726
if (paop == NULL || paop->parse_action_data == NULL || paop->parse_action == NULL)
13727
{
13728
return;
13729
}
13730
13731
if (sdp->choice == Seq_descr_comment)
13732
{
13733
DoParseAction (sdp->data.ptrvalue, paop);
13734
}
13735
else if (sdp->choice == Seq_descr_user && sdp->extended != 0)
13736
{
13737
/* Bankit Comments */
13738
uop = (UserObjectPtr) sdp->data.ptrvalue;
13739
oip = uop->type;
13740
if (oip != NULL && StringCmp (oip->str, "Submission") == 0)
13741
{
13742
for (ufp = uop->data; ufp != NULL; ufp = ufp->next)
13743
{
13744
oip = ufp->label;
13745
if (oip != NULL && StringCmp (oip->str, "AdditionalComment") == 0)
13746
{
13747
DoParseAction (ufp->data.ptrvalue, paop);
13748
}
13749
}
13750
}
13751
}
13752
}
13753
13754
static void ParseActionCommentFeature (SeqFeatPtr sfp, Pointer userdata)
13755
{
13756
ParseActionOpPtr paop;
13757
13758
if (sfp == NULL || sfp->data.choice != SEQFEAT_COMMENT || userdata == NULL)
13759
{
13760
return;
13761
}
13762
paop = (ParseActionOpPtr) userdata;
13763
DoParseAction (sfp->comment, paop);
13764
}
13765
13766
13767
static void ParseActionStructuredComment(SeqDescrPtr sdp, Pointer userdata)
13768
{
13769
ParseActionOpPtr paop;
13770
UserObjectPtr uop;
13771
ObjectIdPtr oip;
13772
UserFieldPtr ufp;
13773
13774
if (sdp == NULL || userdata == NULL || sdp->data.ptrvalue == NULL)
13775
{
13776
return;
13777
}
13778
13779
paop = (ParseActionOpPtr) userdata;
13780
if (paop == NULL || paop->parse_action_data == NULL || paop->parse_action == NULL)
13781
{
13782
return;
13783
}
13784
13785
if (sdp->choice == Seq_descr_comment)
13786
{
13787
DoParseAction (sdp->data.ptrvalue, paop);
13788
}
13789
else if (sdp->choice == Seq_descr_user && sdp->extended != 0)
13790
{
13791
/* Bankit Comments */
13792
uop = (UserObjectPtr) sdp->data.ptrvalue;
13793
oip = uop->type;
13794
if (oip != NULL && StringCmp (oip->str, "Submission") == 0)
13795
{
13796
for (ufp = uop->data; ufp != NULL; ufp = ufp->next)
13797
{
13798
oip = ufp->label;
13799
if (oip != NULL && StringCmp (oip->str, "AdditionalComment") == 0)
13800
{
13801
DoParseAction (ufp->data.ptrvalue, paop);
13802
}
13803
}
13804
}
13805
}
13806
}
13807
13808
15966
static void SetSourceAndTitle (ParseActionPtr pap, SeqDescrPtr sdp, SeqAnnotPtr sap)
13809
15967
{
13810
15968
SeqFeatPtr sfp;
13855
16013
}
13856
16014
}
13857
16015
13858
static void ParseFromSource (BioSourcePtr biop, ParseActionPtr pap, ParseActionOpPtr paop)
13859
{
13860
if (biop == NULL || pap == NULL || paop == NULL)
13861
{
13862
return;
13863
}
13864
13865
if (pap->src_field == PARSE_FIELD_SRC_TAXNAME)
13866
{
13867
ParseActionTaxnameText (biop, paop);
13868
}
13869
}
13870
13871
16016
typedef struct parsesourceinfo
13872
16017
{
13873
16018
BioseqPtr bsp;
13940
16085
typedef struct parsesource
13941
16086
{
13942
16087
Int4 src_field;
16088
SourceQualDescPtr sqdp;
13943
16089
CharPtr comment_field;
13944
16090
FilterSetPtr fsp;
13945
16091
ParseFieldPtr dst_field_data;
13946
16092
ValNodePtr source_list; /* ptrvalue points to ParseSourceInfo struct */
13947
TextPortionPtr tp;
16093
TextPortionXPtr tp;
13948
16094
} ParseSourceData, PNTR ParseSourcePtr;
13949
16095
13950
16096
13952
16098
GetDeflineSourcesForBioseq
13953
16099
(BioseqPtr bsp,
13954
16100
FilterSetPtr fsp,
13955
TextPortionPtr tp,
16101
TextPortionXPtr tp,
13956
16102
ValNodePtr PNTR source_list)
13957
16103
{
13958
16104
SeqDescrPtr sdp;
13971
16117
{
13972
16118
if (fsp == NULL
13973
16119
|| fsp->ccp == NULL
13974
|| DoesStringMatchConstraint (sdp->data.ptrvalue, fsp->ccp->string_constraint))
16120
|| DoesStringMatchConstraintX (sdp->data.ptrvalue, fsp->ccp->string_constraint))
13975
16121
{
13976
FindTextPortionInString (sdp->data.ptrvalue, tp, &found_loc, &found_len);
16122
FindTextPortionXInString (sdp->data.ptrvalue, tp, &found_loc, &found_len);
13977
16123
if (found_loc != NULL)
13978
16124
{
13979
16125
parse_src_txt = (CharPtr) MemNew (sizeof (Char) + (found_len + 1));
14001
16147
}
14002
16148
}
14003
16149
16150
16151
static CharPtr GetIDSrc (SeqIdPtr sip, Uint1 id_type, CharPtr tag, FilterSetPtr fsp)
16152
{
16153
DbtagPtr dbt = NULL;
16154
ObjectIdPtr oip = NULL;
16155
Char id_str[128];
16156
CharPtr str_src = NULL;
16157
16158
if (sip == NULL || sip->choice != id_type) return NULL;
16159
16160
if (id_type == SEQID_GENERAL)
16161
{
16162
dbt = (DbtagPtr) sip->data.ptrvalue;
16163
if (dbt == NULL || (tag != NULL && StringCmp (dbt->db, tag) != 0)) return NULL;
16164
oip = dbt->tag;
16165
}
16166
else if (id_type == SEQID_LOCAL)
16167
{
16168
oip = sip->data.ptrvalue;
16169
}
16170
16171
id_str[0] = 0;
16172
if (fsp != NULL && fsp->ccp != NULL)
16173
{
16174
SeqIdWrite (sip, id_str, PRINTID_REPORT, sizeof (id_str));
16175
if (!DoesStringMatchConstraintX (id_str, fsp->ccp->string_constraint))
16176
{
16177
return NULL;
16178
}
16179
}
16180
16181
if (oip == NULL)
16182
{
16183
if (id_str[0] == 0)
16184
{
16185
SeqIdWrite (sip, id_str, PRINTID_REPORT, sizeof (id_str));
16186
}
16187
str_src = StringSave (id_str);
16188
}
16189
else
16190
{
16191
if (oip->str == NULL)
16192
{
16193
sprintf (id_str, "%d", oip->id);
16194
str_src = StringSave (id_str);
16195
}
16196
else
16197
{
16198
str_src = StringSave (oip->str);
16199
}
16200
}
16201
return str_src;
16202
}
16203
16204
14004
16205
static void
14005
GetLocalIDSourcesForBioseq
16206
GetIDSourcesForBioseq
14006
16207
(BioseqPtr bsp,
14007
16208
FilterSetPtr fsp,
14008
TextPortionPtr tp,
16209
TextPortionXPtr tp,
16210
Uint1 id_type,
16211
CharPtr tag,
14009
16212
ValNodePtr PNTR source_list)
14010
16213
{
14011
16214
SeqIdPtr sip;
14012
16215
ParseSourceInfoPtr psip;
14013
Char id_str [128];
14014
16216
CharPtr src_str, found_loc = NULL, parse_src_txt;
14015
16217
Int4 found_len;
14016
ObjectIdPtr oip;
14017
16218
14018
16219
if (bsp == NULL || source_list == NULL)
14019
16220
{
14023
16224
sip = bsp->id;
14024
16225
while (sip != NULL)
14025
16226
{
14026
if (sip->choice == SEQID_LOCAL)
14027
{
14028
SeqIdWrite (sip, id_str, PRINTID_REPORT, sizeof (id_str));
14029
if (fsp == NULL
14030
|| fsp->ccp == NULL
14031
|| DoesStringMatchConstraint (id_str, fsp->ccp->string_constraint))
16227
if ((src_str = GetIDSrc (sip, id_type, tag, fsp)) != NULL)
16228
{
16229
FindTextPortionXInString (src_str, tp, &found_loc, &found_len);
16230
if (found_loc != NULL)
14032
16231
{
14033
oip = (ObjectIdPtr) sip->data.ptrvalue;
14034
if (oip->str == NULL)
16232
parse_src_txt = (CharPtr) MemNew (sizeof (Char) + (found_len + 1));
16233
StringNCpy (parse_src_txt, found_loc, found_len);
16234
parse_src_txt [found_len] = 0;
16235
psip = (ParseSourceInfoPtr) MemNew (sizeof (ParseSourceInfoData));
16236
if (psip != NULL)
14035
16237
{
14036
sprintf (id_str, "%d", oip->id);
14037
src_str = id_str;
16238
psip->bsp = bsp;
16239
psip->sdp = NULL;
16240
psip->sfp = NULL;
16241
psip->sip = sip;
16242
psip->dest_list = NULL;
16243
psip->parse_src_txt = parse_src_txt;
16244
ValNodeAddPointer (source_list, 0, psip);
14038
16245
}
14039
16246
else
14040
16247
{
14041
src_str = oip->str;
14042
}
14043
FindTextPortionInString (src_str, tp, &found_loc, &found_len);
14044
if (found_loc != NULL)
14045
{
14046
parse_src_txt = (CharPtr) MemNew (sizeof (Char) + (found_len + 1));
14047
StringNCpy (parse_src_txt, found_loc, found_len);
14048
parse_src_txt [found_len] = 0;
14049
psip = (ParseSourceInfoPtr) MemNew (sizeof (ParseSourceInfoData));
14050
if (psip != NULL)
14051
{
14052
psip->bsp = bsp;
14053
psip->sdp = NULL;
14054
psip->sfp = NULL;
14055
psip->sip = sip;
14056
psip->dest_list = NULL;
14057
psip->parse_src_txt = parse_src_txt;
14058
ValNodeAddPointer (source_list, 0, psip);
14059
}
14060
else
14061
{
14062
parse_src_txt = MemFree (parse_src_txt);
14063
}
16248
parse_src_txt = MemFree (parse_src_txt);
14064
16249
}
14065
16250
}
16251
src_str = MemFree (src_str);
14066
16252
}
14067
16253
sip = sip->next;
14068
16254
}
14069
16255
}
14070
16256
16257
16258
static void
16259
GetLocalIDSourcesForBioseq
16260
(BioseqPtr bsp,
16261
FilterSetPtr fsp,
16262
TextPortionXPtr tp,
16263
ValNodePtr PNTR source_list)
16264
{
16265
GetIDSourcesForBioseq (bsp, fsp, tp, SEQID_LOCAL, NULL, source_list);
16266
}
16267
16268
16269
static void GetNcbiFileSourceForBioseq
16270
(BioseqPtr bsp,
16271
FilterSetPtr fsp,
16272
TextPortionXPtr tp,
16273
ValNodePtr PNTR source_list)
16274
{
16275
GetIDSourcesForBioseq (bsp, fsp, tp, SEQID_GENERAL, "NCBIFILE", source_list);
16276
}
16277
16278
16279
const CharPtr nomial_keywordsx[] = {
16280
"f. sp. ",
16281
"var.",
16282
"pv.",
16283
"bv.",
16284
"serovar",
16285
"subsp." };
16286
16287
const Int4 num_nomial_keywordsx = sizeof(nomial_keywordsx) / sizeof (CharPtr);
16288
16289
static CharPtr GetTextAfterNomial (CharPtr taxname)
16290
16291
{
16292
CharPtr ptr, nomial_end;
16293
Int4 i;
16294
Boolean found_keyword = TRUE;
16295
16296
ptr = StringChr (taxname, ' ');
16297
if (ptr == NULL) return NULL;
16298
/* skip over the first word and the spaces after it. */
16299
while (*ptr == ' ')
16300
{
16301
ptr++;
16302
}
16303
ptr = StringChr (ptr, ' ');
16304
/* if there are only two words, give up. */
16305
if (ptr == NULL)
16306
{
16307
return NULL;
16308
}
16309
nomial_end = ptr;
16310
while (*ptr == ' ')
16311
{
16312
ptr++;
16313
}
16314
16315
while (found_keyword) {
16316
found_keyword = FALSE;
16317
/* if the next word is a nomial keyword, skip that plus the first word that follows it. */
16318
for (i = 0; i < num_nomial_keywordsx && *nomial_end != 0; i++) {
16319
if (StringNCmp (ptr, nomial_keywordsx[i], StringLen(nomial_keywordsx[i])) == 0)
16320
{
16321
ptr += StringLen(nomial_keywordsx[i]);
16322
while (*ptr == ' ' )
16323
{
16324
ptr++;
16325
}
16326
nomial_end = StringChr (ptr, ' ');
16327
if (nomial_end == NULL)
16328
{
16329
nomial_end = ptr + StringLen (ptr);
16330
}
16331
else
16332
{
16333
ptr = nomial_end;
16334
while (*ptr == ' ') {
16335
ptr++;
16336
}
16337
found_keyword = TRUE;
16338
}
16339
}
16340
}
16341
}
16342
return nomial_end;
16343
}
16344
14071
16345
static void
14072
GetTaxNameSourcesForBioseq
16346
GetTaxNameSourcesForBioseqEx
14073
16347
(BioseqPtr bsp,
14074
16348
FilterSetPtr fsp,
14075
TextPortionPtr tp,
14076
ValNodePtr PNTR source_list)
16349
TextPortionXPtr tp,
16350
ValNodePtr PNTR source_list,
16351
Boolean skip_nomial)
14077
16352
{
14078
16353
SeqDescrPtr sdp;
14079
16354
SeqFeatPtr sfp;
14083
16358
CharPtr found_loc = NULL, parse_src_txt;
14084
16359
Int4 found_len;
14085
16360
BioSourcePtr biop;
16361
CharPtr nomial;
14086
16362
14087
16363
if (bsp == NULL || source_list == NULL)
14088
16364
{
14098
16374
|| fsp->ccp == NULL
14099
16375
|| DoesOneSourceMatchConstraint (biop, fsp->ccp)))
14100
16376
{
14101
FindTextPortionInString (biop->org->taxname, tp, &found_loc, &found_len);
16377
if (skip_nomial) {
16378
nomial = GetTextAfterNomial(biop->org->taxname);
16379
FindTextPortionXInString (nomial, tp, &found_loc, &found_len);
16380
} else {
16381
FindTextPortionXInString (biop->org->taxname, tp, &found_loc, &found_len);
16382
}
14102
16383
if (found_loc != NULL)
14103
16384
{
14104
16385
parse_src_txt = (CharPtr) MemNew (sizeof (Char) + (found_len + 1));
14134
16415
|| fsp->ccp == NULL
14135
16416
|| DoesOneSourceMatchConstraint (sfp->data.value.ptrvalue, fsp->ccp)))
14136
16417
{
14137
FindTextPortionInString (biop->org->taxname, tp, &found_loc, &found_len);
16418
FindTextPortionXInString (biop->org->taxname, tp, &found_loc, &found_len);
14138
16419
if (found_loc != NULL)
14139
16420
{
14140
16421
parse_src_txt = (CharPtr) MemNew (sizeof (Char) + (found_len + 1));
14162
16443
}
14163
16444
}
14164
16445
16446
16447
static void
16448
GetTaxNameSourcesForBioseq
16449
(BioseqPtr bsp,
16450
FilterSetPtr fsp,
16451
TextPortionXPtr tp,
16452
ValNodePtr PNTR source_list)
16453
{
16454
GetTaxNameSourcesForBioseqEx (bsp, fsp, tp, source_list, FALSE);
16455
}
16456
16457
16458
static void
16459
GetTaxNameAfterNomialSourcesForBioseq
16460
(BioseqPtr bsp,
16461
FilterSetPtr fsp,
16462
TextPortionXPtr tp,
16463
ValNodePtr PNTR source_list)
16464
{
16465
GetTaxNameSourcesForBioseqEx (bsp, fsp, tp, source_list, TRUE);
16466
}
16467
16468
16469
static CharPtr
16470
GetSourceQualSourceTextForBioSource
16471
(BioSourcePtr biop,
16472
SourceQualDescPtr sqdp,
16473
FilterSetPtr fsp,
16474
TextPortionXPtr tp)
16475
{
16476
CharPtr str;
16477
CharPtr found_loc = NULL, parse_src_txt = NULL;
16478
Int4 found_len;
16479
16480
if (biop == NULL || biop->org == NULL || sqdp == NULL
16481
|| (fsp != NULL
16482
&& fsp->ccp != NULL
16483
&& !DoesOneSourceMatchConstraint (biop, fsp->ccp)))
16484
{
16485
return NULL;
16486
}
16487
16488
str = GetSourceQualQualValueFromBiop (biop, sqdp, fsp);
16489
if (!StringHasNoText (str))
16490
{
16491
FindTextPortionXInString (str, tp, &found_loc, &found_len);
16492
if (found_loc != NULL)
16493
{
16494
parse_src_txt = (CharPtr) MemNew (sizeof (Char) + (found_len + 1));
16495
StringNCpy (parse_src_txt, found_loc, found_len);
16496
parse_src_txt [found_len] = 0;
16497
}
16498
}
16499
str = MemFree (str);
16500
return parse_src_txt;
16501
}
16502
16503
16504
static void
16505
GetSourceQualSourcesForBioseq
16506
(BioseqPtr bsp,
16507
SourceQualDescPtr sqdp,
16508
FilterSetPtr fsp,
16509
TextPortionXPtr tp,
16510
ValNodePtr PNTR source_list)
16511
{
16512
SeqDescrPtr sdp;
16513
SeqFeatPtr sfp;
16514
SeqMgrFeatContext fcontext;
16515
SeqMgrDescContext dcontext;
16516
ParseSourceInfoPtr psip;
16517
CharPtr parse_src_txt;
16518
BioSourcePtr biop;
16519
16520
if (bsp == NULL || source_list == NULL)
16521
{
16522
return;
16523
}
16524
16525
sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_source, &dcontext);
16526
while (sdp != NULL)
16527
{
16528
if ((biop = sdp->data.ptrvalue) != NULL
16529
&& (parse_src_txt = GetSourceQualSourceTextForBioSource (biop, sqdp, fsp, tp)) != NULL)
16530
{
16531
psip = (ParseSourceInfoPtr) MemNew (sizeof (ParseSourceInfoData));
16532
if (psip != NULL)
16533
{
16534
psip->bsp = bsp;
16535
psip->sdp = sdp;
16536
psip->sfp = NULL;
16537
psip->sip = NULL;
16538
psip->dest_list = NULL;
16539
psip->parse_src_txt = parse_src_txt;
16540
ValNodeAddPointer (source_list, 0, psip);
16541
}
16542
else
16543
{
16544
parse_src_txt = MemFree (parse_src_txt);
16545
}
16546
}
16547
sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_source, &dcontext);
16548
}
16549
16550
sfp = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_BIOSRC, 0, &fcontext);
16551
while (sfp != NULL)
16552
{
16553
if ((biop = sfp->data.value.ptrvalue) != NULL
16554
&& (parse_src_txt = GetSourceQualSourceTextForBioSource (biop, sqdp, fsp, tp)) != NULL)
16555
{
16556
psip = (ParseSourceInfoPtr) MemNew (sizeof (ParseSourceInfoData));
16557
if (psip != NULL)
16558
{
16559
psip->bsp = bsp;
16560
psip->sdp = NULL;
16561
psip->sfp = sfp;
16562
psip->sip = NULL;
16563
psip->dest_list = NULL;
16564
psip->parse_src_txt = parse_src_txt;
16565
ValNodeAddPointer (source_list, 0, psip);
16566
}
16567
else
16568
{
16569
parse_src_txt = MemFree (parse_src_txt);
16570
}
16571
}
16572
sfp = SeqMgrGetNextFeature (bsp, sfp, SEQFEAT_BIOSRC, 0, &fcontext);
16573
}
16574
}
16575
16576
14165
16577
static void
14166
16578
GetBankitCommentSourcesForBioseq
14167
16579
(BioseqPtr bsp,
14168
16580
FilterSetPtr fsp,
14169
TextPortionPtr tp,
16581
TextPortionXPtr tp,
14170
16582
ValNodePtr PNTR source_list)
14171
16583
{
14172
16584
SeqDescrPtr sdp;
14202
16614
{
14203
16615
if (fsp == NULL
14204
16616
|| fsp->ccp == NULL
14205
|| DoesStringMatchConstraint (ufp->data.ptrvalue, fsp->ccp->string_constraint))
16617
|| DoesStringMatchConstraintX (ufp->data.ptrvalue, fsp->ccp->string_constraint))
14206
16618
{
14207
FindTextPortionInString (ufp->data.ptrvalue, tp, &found_loc, &found_len);
16619
FindTextPortionXInString (ufp->data.ptrvalue, tp, &found_loc, &found_len);
14208
16620
if (found_loc != NULL)
14209
16621
{
14210
16622
parse_src_txt = (CharPtr) MemNew (sizeof (Char) + (found_len + 1));
14241
16653
GetCommentSourcesForBioseq
14242
16654
(BioseqPtr bsp,
14243
16655
FilterSetPtr fsp,
14244
TextPortionPtr tp,
16656
TextPortionXPtr tp,
14245
16657
ValNodePtr PNTR source_list)
14246
16658
{
14247
16659
SeqDescrPtr sdp;
14262
16674
{
14263
16675
if (fsp == NULL
14264
16676
|| fsp->ccp == NULL
14265
|| DoesStringMatchConstraint (sdp->data.ptrvalue, fsp->ccp->string_constraint))
16677
|| DoesStringMatchConstraintX (sdp->data.ptrvalue, fsp->ccp->string_constraint))
14266
16678
{
14267
FindTextPortionInString (sdp->data.ptrvalue, tp, &found_loc, &found_len);
16679
FindTextPortionXInString (sdp->data.ptrvalue, tp, &found_loc, &found_len);
14268
16680
if (found_loc != NULL)
14269
16681
{
14270
16682
parse_src_txt = (CharPtr) MemNew (sizeof (Char) + (found_len + 1));
14296
16708
{
14297
16709
if (fsp == NULL
14298
16710
|| fsp->ccp == NULL
14299
|| DoesStringMatchConstraint (sfp->data.value.ptrvalue, fsp->ccp->string_constraint))
16711
|| DoesStringMatchConstraintX (sfp->data.value.ptrvalue, fsp->ccp->string_constraint))
14300
16712
{
14301
FindTextPortionInString (sdp->data.ptrvalue, tp, &found_loc, &found_len);
16713
FindTextPortionXInString (sdp->data.ptrvalue, tp, &found_loc, &found_len);
14302
16714
if (found_loc != NULL)
14303
16715
{
14304
16716
parse_src_txt = (CharPtr) MemNew (sizeof (Char) + (found_len + 1));
14331
16743
GetStructuredCommentSourcesForBioseq
14332
16744
(BioseqPtr bsp,
14333
16745
FilterSetPtr fsp,
14334
TextPortionPtr tp,
16746
TextPortionXPtr tp,
14335
16747
CharPtr comment_field,
14336
16748
ValNodePtr PNTR source_list)
14337
16749
{
14364
16776
if (oip != NULL && StringCmp (oip->str, comment_field) == 0
14365
16777
&& (fsp == NULL
14366
16778
|| fsp->ccp == NULL
14367
|| DoesStringMatchConstraint (sdp->data.ptrvalue, fsp->ccp->string_constraint)))
16779
|| DoesStringMatchConstraintX (sdp->data.ptrvalue, fsp->ccp->string_constraint)))
14368
16780
{
14369
FindTextPortionInString (ufp->data.ptrvalue, tp, &found_loc, &found_len);
16781
FindTextPortionXInString (ufp->data.ptrvalue, tp, &found_loc, &found_len);
14370
16782
if (found_loc != NULL)
14371
16783
{
14372
16784
parse_src_txt = (CharPtr) MemNew (sizeof (Char) + (found_len + 1));
14393
16805
}
14394
16806
}
14395
16807
}
14396
sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_comment, &dcontext);
16808
sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_user, &dcontext);
14397
16809
}
14398
16810
}
14399
16811
14409
16821
psp = (ParseSourcePtr) userdata;
14410
16822
switch (psp->src_field)
14411
16823
{
14412
case PARSE_FIELD_SRC_DEFLINE:
16824
case eParseFieldSrcDefLine:
14413
16825
if (!ISA_aa (bsp->mol))
14414
16826
{
14415
16827
GetDeflineSourcesForBioseq (bsp, psp->fsp, psp->tp, &(psp->source_list));
14416
16828
}
14417
16829
break;
14418
case PARSE_FIELD_SRC_LOCAL_ID:
16830
case eParseFieldSrcLocalID:
14419
16831
if (! ISA_aa (bsp->mol) && bsp->repr != Seq_repr_seg)
14420
16832
{
14421
16833
GetLocalIDSourcesForBioseq (bsp, psp->fsp, psp->tp, &(psp->source_list));
14422
16834
}
14423
16835
break;
14424
case PARSE_FIELD_SRC_TAXNAME:
14425
GetTaxNameSourcesForBioseq (bsp, psp->fsp, psp->tp, &(psp->source_list));
14426
break;
14427
case PARSE_FIELD_SRC_COMMENT:
16836
case eParseFieldSrcFileID:
16837
GetNcbiFileSourceForBioseq (bsp, psp->fsp, psp->tp, &(psp->source_list));
16838
break;
16839
case eParseFieldSrcTaxName:
16840
if (! ISA_aa (bsp->mol))
16841
{
16842
GetTaxNameSourcesForBioseq (bsp, psp->fsp, psp->tp, &(psp->source_list));
16843
}
16844
break;
16845
case eParseFieldSrcSourceQual:
16846
if (! ISA_aa (bsp->mol))
16847
{
16848
GetSourceQualSourcesForBioseq (bsp, psp->sqdp, psp->fsp, psp->tp, &(psp->source_list));
16849
}
16850
break;
16851
case eParseFieldSrcComment:
14428
16852
GetCommentSourcesForBioseq (bsp, psp->fsp, psp->tp, &(psp->source_list));
14429
16853
break;
14430
case PARSE_FIELD_STRUCTURED_COMMENT:
16854
case eParseFieldSrcStructuredComment:
14431
16855
GetStructuredCommentSourcesForBioseq(bsp, psp->fsp, psp->tp, psp->comment_field, &(psp->source_list));
14432
16856
break;
14433
case PARSE_FIELD_BANKIT_COMMENT:
14434
GetBankitCommentSourcesForBioseq (bsp, psp->fsp, psp->tp, &(psp->source_list));
16857
case eParseFieldSrcBankitComment:
16858
if (!ISA_aa (bsp->mol))
16859
{
16860
GetBankitCommentSourcesForBioseq (bsp, psp->fsp, psp->tp, &(psp->source_list));
16861
}
16862
break;
16863
case eParseFieldSrcTaxNameAfterNomial:
16864
if (! ISA_aa (bsp->mol))
16865
{
16866
GetTaxNameAfterNomialSourcesForBioseq (bsp, psp->fsp, psp->tp, &(psp->source_list));
16867
}
14435
16868
break;
14436
16869
}
14437
16870
}
14438
16871
14439
16872
14440
static void StripFromParsedField (ParseSourceInfoPtr psip, TextPortionPtr tp, Int4 parse_field_type, CharPtr comment_field)
16873
static void StripFromParsedField (ParseSourceInfoPtr psip, TextPortionXPtr tp, Int4 parse_field_type, SourceQualDescPtr sqdp, CharPtr comment_field)
14441
16874
{
14442
CharPtr str_found;
16875
CharPtr str_found, tmp;
14443
16876
BioSourcePtr biop = NULL;
14444
16877
UserObjectPtr uop;
14445
16878
ObjectIdPtr oip;
14446
16879
UserFieldPtr ufp;
16880
ApplyValueData avd;
16881
ValNode vn;
14447
16882
14448
16883
if (psip == NULL || tp == NULL) {
14449
16884
return;
14450
16885
}
14451
16886
switch (parse_field_type) {
14452
case PARSE_FIELD_SRC_DEFLINE:
14453
case PARSE_FIELD_SRC_COMMENT:
16887
case eParseFieldSrcDefLine:
16888
case eParseFieldSrcComment:
14454
16889
if (psip->sdp != NULL) {
14455
16890
str_found = ReplaceStringForParse(psip->sdp->data.ptrvalue, tp);
14456
16891
str_found = MemFree (str_found);
14457
16892
}
14458
16893
break;
14459
case PARSE_FIELD_SRC_TAXNAME:
16894
case eParseFieldSrcTaxName:
14460
16895
if (psip->sdp != NULL) {
14461
16896
biop = psip->sdp->data.ptrvalue;
14462
16897
} else if (psip->sfp != NULL) {
14467
16902
str_found = MemFree (str_found);
14468
16903
}
14469
16904
break;
14470
case PARSE_FIELD_STRUCTURED_COMMENT:
16905
case eParseFieldSrcSourceQual:
16906
if (psip->sdp != NULL) {
16907
biop = psip->sdp->data.ptrvalue;
16908
} else if (psip->sfp != NULL) {
16909
biop = psip->sfp->data.value.ptrvalue;
16910
}
16911
if (biop != NULL) {
16912
tmp = GetSourceQualQualValueFromBiop (biop, sqdp, NULL);
16913
str_found = ReplaceStringForParse (tmp, tp);
16914
str_found = MemFree (str_found);
16915
avd.etp = NULL;
16916
vn.choice = 0;
16917
vn.data.ptrvalue = sqdp;
16918
vn.next = NULL;
16919
avd.field_list = &vn;
16920
avd.new_text = tmp;
16921
avd.text_to_replace = NULL;
16922
avd.where_to_replace = EditApplyFindLocation_anywhere;
16923
16924
ApplySourceQualBioSourceCallback (biop, &avd, NULL);
16925
tmp = MemFree (tmp);
16926
}
16927
break;
16928
case eParseFieldSrcTaxNameAfterNomial:
16929
if (psip->sdp != NULL) {
16930
biop = psip->sdp->data.ptrvalue;
16931
} else if (psip->sfp != NULL) {
16932
biop = psip->sfp->data.value.ptrvalue;
16933
}
16934
if (biop != NULL && biop->org != NULL) {
16935
str_found = GetTextAfterNomial(biop->org->taxname);
16936
str_found = ReplaceStringForParse (str_found, tp);
16937
str_found = MemFree (str_found);
16938
}
16939
break;
16940
case eParseFieldSrcStructuredComment:
14471
16941
if (psip->sdp != NULL
14472
16942
&& psip->sdp->extended != 0
14473
16943
&& psip->sdp->data.ptrvalue != NULL) {
14487
16957
}
14488
16958
}
14489
16959
break;
14490
case PARSE_FIELD_BANKIT_COMMENT:
16960
case eParseFieldSrcBankitComment:
14491
16961
if (psip->sdp != NULL
14492
16962
&& psip->sdp->extended != 0
14493
16963
&& psip->sdp->data.ptrvalue != NULL) {
14511
16981
}
14512
16982
14513
16983
14514
static void GetBioSourceDestinationsForBioseq (BioseqPtr bsp, ValNodePtr PNTR dest_list)
16984
static void GetBioSourceDestinationsForBioseq (BioseqPtr bsp, Boolean do_feat, Boolean do_desc, ValNodePtr PNTR dest_list)
14515
16985
{
14516
16986
SeqDescrPtr sdp;
14517
16987
SeqFeatPtr sfp;
14523
16993
return;
14524
16994
}
14525
16995
14526
sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_source, &dcontext);
14527
while (sdp != NULL)
16996
if (do_desc)
14528
16997
{
14529
ValNodeAddPointer (dest_list, 2, sdp);
14530
sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_source, &dcontext);
16998
sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_source, &dcontext);
16999
while (sdp != NULL)
17000
{
17001
ValNodeAddPointer (dest_list, 2, sdp);
17002
sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_source, &dcontext);
17003
}
14531
17004
}
14532
17005
14533
sfp = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_BIOSRC, 0, &fcontext);
14534
while (sfp != NULL)
17006
if (do_feat)
14535
17007
{
14536
ValNodeAddPointer (dest_list, 1, sfp);
14537
sfp = SeqMgrGetNextFeature (bsp, sfp, SEQFEAT_BIOSRC, 0, &fcontext);
14538
}
17008
sfp = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_BIOSRC, 0, &fcontext);
17009
while (sfp != NULL)
17010
{
17011
ValNodeAddPointer (dest_list, 1, sfp);
17012
sfp = SeqMgrGetNextFeature (bsp, sfp, SEQFEAT_BIOSRC, 0, &fcontext);
17013
}
17014
}
14539
17015
}
14540
17016
14541
17017
static void GetDeflineDestinationsForBioseq (BioseqPtr bsp, ValNodePtr PNTR dest_list)
14580
17056
SeqFeatPtr sfp;
14581
17057
SeqMgrFeatContext fcontext;
14582
17058
SeqAnnotPtr sap;
17059
ProtRefPtr prp;
14583
17060
14584
17061
if (bsp == NULL || dest_list == NULL)
14585
17062
{
14587
17064
}
14588
17065
14589
17066
sfp = SeqMgrGetNextFeature (bsp, NULL, seqFeatChoice, featDefChoice, &fcontext);
14590
while (sfp != NULL)
14591
{
17067
if (sfp == NULL
17068
&& (featDefChoice == FEATDEF_PROT
17069
|| (seqFeatChoice == SEQFEAT_PROT && featDefChoice == 0))) {
17070
sfp = CreateNewFeatureOnBioseq (bsp, SEQFEAT_PROT, NULL);
17071
prp = ProtRefNew ();
17072
sfp->data.value.ptrvalue = prp;
17073
SeqMgrIndexFeatures (bsp->idx.entityID, NULL);
14592
17074
ValNodeAddPointer (dest_list, 1, sfp);
14593
sfp = SeqMgrGetNextFeature (bsp, sfp, seqFeatChoice, featDefChoice, &fcontext);
14594
}
17075
} else {
17076
while (sfp != NULL)
17077
{
17078
ValNodeAddPointer (dest_list, 1, sfp);
17079
sfp = SeqMgrGetNextFeature (bsp, sfp, seqFeatChoice, featDefChoice, &fcontext);
17080
}
17081
}
14595
17082
14596
17083
sap = bsp->annot;
14597
17084
while (sap != NULL)
14684
17171
switch (dst_field_data->parse_field_type)
14685
17172
{
14686
17173
case PARSE_FIELD_SOURCE_QUAL:
14687
GetBioSourceDestinationsForBioseq (psip->bsp, &(psip->dest_list));
17174
case PARSE_FIELD_BIOSRC_STRING :
17175
case PARSE_FIELD_DBXREF :
17176
if ((dst_field_data->do_desc && psip->sdp != NULL && psip->sdp->choice == Seq_descr_source)
17177
|| (dst_field_data->do_feat && psip->sfp != NULL && psip->sfp->data.choice == SEQFEAT_BIOSRC))
17178
{
17179
if (dst_field_data->do_desc && psip->sdp != NULL)
17180
{
17181
ValNodeAddPointer (&(psip->dest_list), 2, psip->sdp);
17182
}
17183
if (dst_field_data->do_feat && psip->sfp != NULL)
17184
{
17185
ValNodeAddPointer (&(psip->dest_list), 1, psip->sfp);
17186
}
17187
}
17188
else
17189
{
17190
GetBioSourceDestinationsForBioseq (psip->bsp, dst_field_data->do_feat, dst_field_data->do_desc, &(psip->dest_list));
17191
}
14688
17192
break;
14689
17193
case PARSE_FIELD_DEFLINE :
14690
17194
GetDeflineDestinationsForBioseq (psip->bsp, &(psip->dest_list));
14691
17195
break;
14692
case PARSE_FIELD_BIOSRC_STRING :
14693
GetBioSourceDestinationsForBioseq (psip->bsp, &(psip->dest_list));
14694
break;
14695
17196
case PARSE_FIELD_GENE_FIELD :
14696
17197
GetFeatureDestinationsForBioseq (psip->bsp, SEQFEAT_GENE, 0, &(psip->dest_list));
14697
17198
break;
14698
case PARSE_FIELD_MRNA_FIELD :
14699
GetFeatureDestinationsForBioseq (psip->bsp, SEQFEAT_RNA, FEATDEF_mRNA, &(psip->dest_list));
17199
case PARSE_FIELD_RNA_FIELD :
17200
GetFeatureDestinationsForBioseq (psip->bsp, SEQFEAT_RNA,
17201
dst_field_data->feature_subtype == NULL ? 0 : dst_field_data->feature_subtype->data.intvalue,
17202
&(psip->dest_list));
14700
17203
break;
14701
17204
case PARSE_FIELD_CDS_COMMENT:
14702
17205
GetFeatureDestinationsForBioseq (psip->bsp, SEQFEAT_CDREGION, FEATDEF_CDS, &(psip->dest_list));
14710
17213
vnp = vnp->next)
14711
17214
{
14712
17215
GetFeatureDestinationsForBioseq (psip->bsp,
14713
SEQFEAT_IMP,
14714
dst_field_data->parse_field_type,
17216
0,
17217
vnp->choice,
14715
17218
&(psip->dest_list));
14716
17219
}
14717
17220
break;
14985
17488
gsp->copy_vn_proc = IntValNodeCopy;
14986
17489
gsp->requested_field = IntValNodeCopy (psp->dst_field_data->feature_field);
14987
17490
break;
14988
case PARSE_FIELD_MRNA_FIELD:
14989
gsp->fieldstring_func = GetmRNAFieldString;
17491
case PARSE_FIELD_RNA_FIELD:
17492
gsp->fieldstring_func = GetRNAFieldString;
14990
17493
gsp->copy_vn_proc = IntValNodeCopy;
14991
17494
gsp->requested_field = IntValNodeCopy (psp->dst_field_data->feature_field);
14992
17495
break;
15016
17519
gsp->copy_vn_proc = ValNodeStringCopy;
15017
17520
gsp->requested_field = ValNodeStringCopy (psp->dst_field_data->feature_field);
15018
17521
break;
17522
case PARSE_FIELD_DBXREF:
17523
gsp->fieldstring_func = GetBioSourceFeatureDbxrefString;
17524
gsp->descrstring_func = GetBioSourceDescriptorDbxrefString;
17525
gsp->free_vn_proc = ValNodeSimpleDataFree;
17526
gsp->copy_vn_proc = ValNodeStringCopy;
17527
gsp->requested_field = ValNodeStringCopy (psp->dst_field_data->feature_field);
17528
break;
15019
17529
}
15020
17530
15021
17531
for (vnp = psp->source_list; vnp != NULL; vnp = vnp->next)
15064
17574
case PARSE_FIELD_GENE_FIELD :
15065
17575
set_string_func = SetGeneFieldString;
15066
17576
break;
15067
case PARSE_FIELD_MRNA_FIELD :
15068
set_string_func = SetmRNAFieldString;
17577
case PARSE_FIELD_RNA_FIELD :
17578
set_string_func = SetRNAFieldString;
15069
17579
break;
15070
17580
case PARSE_FIELD_CDS_COMMENT:
15071
17581
set_string_func = SetCDSComment;
15101
17611
if (prot_bsp == NULL)
15102
17612
{
15103
17613
bsp = BioseqFindFromSeqLoc (sfp->location);
15104
SeqEdTranslateOneCDS (sfp, bsp, sfp->idx.entityID);
17614
SeqEdTranslateOneCDS (sfp, bsp, sfp->idx.entityID, Sequin_GlobalAlign2Seq);
15105
17615
SeqMgrIndexFeatures (sfp->idx.entityID, NULL);
15106
17616
prot_bsp = BioseqFindFromSeqLoc (sfp->product);
15107
17617
}
15271
17781
(ParseSourceInfoPtr psip,
15272
17782
Int4 src_field,
15273
17783
ParseFieldPtr dst_field_data,
15274
TextPortionPtr tp,
17784
TextPortionXPtr tp,
15275
17785
ExistingTextPtr etp)
15276
17786
{
15277
17787
ApplyValueData avd;
15289
17799
avd.new_text = psip->parse_src_txt;
15290
17800
avd.etp = etp;
15291
17801
avd.text_to_replace = NULL;
17802
avd.where_to_replace = EditApplyFindLocation_anywhere;
15292
17803
15293
17804
switch (dst_field_data->parse_field_type)
15294
17805
{
15316
17827
#endif
15317
17828
break;
15318
17829
case PARSE_FIELD_GENE_FIELD :
15319
case PARSE_FIELD_MRNA_FIELD :
17830
case PARSE_FIELD_RNA_FIELD :
15320
17831
case PARSE_FIELD_CDS_COMMENT:
15321
17832
case PARSE_FIELD_PROTEIN_FIELD:
15322
17833
case PARSE_FIELD_IMPORT_QUAL :
15323
17834
case PARSE_FIELD_FEATURE_NOTE :
15324
17835
avd.field_list = dst_field_data->feature_field;
15325
17836
break;
17837
case PARSE_FIELD_DBXREF :
17838
avd.field_list = dst_field_data->feature_field;
17839
feature_action = ApplyBioSourceDbxrefFeatureCallback;
17840
descriptor_action = ApplyBioSourceDbxrefDescriptorCallback;
17841
break;
15326
17842
}
15327
17843
15328
17844
for (dest_vnp = psip->dest_list; dest_vnp != NULL; dest_vnp = dest_vnp->next)
15337
17853
}
15338
17854
else if (dest_vnp->choice == 1
15339
17855
&& (dst_field_data->parse_field_type == PARSE_FIELD_GENE_FIELD
15340
|| dst_field_data->parse_field_type == PARSE_FIELD_MRNA_FIELD
17856
|| dst_field_data->parse_field_type == PARSE_FIELD_RNA_FIELD
15341
17857
|| dst_field_data->parse_field_type == PARSE_FIELD_CDS_COMMENT
15342
17858
|| dst_field_data->parse_field_type == PARSE_FIELD_PROTEIN_FIELD
15343
17859
|| dst_field_data->parse_field_type == PARSE_FIELD_IMPORT_QUAL
15354
17870
FindParseActionPairList
15355
17871
(SeqEntryPtr sep,
15356
17872
Int4 src_field,
17873
SourceQualDescPtr sqdp,
15357
17874
CharPtr comment_field,
15358
17875
ParseFieldPtr dst_field_data,
15359
17876
FilterSetPtr fsp,
15360
TextPortionPtr tp,
15361
Boolean remove_from_parsed)
17877
TextPortionXPtr tp,
17878
Boolean remove_from_parsed,
17879
ChangeCasePtr ccp)
15362
17880
{
15363
17881
ParseSourceData psd;
15364
17882
ValNodePtr vnp;
15367
17885
ExistingTextPtr etp;
15368
17886
Boolean rval = FALSE;
15369
17887
ValNodePtr source_list_for_removal = NULL;
17888
ValNodePtr orgnames = NULL;
15370
17889
15371
17890
psd.fsp = fsp;
15372
17891
psd.source_list = NULL;
15373
17892
psd.src_field = src_field;
15374
17893
psd.comment_field = comment_field;
17894
psd.sqdp = sqdp;
15375
17895
psd.dst_field_data = dst_field_data;
15376
17896
psd.fsp = fsp;
15377
17897
psd.tp = tp;
15379
17899
/* first, we need to get a list of the parse sources */
15380
17900
VisitBioseqsInSep (sep, &psd, FindParseSourceBioseqCallback);
15381
17901
17902
if (ccp != NULL && ccp->change != eChangeCaseNone) {
17903
/* if we will be fixing capitalization, get org names to use in fixes */
17904
VisitBioSourcesInSep (sep, &orgnames, GetOrgNamesInRecordCallback);
17905
}
17906
15382
17907
/* for each parse source, we need to get a list of the destinations */
15383
17908
for (vnp = psd.source_list; vnp != NULL; vnp = vnp->next)
15384
17909
{
15387
17912
if (remove_from_parsed) {
15388
17913
ValNodeAddPointer (&source_list_for_removal, 0, ParseSourceInfoCopy (psip));
15389
17914
}
17915
/* fix source text */
17916
ChangeCase (&(psip->parse_src_txt), ccp, orgnames);
17917
15390
17918
FindDestinationsForParseSourceInfo (psip, dst_field_data);
15391
17919
}
15392
17920
15406
17934
15407
17935
/* check for existing text */
15408
17936
gsp = CheckParseActionPairListForExistingText (&psd);
15409
etp = GetExistingTextHandlerInfo (gsp, FALSE);
17937
etp = GetExistingTextHandlerInfo (gsp == NULL ? 0 : gsp->num_found, FALSE);
15410
17938
gsp = GetSampleFree (gsp);
15411
17939
15412
if (etp == NULL || etp->existing_text_choice != EXISTING_TEXT_CHOICE_CANCEL)
17940
if (etp == NULL || etp->existing_text_choice != eExistingTextChoiceCancel)
15413
17941
{
15414
17942
if (dst_field_data->parse_field_type == PARSE_FIELD_SOURCE_QUAL)
15415
17943
{
15429
17957
{
15430
17958
if (vnp->data.ptrvalue == NULL) continue;
15431
17959
psip = (ParseSourceInfoPtr) vnp->data.ptrvalue;
15432
StripFromParsedField (psip, tp, src_field, comment_field);
17960
StripFromParsedField (psip, tp, src_field, sqdp, comment_field);
15433
17961
}
15434
17962
15435
17963
rval = TRUE;
15436
17964
}
15437
17965
15438
17966
etp = MemFree (etp);
15439
17967
17968
/* free orgname list if we created it */
17969
orgnames = ValNodeFree (orgnames);
17970
17971
comment_field = MemFree (comment_field);
17972
sqdp = MemFree (sqdp);
17973
15440
17974
psd.source_list = ParseSourceListFree (psd.source_list);
15441
17975
source_list_for_removal = ParseSourceListFree (source_list_for_removal);
15442
17976
return rval;
15443
17977
}
15444
17978
15445
static void
15446
VisitSeqEntriesForParseAction
15447
(SeqEntryPtr sep,
15448
ParseActionPtr pap,
15449
ParseActnProc parse_action,
15450
Pointer parse_data,
15451
Boolean ok_to_parse)
15452
{
15453
SeqDescrPtr sdp, sdp_tmp;
15454
SeqAnnotPtr sap, sap_tmp;
15455
SeqFeatPtr sfp;
15456
ParseActionOpData paod;
15457
BioseqSetPtr bssp = NULL;
15458
15459
SeqEntryPtr old_title_sep;
15460
SeqEntryPtr old_biop_sep;
15461
15462
if (sep == NULL || pap == NULL || parse_action == NULL)
15463
{
15464
return;
15465
}
15466
15467
paod.parse_action_data = pap;
15468
paod.parse_action = parse_action;
15469
paod.parse_userdata = parse_data;
15470
paod.parse_complete = FALSE;
15471
15472
pap->sep = sep;
15473
if (IS_Bioseq (pap->sep))
15474
{
15475
pap->bsp = (BioseqPtr) pap->sep->data.ptrvalue;
15476
sdp = pap->bsp->descr;
15477
sap = pap->bsp->annot;
15478
}
15479
else if (IS_Bioseq_set (sep))
15480
{
15481
bssp = (BioseqSetPtr) sep->data.ptrvalue;
15482
pap->bssp = bssp;
15483
sdp = pap->bssp->descr;
15484
sap = pap->bssp->annot;
15485
}
15486
15487
old_title_sep = pap->title_sep;
15488
old_biop_sep = pap->biop_sep;
15489
15490
if (pap->fsp != NULL
15491
&& pap->fsp->ccp != NULL
15492
&& pap->fsp->ccp->constraint_type != CHOICE_CONSTRAINT_ANY)
15493
{
15494
ok_to_parse = FALSE;
15495
/* try to find BioSource descriptor to match source constraint */
15496
sdp_tmp = sdp;
15497
while (sdp_tmp != NULL && ! ok_to_parse)
15498
{
15499
if (sdp_tmp->choice == Seq_descr_source)
15500
{
15501
if (DoesOneSourceMatchConstraint (sdp_tmp->data.ptrvalue, pap->fsp->ccp))
15502
{
15503
ok_to_parse = TRUE;
15504
}
15505
}
15506
sdp_tmp = sdp_tmp->next;
15507
}
15508
/* try to find BioSource feature to match source constraint */
15509
sap_tmp = sap;
15510
while (sap_tmp != NULL && ! ok_to_parse)
15511
{
15512
if (sap_tmp->type == 1)
15513
{
15514
sfp = (SeqFeatPtr) sap_tmp->data;
15515
while (sfp != NULL && !ok_to_parse)
15516
{
15517
if (sfp->data.choice == SEQFEAT_BIOSRC)
15518
{
15519
if (DoesOneSourceMatchConstraint (sfp->data.value.ptrvalue, pap->fsp->ccp))
15520
{
15521
ok_to_parse = TRUE;
15522
}
15523
}
15524
sfp = sfp->next;
15525
}
15526
}
15527
sap_tmp = sap_tmp->next;
15528
}
15529
}
15530
else
15531
{
15532
ok_to_parse = TRUE;
15533
}
15534
if (ok_to_parse)
15535
{
15536
SetSourceAndTitle (pap, sdp, sap);
15537
if (pap->biop_sep != old_biop_sep)
15538
{
15539
sdp_tmp = sdp;
15540
while (sdp_tmp != NULL)
15541
{
15542
if (sdp_tmp->choice == Seq_descr_source)
15543
{
15544
ParseFromSource (sdp_tmp->data.ptrvalue, pap, &paod);
15545
}
15546
sdp_tmp = sdp_tmp->next;
15547
}
15548
sap_tmp = sap;
15549
while (sap_tmp != NULL)
15550
{
15551
if (sap_tmp->type == 1)
15552
{
15553
sfp = sap_tmp->data;
15554
while (sfp != NULL)
15555
{
15556
if (sfp->data.choice == SEQFEAT_BIOSRC)
15557
{
15558
ParseFromSource (sfp->data.value.ptrvalue, pap, &paod);
15559
}
15560
sfp = sfp->next;
15561
}
15562
}
15563
sap_tmp = sap_tmp->next;
15564
}
15565
}
15566
if (pap->title_sep != old_title_sep
15567
&& pap->src_field == PARSE_FIELD_SRC_DEFLINE)
15568
{
15569
sdp_tmp = sdp;
15570
while (sdp_tmp != NULL)
15571
{
15572
if (sdp_tmp->choice == Seq_descr_title)
15573
{
15574
ParseActionDeflineText (sdp_tmp, &paod);
15575
}
15576
sdp_tmp = sdp_tmp->next;
15577
}
15578
}
15579
15580
if (pap->src_field == PARSE_FIELD_SRC_LOCAL_ID && IS_Bioseq (sep))
15581
{
15582
if (pap->biop_sep == NULL)
15583
{
15584
pap->biop_sep = sep;
15585
}
15586
if (pap->title_sep == NULL)
15587
{
15588
pap->title_sep = sep;
15589
}
15590
ParseActionLocalIDText (sep->data.ptrvalue, &paod);
15591
}
15592
if (pap->src_field == PARSE_FIELD_SRC_COMMENT)
15593
{
15594
sdp_tmp = sdp;
15595
while (sdp_tmp != NULL)
15596
{
15597
ParseActionCommentDescriptor (sdp_tmp, &paod);
15598
sdp_tmp = sdp_tmp->next;
15599
}
15600
15601
sap_tmp = sap;
15602
while (sap_tmp != NULL)
15603
{
15604
if (sap_tmp->type == 1)
15605
{
15606
sfp = sap_tmp->data;
15607
while (sfp != NULL)
15608
{
15609
ParseActionCommentFeature (sfp, &paod);
15610
sfp = sfp->next;
15611
}
15612
}
15613
sap_tmp = sap_tmp->next;
15614
}
15615
}
15616
if (pap->src_field == PARSE_FIELD_BANKIT_COMMENT)
15617
{
15618
sdp_tmp = sdp;
15619
while (sdp_tmp != NULL)
15620
{
15621
ParseActionBankitComment (sdp_tmp, &paod);
15622
sdp_tmp = sdp_tmp->next;
15623
}
15624
}
15625
}
15626
15627
if (bssp != NULL && !paod.parse_complete)
15628
{
15629
VisitSeqEntriesForParseAction (bssp->seq_set, pap, parse_action, parse_data, ok_to_parse);
15630
}
15631
15632
pap->title_sep = old_title_sep;
15633
pap->biop_sep = old_biop_sep;
15634
15635
VisitSeqEntriesForParseAction (sep->next, pap, parse_action, parse_data, ok_to_parse);
15636
}
15637
15638
typedef struct parseactionlog
15639
{
15640
FILE *fp;
15641
Boolean data_in_log;
15642
} ParseActionLogData, PNTR ParseActionLogPtr;
15643
15644
static void ParseActionSample (ParseActionPtr pap, Pointer userdata, CharPtr found_text, Int4 found_len)
15645
{
15646
CharPtr log_text;
15647
ParseActionLogPtr palp;
15648
15649
palp = (ParseActionLogPtr) userdata;
15650
if (palp == NULL || found_len == 0 || found_text == NULL || palp->fp == NULL)
15651
{
15652
return;
15653
}
15654
15655
log_text = (CharPtr) MemNew ((found_len + 1) * sizeof (Char));
15656
if (log_text != NULL)
15657
{
15658
StringNCpy (log_text, found_text, found_len);
15659
log_text[found_len] = 0;
15660
fprintf (palp->fp, "%s\n", log_text);
15661
palp->data_in_log = TRUE;
15662
MemFree (log_text);
15663
}
15664
}
17979
typedef ValNodePtr (*AdjustConvertFeatureListFunc) PROTO ((ValNodePtr, Pointer, BaseFormPtr, BoolPtr cancel));
17980
typedef Pointer (*CollectConvertFeatureOptionsFunc) PROTO ((ValNodePtr, BaseFormPtr, BoolPtr cancel));
17981
typedef Pointer (*FreeConvertFeatureOptionsFunc) PROTO ((Pointer));
17982
typedef Boolean (*ConvertFeatureTypeFunc) PROTO ((SeqFeatPtr, Uint2, Pointer));
17983
typedef void (*ConversionCleanupFunc) PROTO ((Uint2, Pointer));
17984
17985
typedef struct convertfeatureprocs {
17986
Uint2 seqfeat_from;
17987
Uint2 featdef_from;
17988
Uint2 seqfeat_to;
17989
Uint2 featdef_to;
17990
AdjustConvertFeatureListFunc adjust_features;
17991
CollectConvertFeatureOptionsFunc collect_options;
17992
FreeConvertFeatureOptionsFunc free_options;
17993
ConvertFeatureTypeFunc convert_func;
17994
ConversionCleanupFunc cleanup_func;
17995
CharPtr help_text;
17996
} ConvertFeatureProcsData, PNTR ConvertFeatureProcsPtr;
17997
17998
static Pointer SimpleOptsFree (Pointer);
17999
static Boolean ConvertCDSToRNA (SeqFeatPtr, Uint2 featdef_to, Pointer extradata);
18000
static Boolean ConvertGeneToRNA (SeqFeatPtr, Uint2 featdef_to, Pointer extradata);
18001
static ValNodePtr AdjustConvertFeaturesForBioSrcToRepeatRegion (ValNodePtr feat_list, Pointer extradata, BaseFormPtr bfp, BoolPtr cancel);
18002
static Boolean ConvertBioSrcToRepeatRegion (SeqFeatPtr, Uint2 featdef_to, Pointer extradata);
18003
static ValNodePtr AdjustCDSToMiscFeatList (ValNodePtr feat_list, Pointer extradata, BaseFormPtr bfp, BoolPtr cancel);
18004
static Pointer GetCDSConversionOpts (ValNodePtr feat_list, BaseFormPtr bfp, BoolPtr cancel);
18005
static Boolean CDSToMiscFeatConvertFunc (SeqFeatPtr, Uint2 featdef_to, Pointer extradata);
18006
static void CDSToMiscFeatConversionCleanup (Uint2 entityID, Pointer extradata);
18007
static Boolean ConvertImpToProt (SeqFeatPtr, Uint2 featdef_to, Pointer extradata);
18008
static Boolean ConvertProtToImp (SeqFeatPtr, Uint2 featdef_to, Pointer extradata);
18009
static Boolean ConvertImpToSpecialRNA (SeqFeatPtr, Uint2 featdef_to, Pointer extradata);
18010
static Boolean ConvertRegionToImp (SeqFeatPtr, Uint2 featdef_to, Pointer extradata);
18011
static Boolean ConvertRegionToRNA (SeqFeatPtr, Uint2 featdef_to, Pointer extradata);
18012
static Boolean ConvertImpToRNA (SeqFeatPtr, Uint2 featdef_to, Pointer extradata);
18013
static Boolean ConvertCommentToMiscFeat (SeqFeatPtr, Uint2 featdef_to, Pointer extradata);
18014
static Boolean ConvertGeneToMiscFeat (SeqFeatPtr, Uint2 featdef_to, Pointer extradata);
18015
static Boolean ConvertRNAToMiscFeat (SeqFeatPtr, Uint2 featdef_to, Pointer extradata);
18016
static Boolean ConvertSiteToMiscFeat (SeqFeatPtr, Uint2 featdef_to, Pointer extradata);
18017
static Boolean ConvertProtToRegion (SeqFeatPtr, Uint2 featdef_to, Pointer extradata);
18018
static Boolean ConvertRegionToProt (SeqFeatPtr, Uint2 featdef_to, Pointer extradata);
18019
static Pointer GetBondOpts (ValNodePtr feat_list, BaseFormPtr bfp, BoolPtr cancel);
18020
static Pointer GetSiteOpts (ValNodePtr feat_list, BaseFormPtr bfp, BoolPtr cancel);
18021
static Boolean ConvertToSiteOrBond (SeqFeatPtr, Uint2 featdef_to, Pointer extradata);
18022
static Pointer GetRegionOpts (ValNodePtr feat_list, BaseFormPtr bfp, BoolPtr cancel);
18023
static ValNodePtr AdjustRegionConversionFeatures (ValNodePtr feat_list, Pointer extradata, BaseFormPtr bfp, BoolPtr cancel);
18024
static Boolean ConvertAnyToRegion (SeqFeatPtr, Uint2 featdef_to, Pointer extradata);
18025
static Boolean ConvertImpToImp (SeqFeatPtr, Uint2 featdef_to, Pointer extradata);
18026
static Boolean ConvertRNAToRNA (SeqFeatPtr, Uint2 featdef_to, Pointer extradata);
18027
static Boolean ConvertProtToProt (SeqFeatPtr, Uint2 featdef_to, Pointer extradata);
18028
18029
18030
static ConvertFeatureProcsData ConvertFeaturesTable[] = {
18031
{ SEQFEAT_CDREGION, FEATDEF_CDS, SEQFEAT_RNA, FEATDEF_ANY,
18032
NULL, GetCDSConversionOpts, SimpleOptsFree, ConvertCDSToRNA, NULL,
18033
"Delete protein product sequence.\nClear product field if transcript ID removal was requested.\nIf converting to tRNA and anticodon value can be parsed from label, set aa value, and add any text that could not be parsed into an anticodon value to the feature note.\nIf converting to other RNA, put label in RNA product." },
18034
{ SEQFEAT_GENE, FEATDEF_GENE, SEQFEAT_RNA, FEATDEF_ANY,
18035
NULL, NULL, NULL, ConvertGeneToRNA, NULL,
18036
"If converting to tRNA and anticodon value can be parsed from label, set aa value, and add any text that could not be parsed into an anticodon value to the feature note. If converting to other RNA, put label in RNA product. Also append gene locus, allele, description, map location, and locus tag to comment (as long as these values are not already in the label and therefore in the RNA product)." },
18037
{ SEQFEAT_BIOSRC, FEATDEF_BIOSRC, SEQFEAT_IMP, FEATDEF_repeat_region,
18038
AdjustConvertFeaturesForBioSrcToRepeatRegion, NULL, NULL, ConvertBioSrcToRepeatRegion, NULL,
18039
"Creates a repeat_region with mobile_element qualifiers for the transposon and/or insertion sequence qualifiers on the BioSource. All other BioSource information is discarded." },
18040
{ SEQFEAT_CDREGION, FEATDEF_CDS, SEQFEAT_IMP, FEATDEF_misc_feature,
18041
AdjustCDSToMiscFeatList, GetCDSConversionOpts, SimpleOptsFree, CDSToMiscFeatConvertFunc, CDSToMiscFeatConversionCleanup,
18042
"Copy comment from coding region to new misc_feature and remove product field. If not pseudo coding region, add product name from protein feature to new misc_feature comment and delete product sequence." },
18043
{ SEQFEAT_IMP, FEATDEF_ANY, SEQFEAT_PROT, FEATDEF_ANY,
18044
NULL, NULL, NULL, ConvertImpToProt, NULL,
18045
"Original feature must be on nucleotide sequence and be contained in coding region location. Coding region must have product protein sequence. New feature is created on product protein sequence so that the translated location will be as close as possible to the original nucleotide location (may not be exact because of codon boundaries)." },
18046
{ SEQFEAT_PROT, FEATDEF_mat_peptide_aa, SEQFEAT_IMP, FEATDEF_ANY,
18047
NULL, NULL, NULL, ConvertProtToImp, NULL,
18048
"Original feature must be on a protein sequence that is a product of a coding region.\nNew feature will be created on same sequence as coding region.\n"
18049
"If protein feature has name, this will be saved as /product qualifier on new feature.\nIf protein feature does not have name but does have description, this will be saved as /product qualifier on new feature.\n"
18050
"EC_number values from the protein feature will be saved as /EC_number qualifiers on the new feature.\nActivity values will be saved as /function qualifiers on the new feature.\n"
18051
"Db_xref values from the protein feature will be saved as /db_xref qualifers on the new feature." },
18052
{ SEQFEAT_PROT, FEATDEF_sig_peptide_aa, SEQFEAT_IMP, FEATDEF_ANY,
18053
NULL, NULL, NULL, ConvertProtToImp, NULL,
18054
"Original feature must be on a protein sequence that is a product of a coding region.\nNew feature will be created on same sequence as coding region.\n"
18055
"If protein feature has name, this will be saved as /product qualifier on new feature.\nIf protein feature does not have name but does have description, this will be saved as /product qualifier on new feature.\n"
18056
"EC_number values from the protein feature will be saved as /EC_number qualifiers on the new feature.\nActivity values will be saved as /function qualifiers on the new feature.\n"
18057
"Db_xref values from the protein feature will be saved as /db_xref qualifers on the new feature." },
18058
{ SEQFEAT_PROT, FEATDEF_transit_peptide_aa, SEQFEAT_IMP, FEATDEF_ANY,
18059
NULL, NULL, NULL, ConvertProtToImp, NULL,
18060
"Original feature must be on a protein sequence that is a product of a coding region.\nNew feature will be created on same sequence as coding region.\n"
18061
"If protein feature has name, this will be saved as /product qualifier on new feature.\nIf protein feature does not have name but does have description, this will be saved as /product qualifier on new feature.\n"
18062
"EC_number values from the protein feature will be saved as /EC_number qualifiers on the new feature.\nActivity values will be saved as /function qualifiers on the new feature.\n"
18063
"Db_xref values from the protein feature will be saved as /db_xref qualifers on the new feature." },
18064
{ SEQFEAT_IMP, FEATDEF_ANY, SEQFEAT_RNA, FEATDEF_misc_RNA,
18065
NULL, NULL, NULL, ConvertImpToSpecialRNA, NULL,
18066
"Creates a misc_RNA. Import feature key is discarded." },
18067
{ SEQFEAT_IMP, FEATDEF_ANY, SEQFEAT_RNA, FEATDEF_precursor_RNA,
18068
NULL, NULL, NULL, ConvertImpToSpecialRNA, NULL,
18069
"Creates a precursor RNA. Import feature key is discarded." },
18070
{ SEQFEAT_REGION, FEATDEF_REGION, SEQFEAT_IMP, FEATDEF_ANY,
18071
NULL, NULL, NULL, ConvertRegionToImp, NULL,
18072
"Creates a misc_feature with the region name saved as a /note qualifier." },
18073
{ SEQFEAT_REGION, FEATDEF_REGION, SEQFEAT_RNA, FEATDEF_misc_RNA,
18074
NULL, NULL, NULL, ConvertRegionToRNA, NULL,
18075
"Creates a misc_RNA feature with the region name as the product name." },
18076
{ SEQFEAT_REGION, FEATDEF_REGION, SEQFEAT_RNA, FEATDEF_precursor_RNA,
18077
NULL, NULL, NULL, ConvertRegionToRNA, NULL,
18078
"Creates a precursor RNA feature with the region name as the product name." },
18079
{ SEQFEAT_IMP, FEATDEF_ANY, SEQFEAT_RNA, FEATDEF_ANY,
18080
NULL, NULL, NULL, ConvertImpToRNA, NULL,
18081
"Creates an RNA feature of the specified type." },
18082
{ SEQFEAT_COMMENT, FEATDEF_ANY, SEQFEAT_IMP, FEATDEF_misc_feature,
18083
NULL, NULL, NULL, ConvertCommentToMiscFeat, NULL,
18084
"Creates a misc_feature with the same note as the original. Note � the flatfile display for the feature is the same." },
18085
{ SEQFEAT_GENE, FEATDEF_GENE, SEQFEAT_IMP, FEATDEF_misc_feature,
18086
NULL, NULL, NULL, ConvertGeneToMiscFeat, NULL,
18087
"Creates a misc_feature with the gene description and locus prepended to the original comment, separated by semicolons." },
18088
{ SEQFEAT_RNA, FEATDEF_ANY, SEQFEAT_IMP, FEATDEF_misc_feature,
18089
NULL, NULL, NULL, ConvertRNAToMiscFeat, NULL,
18090
"Creates a misc_feature and adds the RNA product name to the comment." } ,
18091
{ SEQFEAT_SITE, FEATDEF_ANY, SEQFEAT_IMP, FEATDEF_misc_feature,
18092
NULL, NULL, NULL, ConvertSiteToMiscFeat, NULL,
18093
"Creates a misc_feature with the site type name as a /note qualifier." } ,
18094
{ SEQFEAT_PROT, FEATDEF_mat_peptide_aa, SEQFEAT_REGION, FEATDEF_REGION,
18095
NULL, NULL, NULL, ConvertProtToRegion, NULL,
18096
"Creates a Region feature with the protein name as the region name." },
18097
{ SEQFEAT_PROT, FEATDEF_sig_peptide_aa, SEQFEAT_REGION, FEATDEF_REGION,
18098
NULL, NULL, NULL, ConvertProtToRegion, NULL,
18099
"Creates a Region feature with the protein name as the region name." },
18100
{ SEQFEAT_PROT, FEATDEF_transit_peptide_aa, SEQFEAT_REGION, FEATDEF_REGION,
18101
NULL, NULL, NULL, ConvertProtToRegion, NULL,
18102
"Creates a Region feature with the protein name as the region name." },
18103
{ SEQFEAT_REGION, FEATDEF_REGION, SEQFEAT_PROT, FEATDEF_mat_peptide_aa,
18104
NULL, NULL, NULL, ConvertRegionToProt, NULL,
18105
"If feature is on nucleotide sequence, will create feature on protein product sequence for overlapping coding region. Protein name will be region name." },
18106
{ SEQFEAT_REGION, FEATDEF_REGION, SEQFEAT_PROT, FEATDEF_sig_peptide_aa,
18107
NULL, NULL, NULL, ConvertRegionToProt, NULL,
18108
"If feature is on nucleotide sequence, will create feature on protein product sequence for overlapping coding region. Protein name will be region name." },
18109
{ SEQFEAT_REGION, FEATDEF_REGION, SEQFEAT_PROT, FEATDEF_transit_peptide_aa,
18110
NULL, NULL, NULL, ConvertRegionToProt, NULL,
18111
"If feature is on nucleotide sequence, will create feature on protein product sequence for overlapping coding region. Protein name will be region name." },
18112
{ SEQFEAT_REGION, FEATDEF_REGION, SEQFEAT_PROT, FEATDEF_preprotein,
18113
NULL, NULL, NULL, ConvertRegionToProt, NULL,
18114
"If feature is on nucleotide sequence, will create feature on protein product sequence for overlapping coding region. Protein name will be region name." },
18115
{ 0, FEATDEF_ANY, SEQFEAT_BOND, FEATDEF_BOND,
18116
NULL, GetBondOpts, SimpleOptsFree, ConvertToSiteOrBond, NULL,
18117
"Create Bond feature with specified bond type. Location is a SeqLocBond with a point at the start of the original location and a point at the end of the original location. All feature ID, partialness, except, comment, product, location, genbank qualifiers, title, citation, experimental evidence, gene xrefs, db xrefs, and pseudo-ness information is discarded." },
18118
{ 0, FEATDEF_ANY, SEQFEAT_SITE, FEATDEF_SITE,
18119
NULL, GetSiteOpts, SimpleOptsFree, ConvertToSiteOrBond, NULL,
18120
"Create Site feature with specified site type. All feature ID, partialness, except, comment, product, location, genbank qualifiers, title, citation, experimental evidence, gene xrefs, db xrefs, and pseudo-ness information is discarded." },
18121
{ 0, FEATDEF_ANY, SEQFEAT_REGION, FEATDEF_REGION,
18122
AdjustRegionConversionFeatures, GetRegionOpts, SimpleOptsFree, ConvertAnyToRegion, NULL,
18123
"Create Region feature on nucleotide sequence or protein product sequence of overlapping coding region as specified. Use comment on feature for region name.\n"
18124
"All feature ID, partialness, except, comment, product, location, genbank qualifiers, title, citation, experimental evidence, gene xrefs, db xrefs, and pseudo-ness information is discarded." },
18125
{ SEQFEAT_IMP, FEATDEF_ANY, SEQFEAT_IMP, FEATDEF_ANY,
18126
NULL, NULL, NULL, ConvertImpToImp, NULL,
18127
"Changes type of import feature." },
18128
{ SEQFEAT_RNA, FEATDEF_ANY, SEQFEAT_RNA, FEATDEF_ANY,
18129
NULL, NULL, NULL, ConvertRNAToRNA, NULL,
18130
"Changes type of RNA feature." },
18131
{ SEQFEAT_PROT, FEATDEF_ANY, SEQFEAT_PROT, FEATDEF_ANY,
18132
NULL, NULL, NULL, ConvertProtToProt, NULL,
18133
"Changes type of protein feature." },
18134
};
18135
18136
static Int4 num_convert_feature_table_lines = sizeof (ConvertFeaturesTable) / sizeof (ConvertFeatureProcsData);
18137
18138
static Int4 GetConvertFeatureTableLine (Uint2 seqfeat_from, Uint2 featdef_from, Uint2 seqfeat_to, Uint2 featdef_to)
18139
{
18140
Int4 i, table_line_num = -1;
18141
18142
for (i = 0; i < num_convert_feature_table_lines && table_line_num == -1; i++)
18143
{
18144
if ((ConvertFeaturesTable[i].seqfeat_from == 0 || ConvertFeaturesTable[i].seqfeat_from == seqfeat_from)
18145
&& (ConvertFeaturesTable[i].featdef_from == FEATDEF_ANY || ConvertFeaturesTable[i].featdef_from == featdef_from)
18146
&& (ConvertFeaturesTable[i].seqfeat_to == 0 || ConvertFeaturesTable[i].seqfeat_to == seqfeat_to)
18147
&& (ConvertFeaturesTable[i].featdef_to == FEATDEF_ANY || ConvertFeaturesTable[i].featdef_to == featdef_to))
18148
{
18149
table_line_num = i;
18150
}
18151
}
18152
return table_line_num;
18153
}
18154
15665
18155
15666
18156
typedef struct featureselremconform
15667
18157
{
15678
18168
GrouP convert_grp;
15679
18169
ButtoN clear_constraints_on_action_change;
15680
18170
ButtoN leave_original_feature_btn; /* checkbox for conversion only */
15681
18171
18172
DoC help_text; /* for conversion only - describes conversion */
18173
15682
18174
/* used for convert callback */
15683
18175
Uint1 featdef_to;
15684
CharPtr featname_to;
15685
Boolean ask_for_transcript_id_removal;
15686
Boolean do_remove_transcript_ids;
15687
ValNodePtr productbsp_list;
15688
Int4 site_or_bond_type;
15689
Boolean abort_convert;
18176
Boolean renormalize_nucprot;
15690
18177
Boolean leave_original_feature;
15691
18178
ValNodePtr feat_list;
18179
BaseFormPtr bfp;
15692
18180
} FeatureSelRemConvFormData, PNTR FeatureSelRemConvFormPtr;
15693
18181
15694
18182
static void CleanupFeatureSelRemConvForm (GraphiC g, VoidPtr data)
15698
18186
15699
18187
mrfp = (FeatureSelRemConvFormPtr) data;
15700
18188
if (mrfp != NULL) {
15701
mrfp->featname_to = MemFree (mrfp->featname_to);
15702
18189
}
15703
18190
StdCleanupFormProc (g, data);
15704
18191
}
15739
18226
static void FeatureRemoveChangeNotify (Pointer userdata)
15740
18227
{
15741
18228
FeatureSelRemConvFormPtr mrfp;
15742
ValNodePtr err_list;
18229
ValNodePtr err_list, vnp_from, vnp_to;
18230
Int4 table_line;
18231
RecT r;
18232
Boolean need_original = FALSE;
15743
18233
15744
18234
mrfp = (FeatureSelRemConvFormPtr) userdata;
15745
18235
if (mrfp == NULL) return;
15764
18254
{
15765
18255
err_list = TestDialog (mrfp->feature_select_to);
15766
18256
}
18257
/* set help text */
18258
Reset (mrfp->help_text);
18259
vnp_from = (ValNodePtr) DialogToPointer (mrfp->feature_select_from);
18260
vnp_to = (ValNodePtr) DialogToPointer (mrfp->feature_select_to);
18261
if (vnp_from == NULL || vnp_to == NULL)
18262
{
18263
AppendText (mrfp->help_text, "No conversion selected", NULL, NULL, systemFont);
18264
}
18265
else if (vnp_from->choice == vnp_to->choice)
18266
{
18267
AppendText (mrfp->help_text, "Can't convert from and to the same type", NULL, NULL, systemFont);
18268
ValNodeAddPointer (&err_list, 0, "Can't convert from and to the same type");
18269
}
18270
else
18271
{
18272
/* set help text */
18273
table_line = GetConvertFeatureTableLine (FindFeatFromFeatDefType (vnp_from->choice),
18274
vnp_from->choice,
18275
FindFeatFromFeatDefType (vnp_to->choice),
18276
vnp_to->choice);
18277
if (table_line < 0)
18278
{
18279
AppendText (mrfp->help_text, "Conversion not supported", NULL, NULL, systemFont);
18280
}
18281
else if (ConvertFeaturesTable[table_line].help_text == NULL)
18282
{
18283
AppendText (mrfp->help_text, "No description available", NULL, NULL, systemFont);
18284
}
18285
else
18286
{
18287
AppendText (mrfp->help_text, ConvertFeaturesTable[table_line].help_text, NULL, NULL, systemFont);
18288
}
18289
18290
/* if converting from CDS to site, bond, or region, "leave original" must be checked */
18291
if ((vnp_from->choice == FEATDEF_CDS
18292
|| vnp_from->choice == FEATDEF_ANY)
18293
&& (vnp_to->choice == FEATDEF_SITE
18294
|| vnp_to->choice == FEATDEF_BOND
18295
|| vnp_to->choice == FEATDEF_REGION))
18296
{
18297
need_original = TRUE;
18298
AppendText (mrfp->help_text, "If converting from CDS to site or bond, or region, you must check Leave Original Feature.", NULL, NULL, systemFont);
18299
}
18300
}
18301
vnp_from = ValNodeFreeData (vnp_from);
18302
vnp_to = ValNodeFreeData (vnp_to);
18303
ObjectRect (mrfp->help_text, &r);
18304
InvalRect (&r);
18305
15767
18306
}
15768
18307
else
15769
18308
{
15774
18313
}
15775
18314
}
15776
18315
15777
if (err_list == NULL)
18316
if (err_list == NULL && (!need_original || GetStatus (mrfp->leave_original_feature_btn)))
15778
18317
{
15779
18318
EnableAcceptCancelDialogAccept (mrfp->accept_cancel);
15780
18319
}
15785
18324
ValNodeFree (err_list);
15786
18325
}
15787
18326
18327
18328
static void FeatureRemoveChangeButton (ButtoN b)
18329
{
18330
FeatureSelRemConvFormPtr mrfp;
18331
18332
mrfp = (FeatureSelRemConvFormPtr) GetObjectExtra (b);
18333
if (mrfp == NULL) return;
18334
FeatureRemoveChangeNotify (mrfp);
18335
}
18336
18337
15788
18338
static void FeatureRemoveOrConvertCenterAction (PopuP p)
15789
18339
{
15790
18340
FeatureSelRemConvFormPtr mrfp;
15909
18459
}
15910
18460
15911
18461
15912
static void ConvertRegionToImp (SeqFeatPtr sfp, CharPtr featname_to)
18462
static CharPtr GetImportFeatureName (Uint2 featdef_key)
18463
{
18464
FeatDefPtr curr;
18465
Uint1 key;
18466
CharPtr label = NULL;
18467
18468
curr = FeatDefFindNext (NULL, &key, &label, FEATDEF_ANY, TRUE);
18469
while (curr != NULL)
18470
{
18471
if (featdef_key == key)
18472
{
18473
return curr->typelabel;
18474
}
18475
curr = FeatDefFindNext (curr, &key, &label, FEATDEF_ANY, TRUE);
18476
}
18477
return NULL;
18478
}
18479
18480
18481
static Boolean ConvertRegionToImp (SeqFeatPtr sfp, Uint2 featdef_to, Pointer extradata)
15913
18482
{
15914
18483
GBQualPtr gbqual;
15915
18484
ImpFeatPtr ifp;
15916
18485
CharPtr str;
18486
CharPtr featname_to;
15917
18487
18488
if (sfp == NULL || sfp->data.choice != SEQFEAT_REGION) return FALSE;
18489
featname_to = GetImportFeatureName (featdef_to);
15918
18490
ifp = ImpFeatNew ();
15919
18491
if (NULL == ifp)
15920
return;
18492
return FALSE;
15921
18493
15922
18494
str = (CharPtr) sfp->data.value.ptrvalue;
15923
18495
sfp->data.choice = SEQFEAT_IMP;
15939
18511
gbqual->next = sfp->qual;
15940
18512
sfp->qual = gbqual;
15941
18513
}
15942
}
15943
}
15944
15945
static void AskForTranscriptionIdRemoval (BoolPtr ask, BoolPtr do_remove)
15946
{
15947
if (ask == NULL || do_remove == NULL)
15948
{
15949
return;
15950
}
15951
if (*ask)
15952
{
15953
if (Message (MSG_YN, "Remove transcript IDs?") == ANS_YES)
15954
{
15955
*do_remove = TRUE;
15956
}
15957
*ask = FALSE;
15958
}
15959
}
15960
15961
static void
15962
ConvertGeneToRNA
15963
(SeqFeatPtr sfp,
15964
Int2 toFeatSubType,
15965
Int2 fromFeat,
15966
Boolean do_remove_transcript_ids,
15967
ValNodePtr PNTR productbsp_list)
15968
{
15969
Int2 j;
15970
Char label [256];
15971
BioseqPtr productbsp;
15972
RnaRefPtr rrp;
15973
SeqIdPtr sip;
15974
tRNAPtr trp;
15975
Boolean just_trna_text = FALSE;
15976
Boolean asked_for_replace = TRUE;
15977
Boolean do_replace = FALSE;
15978
Boolean use_semicolon = TRUE;
15979
GeneRefPtr grp = NULL;
15980
15981
rrp = RnaRefNew ();
15982
if (NULL == rrp)
15983
return;
15984
15985
FeatDefLabel (sfp, label, sizeof (label), OM_LABEL_CONTENT);
15986
if (fromFeat == SEQFEAT_GENE) {
15987
grp = (GeneRefPtr) sfp->data.value.ptrvalue;
15988
sfp->data.value.ptrvalue = NULL;
15989
} else if (fromFeat == SEQFEAT_CDREGION) {
15990
if (sfp->product != NULL) {
15991
sip = SeqLocId (sfp->product);
15992
if (sip != NULL) {
15993
productbsp = BioseqFind (sip);
15994
if (productbsp != NULL)
15995
{
15996
ValNodeAddPointer (productbsp_list, 0, (Pointer) productbsp);
15997
}
15998
}
15999
if (do_remove_transcript_ids)
16000
{
16001
sfp->product = SeqLocFree (sfp->product);
16002
}
16003
}
16004
sfp->data.value.ptrvalue =
16005
CdRegionFree ((CdRegionPtr) sfp->data.value.ptrvalue);
16006
}
16007
16008
sfp->data.choice = SEQFEAT_RNA;
16009
sfp->data.value.ptrvalue = (Pointer) rrp;
16010
switch (toFeatSubType) {
16011
case FEATDEF_preRNA :
16012
rrp->type = 1;
16013
break;
16014
case FEATDEF_mRNA :
16015
rrp->type = 2;
16016
break;
16017
case FEATDEF_tRNA :
16018
rrp->type = 3;
16019
break;
16020
case FEATDEF_rRNA :
16021
rrp->type = 4;
16022
break;
16023
case FEATDEF_snRNA :
16024
rrp->type = 5;
16025
break;
16026
case FEATDEF_scRNA :
16027
rrp->type = 6;
16028
break;
16029
case FEATDEF_snoRNA :
16030
rrp->type = 7;
16031
break;
16032
case FEATDEF_otherRNA :
16033
rrp->type = 255;
16034
break;
16035
default :
16036
break;
16037
}
16038
16039
if (toFeatSubType == FEATDEF_tRNA) {
16040
trp = (tRNAPtr) MemNew (sizeof (tRNA));
16041
rrp->ext.choice = 2;
16042
rrp->ext.value.ptrvalue = (Pointer) trp;
16043
if (trp != NULL) {
16044
trp->aa = ParseTRnaString (label, &just_trna_text, NULL, FALSE);
16045
trp->aatype = 2;
16046
for (j = 0; j < 6; j++) {
16047
trp->codon [j] = 255;
16048
}
16049
}
16050
if (!just_trna_text)
16051
{
16052
AppendOrReplaceString (&(sfp->comment), label,
16053
&asked_for_replace,
16054
&do_replace,
16055
&use_semicolon);
16056
}
16057
} else if (! StringHasNoText (label)) {
16058
rrp->ext.choice = 1;
16059
rrp->ext.value.ptrvalue = StringSave (label);
16060
}
16061
16062
if (grp != NULL)
16063
{
16064
/* append unused gene qualifiers */
16065
if (StringCmp (grp->locus, label) != 0)
16066
{
16067
AppendOrReplaceString (&(sfp->comment), grp->locus,
16068
&asked_for_replace,
16069
&do_replace,
16070
&use_semicolon);
16071
}
16072
if (StringCmp (grp->allele, label) != 0)
16073
{
16074
AppendOrReplaceString (&(sfp->comment), grp->allele,
16075
&asked_for_replace,
16076
&do_replace,
16077
&use_semicolon);
16078
}
16079
if (StringCmp (grp->desc, label) != 0)
16080
{
16081
AppendOrReplaceString (&(sfp->comment), grp->desc,
16082
&asked_for_replace,
16083
&do_replace,
16084
&use_semicolon);
16085
}
16086
if (StringCmp (grp->maploc, label) != 0)
16087
{
16088
AppendOrReplaceString (&(sfp->comment), grp->maploc,
16089
&asked_for_replace,
16090
&do_replace,
16091
&use_semicolon);
16092
}
16093
if (StringCmp (grp->locus_tag, label) != 0)
16094
{
16095
AppendOrReplaceString (&(sfp->comment), grp->locus_tag,
16096
&asked_for_replace,
16097
&do_replace,
16098
&use_semicolon);
16099
}
16100
16101
/* free generef */
16102
grp = GeneRefFree (grp);
16103
}
16104
}
16105
16106
static void GetSiteOrBondType (FeatureSelRemConvFormPtr mrfp, Uint2 toFeat)
16107
{
16108
EnumFieldAssocPtr al;
16109
CharPtr mssg;
16110
UIEnum val;
16111
if (mrfp == NULL || mrfp->site_or_bond_type != -1 || toFeat == SEQFEAT_REGION)
16112
{
16113
return;
16114
}
16115
al = NULL;
16116
mssg = NULL;
16117
if (toFeat == SEQFEAT_BOND) {
16118
al = enum_bond_alist;
16119
mssg = "Select type of bond";
16120
} else if (toFeat == SEQFEAT_SITE) {
16121
al = enum_site_alist;
16122
mssg = "Select type of site";
16123
}
16124
if (al == NULL) return;
16125
if (! AlistMessage (al, &val, 1, mssg)) return;
16126
mrfp->site_or_bond_type = (Int4) val;
16127
}
16128
16129
static void
18514
}
18515
return TRUE;
18516
}
18517
18518
18519
static SeqLocPtr GetProteinLocationForNucleotideFeatureConversion (SeqLocPtr nuc_slp, BoolPtr no_cds)
18520
{
18521
SeqFeatPtr cds;
18522
SeqMgrFeatContext cds_context;
18523
SeqLocPtr prot_slp;
18524
18525
cds = SeqMgrGetOverlappingCDS (nuc_slp, &cds_context);
18526
if (cds == NULL) {
18527
if (no_cds != NULL) {
18528
*no_cds = TRUE;
18529
}
18530
return NULL;
18531
} else if (no_cds != NULL) {
18532
*no_cds = FALSE;
18533
}
18534
18535
prot_slp = BuildProtLoc (cds, nuc_slp, NULL);
18536
return prot_slp;
18537
}
18538
18539
18540
static Boolean
16130
18541
ConvertToBondSiteOrRegion
16131
18542
(SeqFeatPtr sfp,
16132
18543
Int4 site_or_bond_type,
16133
Uint1 toFeat)
18544
Uint2 featdef_to,
18545
Boolean create_prot_feats)
16134
18546
{
16135
SeqFeatPtr cds;
16136
18547
BioseqPtr bsp;
16137
18548
SeqLocPtr slp;
16138
18549
SeqEntryPtr sep;
16139
SeqMgrFeatContext context, cds_context;
18550
SeqMgrFeatContext context;
16140
18551
SeqFeatPtr newsfp;
16141
18552
SeqIdPtr sip;
16142
18553
CharPtr comment;
16143
18554
SeqBondPtr sbp;
16144
18555
SeqPntPtr spp;
18556
Boolean no_cds = FALSE;
16145
18557
16146
18558
if (sfp == NULL)
16147
18559
{
16148
return;
18560
return FALSE;
16149
18561
}
16150
18562
16151
if (site_or_bond_type == -1 && toFeat != SEQFEAT_REGION)
18563
if (site_or_bond_type == -1 && featdef_to != FEATDEF_REGION)
16152
18564
{
16153
return;
18565
return FALSE;
16154
18566
}
16155
18567
16156
18568
bsp = BioseqFindFromSeqLoc (sfp->location);
16157
18569
sfp = SeqMgrGetDesiredFeature (0, bsp, 0, 0, sfp, &context);
16158
if (sfp == NULL) return;
16159
16160
16161
cds = SeqMgrGetOverlappingCDS (sfp->location, &cds_context);
16162
if (cds == NULL) {
16163
Message (MSG_ERROR, "Unable to find CDS covering %s", context.label);
16164
return;
16165
}
16166
bsp = GetBioseqGivenSeqLoc (cds->location, context.entityID);
16167
if (bsp == NULL || ISA_aa (bsp->mol)) {
16168
Message (MSG_ERROR, "Unable to find DNA bioseq for %s", context.label);
16169
return;
16170
}
16171
slp = BuildProtLoc (cds, sfp->location, NULL);
16172
if (slp == NULL) {
16173
Message (MSG_ERROR, "Unable to convert to protein coordinate for %s", context.label);
16174
return;
16175
}
18570
if (sfp == NULL || bsp == NULL) return FALSE;
18571
18572
if (ISA_aa (bsp->mol))
18573
{
18574
if (create_prot_feats)
18575
{
18576
slp = (SeqLocPtr) AsnIoMemCopy (sfp->location, (AsnReadFunc) SeqLocAsnRead, (AsnWriteFunc) SeqLocAsnWrite);
18577
}
18578
else
18579
{
18580
slp = FindNucleotideLocationForProteinFeatureConversion (sfp->location, sfp->idx.entityID);
18581
}
18582
}
18583
else if (create_prot_feats)
18584
{
18585
slp = GetProteinLocationForNucleotideFeatureConversion (sfp->location, &no_cds);
18586
if (no_cds) {
18587
Message (MSG_ERROR, "Unable to find CDS covering %s", context.label);
18588
return FALSE;
18589
}
18590
} else {
18591
slp = (SeqLocPtr) AsnIoMemCopy (sfp->location, (AsnReadFunc) SeqLocAsnRead, (AsnWriteFunc) SeqLocAsnWrite);
18592
}
18593
16176
18594
bsp = GetBioseqGivenSeqLoc (slp, context.entityID);
16177
18595
if (bsp == NULL) {
16178
Message (MSG_ERROR, "Unable to find target protein bioseq for %s", context.label);
16179
return;
16180
}
18596
Message (MSG_ERROR, "Unable to find target %s bioseq for %s", create_prot_feats ? "protein" : "nucleotide", context.label);
18597
slp = SeqLocFree (slp);
18598
return FALSE;
18599
}
18600
16181
18601
sep = SeqMgrGetSeqEntryForData (bsp);
16182
18602
if (sep == NULL) {
16183
Message (MSG_ERROR, "Unable to find target protein seq-entry for %s", context.label);
16184
return;
18603
Message (MSG_ERROR, "Unable to find target %s seq-entry for %s", create_prot_feats ? "protein" : "nucleotide", context.label);
18604
return FALSE;
16185
18605
}
16186
18606
16187
18607
comment = sfp->comment;
16188
18608
16189
18609
newsfp = NULL;
16190
if (toFeat == SEQFEAT_BOND || toFeat == SEQFEAT_SITE) {
18610
if (featdef_to == FEATDEF_BOND || featdef_to == FEATDEF_SITE) {
16191
18611
newsfp = SeqFeatNew ();
16192
if (newsfp != NULL) {
16193
newsfp->data.choice = toFeat;
18612
if (newsfp != NULL)
18613
{
18614
newsfp->data.choice = FindFeatFromFeatDefType(featdef_to);
16194
18615
newsfp->data.value.intvalue = site_or_bond_type;
16195
sfp->comment = NULL;
18616
sfp->comment = NULL;
16196
18617
}
16197
} else if (toFeat == SEQFEAT_REGION) {
18618
} else if (featdef_to == FEATDEF_REGION) {
16198
18619
newsfp = SeqFeatNew ();
16199
if (newsfp != NULL) {
16200
newsfp->data.choice = toFeat;
18620
if (newsfp != NULL)
18621
{
18622
newsfp->data.choice = FindFeatFromFeatDefType(featdef_to);
16201
18623
newsfp->data.value.ptrvalue = sfp->comment;
16202
18624
sfp->comment = NULL;
16203
comment = NULL;
18625
comment = NULL;
16204
18626
}
16205
18627
}
16206
18628
if (newsfp != NULL) {
16207
18629
sfp->idx.deleteme = TRUE;
16208
DeleteMarkedObjects (context.entityID, 0, NULL);
16209
CreateNewFeature (sep, NULL, toFeat, newsfp);
18630
CreateNewFeature (sep, NULL, FindFeatFromFeatDefType(featdef_to), newsfp);
16210
18631
newsfp->location = slp;
16211
18632
newsfp->comment = comment;
16212
if (toFeat == SEQFEAT_BOND) {
18633
if (featdef_to == FEATDEF_BOND) {
16213
18634
if (slp->choice != SEQLOC_BOND) {
16214
18635
sip = SeqLocId (slp);
16215
18636
if (sip != NULL) {
16241
18662
}
16242
18663
}
16243
18664
}
16244
}
16245
16246
16247
static void ConvertImpToImp (SeqFeatPtr sfp, CharPtr featname_to)
16248
{
16249
ImpFeatPtr ifp;
16250
16251
ifp = (ImpFeatPtr) sfp->data.value.ptrvalue;
16252
if (NULL == ifp)
16253
return;
16254
16255
ifp->key = MemFree (ifp->key);
16256
if (featname_to == NULL)
18665
if (newsfp == NULL)
16257
18666
{
16258
ifp->key = StringSave ("misc_feature");
16259
}
18667
return FALSE;
18668
}
16260
18669
else
16261
18670
{
16262
ifp->key = StringSave (featname_to);
18671
return TRUE;
16263
18672
}
16264
18673
}
16265
18674
16271
18680
} OrigFeatData, PNTR OrigFeatPtr;
16272
18681
16273
18682
16274
static void AddDuplicateFeature (SeqFeatPtr sfp_orig, ValNodePtr PNTR feat_list)
18683
static ValNodePtr AddDuplicateFeature (SeqFeatPtr sfp_orig, ValNodePtr PNTR feat_list)
16275
18684
{
16276
18685
SeqEntryPtr sep;
16277
18686
BioseqPtr bsp;
16278
18687
OrigFeatPtr ofp;
16279
18688
16280
if (sfp_orig == NULL || feat_list == NULL) return;
18689
if (sfp_orig == NULL || feat_list == NULL) return NULL;
16281
18690
bsp = BioseqFindFromSeqLoc (sfp_orig->location);
16282
if (bsp == NULL) return;
18691
if (bsp == NULL) return NULL;
16283
18692
sep = SeqMgrGetSeqEntryForData (bsp);
16284
if (sep == NULL) return;
18693
if (sep == NULL) return NULL;
16285
18694
16286
18695
ofp = (OrigFeatPtr) MemNew (sizeof (OrigFeatData));
16287
if (ofp == NULL) return;
18696
if (ofp == NULL) return NULL;
16288
18697
16289
18698
ofp->sep = sep;
16290
18699
ofp->sfp = (SeqFeatPtr) AsnIoMemCopy (sfp_orig, (AsnReadFunc) SeqFeatAsnRead,
16291
18700
(AsnWriteFunc) SeqFeatAsnWrite);
16292
18701
16293
ValNodeAddPointer (feat_list, 0, ofp);
16294
}
16295
16296
16297
static void ConvertFeatureCallback (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
16298
{
16299
FeatureSelRemConvFormPtr mrfp;
16300
Uint1 fromFeat;
16301
Uint1 toFeat;
16302
16303
mrfp = (FeatureSelRemConvFormPtr) userdata;
16304
16305
if (sfp == NULL || mrfp == NULL || mrfp->abort_convert)
16306
{
16307
return;
16308
}
16309
16310
fromFeat = sfp->data.choice;
16311
toFeat = FindFeatFromFeatDefType (mrfp->featdef_to);
16312
16313
if (mrfp->leave_original_feature)
16314
{
16315
/* need a list of duplicate features that we can add to the appropriate SeqEntrys
16316
* when we are done with the conversions.
16317
*/
16318
AddDuplicateFeature (sfp, &(mrfp->feat_list));
16319
}
16320
16321
if (fromFeat == SEQFEAT_IMP
16322
&& toFeat == SEQFEAT_CDREGION)
16323
{
16324
Message (MSG_ERROR, "Conversion not yet supported");
16325
mrfp->abort_convert = TRUE;
16326
}
16327
else if (fromFeat == SEQFEAT_IMP &&
16328
toFeat == SEQFEAT_PROT)
16329
FeatConvertImpToPeptide (sfp, mrfp->featdef_to, mrfp->input_entityID);
16330
else if (fromFeat == SEQFEAT_PROT &&
16331
toFeat == SEQFEAT_IMP &&
16332
sfp->idx.subtype == FEATDEF_mat_peptide_aa)
16333
FeatConvertPeptideToImp (sfp, mrfp->input_entityID);
16334
else if (fromFeat == SEQFEAT_PROT &&
16335
toFeat == SEQFEAT_IMP &&
16336
sfp->idx.subtype == FEATDEF_sig_peptide_aa)
16337
FeatConvertPeptideToImp (sfp, mrfp->input_entityID);
16338
else if (fromFeat == SEQFEAT_PROT &&
16339
toFeat == SEQFEAT_IMP &&
16340
sfp->idx.subtype == FEATDEF_transit_peptide_aa)
16341
FeatConvertPeptideToImp (sfp, mrfp->input_entityID);
16342
else if (fromFeat == SEQFEAT_IMP &&
16343
(mrfp->featdef_to == FEATDEF_misc_RNA ||
16344
mrfp->featdef_to == FEATDEF_precursor_RNA))
16345
FeatConvertImpToSpecialRNA (sfp, mrfp->featdef_to);
16346
else if ((fromFeat == SEQFEAT_GENE ||
16347
fromFeat == SEQFEAT_CDREGION) &&
16348
toFeat == SEQFEAT_RNA)
16349
{
16350
AskForTranscriptionIdRemoval (&(mrfp->ask_for_transcript_id_removal),
16351
&(mrfp->do_remove_transcript_ids));
16352
ConvertGeneToRNA (sfp, mrfp->featdef_to, fromFeat,
16353
mrfp->do_remove_transcript_ids, &(mrfp->productbsp_list));
16354
}
16355
else if (fromFeat == SEQFEAT_REGION &&
16356
toFeat == SEQFEAT_IMP)
16357
ConvertRegionToImp (sfp, mrfp->featname_to);
16358
else if (fromFeat == SEQFEAT_REGION &&
16359
(mrfp->featdef_to == FEATDEF_misc_RNA ||
16360
mrfp->featdef_to == FEATDEF_precursor_RNA))
16361
FeatConvertRegionToRNA (sfp, mrfp->featdef_to);
16362
else if (fromFeat == SEQFEAT_IMP &&
16363
toFeat == SEQFEAT_RNA)
16364
FeatConvertImpToRNA (sfp, mrfp->featdef_to);
16365
else if (fromFeat == SEQFEAT_COMMENT &&
16366
mrfp->featdef_to == FEATDEF_misc_feature)
16367
FeatConvertCommentToMiscFeature (sfp);
16368
else if (fromFeat == SEQFEAT_GENE &&
16369
mrfp->featdef_to == FEATDEF_misc_feature)
16370
FeatConvertGeneToMiscFeature (sfp);
16371
else if (fromFeat == SEQFEAT_RNA &&
16372
mrfp->featdef_to == FEATDEF_misc_feature)
16373
FeatConvertRNAToMiscFeature (sfp);
16374
else if (fromFeat == SEQFEAT_SITE &&
16375
mrfp->featdef_to == FEATDEF_misc_feature)
16376
FeatConvertSiteToMiscFeature (sfp);
16377
else if (fromFeat == SEQFEAT_PROT &&
16378
(sfp->idx.subtype == FEATDEF_mat_peptide_aa ||
16379
sfp->idx.subtype == FEATDEF_sig_peptide_aa ||
16380
sfp->idx.subtype == FEATDEF_transit_peptide_aa) &&
16381
toFeat == SEQFEAT_REGION)
16382
FeatConvertPeptideToRegion (sfp);
16383
else if (fromFeat == SEQFEAT_BIOSRC &&
16384
toFeat == SEQFEAT_IMP &&
16385
mrfp->featdef_to == FEATDEF_repeat_region)
16386
FeatConvertBioSrcToRepeatRegion (sfp);
16387
else if (fromFeat == SEQFEAT_REGION
16388
&& toFeat == SEQFEAT_PROT
16389
&& (mrfp->featdef_to == FEATDEF_mat_peptide_aa ||
16390
mrfp->featdef_to == FEATDEF_sig_peptide_aa ||
16391
mrfp->featdef_to == FEATDEF_transit_peptide_aa ||
16392
mrfp->featdef_to == FEATDEF_preprotein))
16393
{
16394
FeatConvertRegionToProt (sfp, mrfp->featdef_to);
16395
}
16396
else if (toFeat == SEQFEAT_BOND || toFeat == SEQFEAT_REGION || toFeat == SEQFEAT_SITE)
16397
{
16398
GetSiteOrBondType (mrfp, toFeat);
16399
ConvertToBondSiteOrRegion (sfp, mrfp->site_or_bond_type, toFeat);
16400
}
16401
16402
else if (fromFeat != toFeat)
16403
{
16404
ArrowCursor ();
16405
Message (MSG_OK, "This conversion not supported - contact"
18702
return ValNodeAddPointer (feat_list, 0, ofp);
18703
}
18704
18705
static Pointer SimpleOptsFree (Pointer data)
18706
{
18707
return MemFree (data);
18708
}
18709
18710
static RnaRefPtr RnaRefFromLabel (Uint2 featdef_to, CharPtr label, BoolPtr add_label_to_comment)
18711
{
18712
RnaRefPtr rrp;
18713
tRNAPtr trp = NULL;
18714
Boolean just_trna_text;
18715
Int4 j;
18716
18717
rrp = RnaRefNew ();
18718
if (NULL == rrp)
18719
return NULL;
18720
18721
*add_label_to_comment = FALSE;
18722
18723
switch (featdef_to)
18724
{
18725
case FEATDEF_preRNA :
18726
rrp->type = 1;
18727
break;
18728
case FEATDEF_mRNA :
18729
rrp->type = 2;
18730
break;
18731
case FEATDEF_tRNA :
18732
rrp->type = 3;
18733
break;
18734
case FEATDEF_rRNA :
18735
rrp->type = 4;
18736
break;
18737
case FEATDEF_snRNA :
18738
rrp->type = 5;
18739
break;
18740
case FEATDEF_scRNA :
18741
rrp->type = 6;
18742
break;
18743
case FEATDEF_snoRNA :
18744
rrp->type = 7;
18745
break;
18746
case FEATDEF_otherRNA :
18747
rrp->type = 255;
18748
break;
18749
default :
18750
break;
18751
}
18752
18753
if (featdef_to == FEATDEF_tRNA)
18754
{
18755
trp = (tRNAPtr) MemNew (sizeof (tRNA));
18756
rrp->ext.choice = 2;
18757
rrp->ext.value.ptrvalue = (Pointer) trp;
18758
trp->aa = ParseTRnaString (label, &just_trna_text, NULL, FALSE);
18759
trp->aatype = 2;
18760
for (j = 0; j < 6; j++) {
18761
trp->codon [j] = 255;
18762
}
18763
if (!just_trna_text)
18764
{
18765
*add_label_to_comment = TRUE;
18766
}
18767
}
18768
else if (! StringHasNoText (label))
18769
{
18770
rrp->ext.choice = 1;
18771
rrp->ext.value.ptrvalue = StringSave (label);
18772
}
18773
return rrp;
18774
}
18775
18776
static Boolean
18777
ConvertCDSToRNA
18778
(SeqFeatPtr sfp,
18779
Uint2 toFeatSubType,
18780
Pointer extradata)
18781
{
18782
Char label [256];
18783
BioseqPtr product_bsp;
18784
CharPtr new_comment;
18785
Int4 comment_len = 0;
18786
CDSConversionOptsPtr opts;
18787
Boolean add_label_to_comment = FALSE;
18788
SeqFeatPtr mrna, gene;
18789
SeqMgrFeatContext fcontext;
18790
18791
if (sfp == NULL || sfp->data.choice != SEQFEAT_CDREGION) return FALSE;
18792
18793
opts = (CDSConversionOptsPtr) extradata;
18794
18795
FeatDefLabel (sfp, label, sizeof (label), OM_LABEL_CONTENT);
18796
18797
if (sfp->product != NULL) {
18798
product_bsp = BioseqFindFromSeqLoc (sfp->product);
18799
if (product_bsp != NULL)
18800
{
18801
product_bsp->idx.deleteme = TRUE;
18802
}
18803
if (!IsFeatInGPS (sfp) || (opts != NULL && opts->remove_transcript_id))
18804
{
18805
sfp->product = SeqLocFree (sfp->product);
18806
}
18807
}
18808
18809
if (opts != NULL && opts->remove_gene)
18810
{
18811
gene = SeqMgrGetOverlappingGene (sfp->location, &fcontext);
18812
if (gene != NULL)
18813
{
18814
gene->idx.deleteme = TRUE;
18815
}
18816
}
18817
18818
if (opts != NULL && opts->remove_mrna)
18819
{
18820
mrna = SeqMgrGetOverlappingmRNA (sfp->location, &fcontext);
18821
if (mrna != NULL)
18822
{
18823
mrna->idx.deleteme = TRUE;
18824
}
18825
}
18826
18827
sfp->data.value.ptrvalue =
18828
CdRegionFree ((CdRegionPtr) sfp->data.value.ptrvalue);
18829
18830
sfp->data.choice = SEQFEAT_RNA;
18831
sfp->data.value.ptrvalue = RnaRefFromLabel (toFeatSubType, label, &add_label_to_comment);
18832
18833
if (add_label_to_comment && StringCmp (label, sfp->comment) != 0)
18834
{
18835
if (StringHasNoText (sfp->comment))
18836
{
18837
new_comment = StringSave (label);
18838
}
18839
else
18840
{
18841
comment_len = StringLen (sfp->comment) + StringLen (label) + 3;
18842
new_comment = (CharPtr) MemNew (sizeof (Char) * comment_len);
18843
sprintf (new_comment, "%s; %s", sfp->comment, label);
18844
}
18845
sfp->comment = MemFree (sfp->comment);
18846
sfp->comment = new_comment;
18847
}
18848
18849
return TRUE;
18850
}
18851
18852
18853
static Boolean ConvertGeneToRNA (SeqFeatPtr sfp, Uint2 featdef_to, Pointer extradata)
18854
{
18855
Char label [256];
18856
GeneRefPtr grp;
18857
Boolean add_label_to_comment = FALSE;
18858
CharPtr new_comment;
18859
Int4 comment_len = 0;
18860
18861
if (sfp == NULL || sfp->data.choice != SEQFEAT_GENE) return FALSE;
18862
18863
FeatDefLabel (sfp, label, sizeof (label), OM_LABEL_CONTENT);
18864
18865
grp = (GeneRefPtr) sfp->data.value.ptrvalue;
18866
18867
sfp->data.choice = SEQFEAT_RNA;
18868
sfp->data.value.ptrvalue = RnaRefFromLabel (featdef_to, label, &add_label_to_comment);
18869
18870
if (add_label_to_comment)
18871
{
18872
comment_len += StringLen (label) + 2;
18873
}
18874
if (grp != NULL)
18875
{
18876
if (!StringHasNoText (grp->locus) && StringCmp (grp->locus, label) != 0)
18877
{
18878
comment_len += StringLen (grp->locus) + 2;
18879
}
18880
if (!StringHasNoText (grp->allele) && StringCmp (grp->allele, label) != 0)
18881
{
18882
comment_len += StringLen (grp->allele) + 2;
18883
}
18884
if (!StringHasNoText (grp->desc) && StringCmp (grp->desc, label) != 0)
18885
{
18886
comment_len += StringLen (grp->desc) + 2;
18887
}
18888
if (!StringHasNoText (grp->maploc) && StringCmp (grp->maploc, label) != 0)
18889
{
18890
comment_len += StringLen (grp->maploc) + 2;
18891
}
18892
if (!StringHasNoText (grp->locus_tag) && StringCmp (grp->locus_tag, label) != 0)
18893
{
18894
comment_len += StringLen (grp->locus_tag) + 2;
18895
}
18896
}
18897
if (comment_len > 0)
18898
{
18899
comment_len += StringLen (sfp->comment) + 3;
18900
new_comment = (CharPtr) MemNew (sizeof (Char) * comment_len);
18901
if (!StringHasNoText (sfp->comment))
18902
{
18903
StringCat (new_comment, sfp->comment);
18904
StringCat (new_comment, "; ");
18905
}
18906
if (add_label_to_comment)
18907
{
18908
StringCat (new_comment, label);
18909
StringCat (new_comment, "; ");
18910
}
18911
/* append unused gene qualifiers */
18912
if (grp != NULL)
18913
{
18914
if (!StringHasNoText (grp->locus) && StringCmp (grp->locus, label) != 0)
18915
{
18916
StringCat (new_comment, grp->locus);
18917
StringCat (new_comment, "; ");
18918
}
18919
if (!StringHasNoText (grp->allele) && StringCmp (grp->allele, label) != 0)
18920
{
18921
StringCat (new_comment, grp->allele);
18922
StringCat (new_comment, "; ");
18923
}
18924
if (!StringHasNoText (grp->desc) && StringCmp (grp->desc, label) != 0)
18925
{
18926
StringCat (new_comment, grp->desc);
18927
StringCat (new_comment, "; ");
18928
}
18929
if (!StringHasNoText (grp->maploc) && StringCmp (grp->maploc, label) != 0)
18930
{
18931
StringCat (new_comment, grp->maploc);
18932
StringCat (new_comment, "; ");
18933
}
18934
if (!StringHasNoText (grp->locus_tag) && StringCmp (grp->locus_tag, label) != 0)
18935
{
18936
StringCat (new_comment, grp->locus_tag);
18937
StringCat (new_comment, "; ");
18938
}
18939
}
18940
/* remove last semicolon */
18941
new_comment[StringLen (new_comment) - 2] = 0;
18942
sfp->comment = MemFree (sfp->comment);
18943
sfp->comment = new_comment;
18944
18945
}
18946
18947
/* free generef */
18948
grp = GeneRefFree (grp);
18949
18950
return TRUE;
18951
}
18952
18953
18954
static ValNodePtr CreateClickableListForSourceFeats (ValNodePtr feat_list)
18955
{
18956
ValNodePtr transposon_only_list = NULL;
18957
ValNodePtr insertion_seq_only_list = NULL;
18958
ValNodePtr transposon_and_insertion_seq_list = NULL;
18959
ValNodePtr note_only_list = NULL;
18960
ValNodePtr no_data_list = NULL;
18961
ValNodePtr vnp;
18962
CharPtr transposon_txt, insertion_seq_txt, note_txt;
18963
SeqFeatPtr sfp;
18964
BioSourcePtr biop;
18965
Boolean is_transposon;
18966
Boolean is_insertion_seq;
18967
ClickableItemPtr cip;
18968
ValNodePtr clickable_list = NULL;
18969
18970
for (vnp = feat_list; vnp != NULL; vnp = vnp->next) {
18971
sfp = (SeqFeatPtr) vnp->data.ptrvalue;
18972
biop = (BioSourcePtr) sfp->data.value.ptrvalue;
18973
is_transposon = FALSE;
18974
is_insertion_seq = FALSE;
18975
transposon_txt = SubSourceText (biop, SUBSRC_transposon_name, &is_transposon);
18976
insertion_seq_txt = SubSourceText (biop, SUBSRC_insertion_seq_name, &is_insertion_seq);
18977
note_txt = NoteText (biop, sfp->comment);
18978
18979
if (is_transposon && is_insertion_seq) {
18980
ValNodeAddPointer (&transposon_and_insertion_seq_list, OBJ_SEQFEAT, vnp->data.ptrvalue);
18981
} else if (is_transposon) {
18982
ValNodeAddPointer (&transposon_only_list, OBJ_SEQFEAT, vnp->data.ptrvalue);
18983
} else if (is_insertion_seq) {
18984
ValNodeAddPointer (&insertion_seq_only_list, OBJ_SEQFEAT, vnp->data.ptrvalue);
18985
} else if (!StringHasNoText (note_txt)) {
18986
ValNodeAddPointer (¬e_only_list, OBJ_SEQFEAT, vnp->data.ptrvalue);
18987
} else {
18988
ValNodeAddPointer (&no_data_list, OBJ_SEQFEAT, vnp->data.ptrvalue);
18989
}
18990
}
18991
18992
if (transposon_and_insertion_seq_list != NULL) {
18993
cip = NewClickableItem (0, "%d source features have both transposon-name and insertion-seq-name.", transposon_and_insertion_seq_list);
18994
ValNodeAddPointer (&clickable_list, 0, cip);
18995
}
18996
if (transposon_only_list != NULL) {
18997
cip = NewClickableItem (0, "%d source features have transposon-name.", transposon_only_list);
18998
cip->chosen = TRUE;
18999
ValNodeAddPointer (&clickable_list, 0, cip);
19000
}
19001
if (insertion_seq_only_list != NULL) {
19002
cip = NewClickableItem (0, "%d source features have insertion-seq-name.", insertion_seq_only_list);
19003
cip->chosen = TRUE;
19004
ValNodeAddPointer (&clickable_list, 0, cip);
19005
}
19006
if (note_only_list != NULL) {
19007
cip = NewClickableItem (0, "%d source features have notes, but neither transposon-name nor insertion-seq-name.", note_only_list);
19008
ValNodeAddPointer (&clickable_list, 0, cip);
19009
}
19010
if (no_data_list != NULL) {
19011
cip = NewClickableItem (0, "%d source features have no notes, no transposon-name, and no insertion-seq-name.", no_data_list);
19012
ValNodeAddPointer (&clickable_list, 0, cip);
19013
}
19014
19015
return clickable_list;
19016
}
19017
19018
19019
static ValNodePtr AdjustConvertFeaturesForBioSrcToRepeatRegion (ValNodePtr feat_list, Pointer extradata, BaseFormPtr bfp, BoolPtr cancel)
19020
{
19021
ValNodePtr clickable_list;
19022
19023
*cancel = FALSE;
19024
clickable_list = CreateClickableListForSourceFeats (feat_list);
19025
feat_list = ValNodeFree (feat_list);
19026
feat_list = ChooseFeaturesForConversion (clickable_list, bfp, "Available Data", "Features");
19027
/* NOTE - the clickable_list will be freed by the dialog - do not free it again here */
19028
if (feat_list == NULL)
19029
{
19030
*cancel = TRUE;
19031
}
19032
return feat_list;
19033
}
19034
19035
static Boolean AllFeaturesArePseudo (ValNodePtr feat_list)
19036
{
19037
Boolean all_pseudo = TRUE;
19038
SeqFeatPtr sfp;
19039
19040
while (feat_list != NULL && all_pseudo) {
19041
sfp = (SeqFeatPtr) feat_list->data.ptrvalue;
19042
if (sfp != NULL && !sfp->pseudo) {
19043
all_pseudo = FALSE;
19044
}
19045
feat_list = feat_list->next;
19046
}
19047
return all_pseudo;
19048
}
19049
19050
19051
static Boolean AnyFeaturesArePseudo (ValNodePtr feat_list)
19052
{
19053
Boolean any_pseudo = FALSE;
19054
19055
SeqFeatPtr sfp;
19056
19057
while (feat_list != NULL && !any_pseudo) {
19058
sfp = (SeqFeatPtr) feat_list->data.ptrvalue;
19059
if (sfp != NULL && sfp->pseudo) {
19060
any_pseudo = TRUE;
19061
}
19062
feat_list = feat_list->next;
19063
}
19064
return any_pseudo;
19065
}
19066
19067
19068
static void RemoveNonPseudoFeatures (ValNodePtr PNTR feat_list)
19069
{
19070
ValNodePtr prev = NULL, next_vnp, vnp;
19071
SeqFeatPtr sfp;
19072
19073
vnp = *feat_list;
19074
while (vnp != NULL) {
19075
next_vnp = vnp->next;
19076
sfp = (SeqFeatPtr) vnp->data.ptrvalue;
19077
if (sfp != NULL && !sfp->pseudo) {
19078
if (prev == NULL) {
19079
*feat_list = vnp->next;
19080
} else {
19081
prev->next = vnp->next;
19082
}
19083
vnp->next = NULL;
19084
vnp = ValNodeFree (vnp);
19085
} else {
19086
prev = vnp;
19087
}
19088
vnp = next_vnp;
19089
}
19090
}
19091
19092
19093
static Pointer GetCDSConversionOpts (ValNodePtr feat_list, BaseFormPtr bfp, BoolPtr cancel)
19094
{
19095
Boolean all_are_pseudo = TRUE, any_are_pseudo = FALSE, any_gps = FALSE;
19096
CDSConversionOptsPtr opts;
19097
ValNodePtr vnp;
19098
SeqFeatPtr sfp;
19099
19100
for (vnp = feat_list; vnp != NULL; vnp = vnp->next)
19101
{
19102
sfp = (SeqFeatPtr) vnp->data.ptrvalue;
19103
if (sfp != NULL)
19104
{
19105
if (sfp->pseudo)
19106
{
19107
any_are_pseudo = TRUE;
19108
}
19109
else
19110
{
19111
all_are_pseudo = FALSE;
19112
}
19113
if (!any_gps)
19114
{
19115
any_gps = IsFeatInGPS (sfp);
19116
}
19117
}
19118
}
19119
19120
opts = GetCDSConversionOptions (all_are_pseudo, any_are_pseudo, any_gps, cancel);
19121
19122
return opts;
19123
}
19124
19125
19126
static ValNodePtr AdjustCDSToMiscFeatList (ValNodePtr feat_list, Pointer extradata, BaseFormPtr bfp, BoolPtr cancel)
19127
{
19128
CDSConversionOptsPtr opts;
19129
19130
if (feat_list == NULL || extradata == NULL || cancel == NULL) return feat_list;
19131
opts = (CDSConversionOptsPtr) extradata;
19132
*cancel = FALSE;
19133
if (opts->only_pseudo) {
19134
/* remove features that are not pseudo */
19135
RemoveNonPseudoFeatures (&feat_list);
19136
}
19137
return feat_list;
19138
}
19139
19140
19141
static void CDSToMiscFeatConversionCleanup (Uint2 entityID, Pointer extradata)
19142
{
19143
SeqEntryPtr sep;
19144
19145
DeleteMarkedObjects (entityID, 0, NULL);
19146
sep = GetTopSeqEntryForEntityID (entityID);
19147
RenormalizeNucProtSets (sep, TRUE);
19148
}
19149
19150
19151
static Boolean CDSToMiscFeatConvertFunc (SeqFeatPtr sfp, Uint2 featdef_to, Pointer extradata)
19152
{
19153
CDSConversionOptsPtr opts;
19154
Boolean rval = FALSE;
19155
19156
opts = (CDSConversionOptsPtr) extradata;
19157
if (opts == NULL || sfp == NULL || sfp->data.choice != SEQFEAT_CDREGION)
19158
{
19159
return FALSE;
19160
}
19161
else if (sfp->pseudo)
19162
{
19163
rval = ConvertOnePseudoCDSToMiscFeat (sfp);
19164
}
19165
else
19166
{
19167
/* do other here */
19168
19169
rval = ConvertOneCDSToMiscFeat (sfp, FALSE, FALSE, opts);
19170
}
19171
return TRUE;
19172
}
19173
19174
19175
typedef struct siteorbond {
19176
Int4 site_or_bond_type;
19177
} SiteOrBondData, PNTR SiteOrBondPtr;
19178
19179
static Pointer GetSiteOrBondOpts (ValNodePtr feat_list, BaseFormPtr bfp, BoolPtr cancel, Uint2 toFeat)
19180
{
19181
EnumFieldAssocPtr al;
19182
CharPtr mssg;
19183
UIEnum val;
19184
SiteOrBondPtr opts = NULL;
19185
19186
*cancel = FALSE;
19187
al = NULL;
19188
mssg = NULL;
19189
if (toFeat == FEATDEF_BOND) {
19190
al = enum_bond_alist;
19191
mssg = "Select type of bond";
19192
} else if (toFeat == FEATDEF_SITE) {
19193
al = enum_site_alist;
19194
mssg = "Select type of site";
19195
} else {
19196
*cancel = TRUE;
19197
return NULL;
19198
}
19199
19200
if (al == NULL || ! AlistMessage (al, &val, 1, mssg))
19201
{
19202
*cancel = TRUE;
19203
}
19204
else
19205
{
19206
opts = (SiteOrBondPtr) MemNew (sizeof (SiteOrBondData));
19207
opts->site_or_bond_type = (Int4) val;
19208
}
19209
return opts;
19210
}
19211
19212
19213
static Pointer GetSiteOpts (ValNodePtr feat_list, BaseFormPtr bfp, BoolPtr cancel)
19214
{
19215
return GetSiteOrBondOpts (feat_list, bfp, cancel, FEATDEF_SITE);
19216
}
19217
19218
19219
static Pointer GetBondOpts (ValNodePtr feat_list, BaseFormPtr bfp, BoolPtr cancel)
19220
{
19221
return GetSiteOrBondOpts (feat_list, bfp, cancel, FEATDEF_BOND);
19222
}
19223
19224
19225
static Boolean ConvertToSiteOrBond (SeqFeatPtr sfp, Uint2 featdef_to, Pointer extradata)
19226
{
19227
SiteOrBondPtr opts = NULL;
19228
19229
opts = (SiteOrBondPtr) extradata;
19230
if (sfp == NULL || opts == NULL) return FALSE;
19231
19232
return ConvertToBondSiteOrRegion (sfp, opts->site_or_bond_type, featdef_to, TRUE);
19233
}
19234
19235
typedef struct regionopts {
19236
Boolean create_prot_feats;
19237
} RegionOptsData, PNTR RegionOptsPtr;
19238
19239
19240
static ValNodePtr GetBadProteinConversionFeatures (ValNodePtr feat_list)
19241
{
19242
ValNodePtr no_cds_list = NULL, bad_coordinates_list = NULL, err_list = NULL, vnp;
19243
Boolean no_cds;
19244
SeqLocPtr slp;
19245
SeqFeatPtr sfp;
19246
BioseqPtr bsp;
19247
19248
for (vnp = feat_list; vnp != NULL; vnp = vnp->next) {
19249
sfp = (SeqFeatPtr) vnp->data.ptrvalue;
19250
bsp = BioseqFindFromSeqLoc (sfp->location);
19251
if (bsp != NULL && ISA_aa (bsp->mol))
19252
{
19253
slp = FindNucleotideLocationForProteinFeatureConversion (sfp->location, sfp->idx.entityID);
19254
if (slp == NULL)
19255
{
19256
no_cds = TRUE;
19257
}
19258
}
19259
else
19260
{
19261
slp = GetProteinLocationForNucleotideFeatureConversion (sfp->location, &no_cds);
19262
}
19263
if (slp == NULL) {
19264
if (no_cds) {
19265
ValNodeAddPointer (&no_cds_list, OBJ_SEQFEAT, sfp);
19266
} else {
19267
ValNodeAddPointer (&bad_coordinates_list, OBJ_SEQFEAT, sfp);
19268
}
19269
} else {
19270
slp = SeqLocFree (slp);
19271
}
19272
}
19273
19274
if (no_cds_list != NULL) {
19275
ValNodeAddPointer (&err_list, 0, NewClickableItem (0, "%d features have no overlapping coding region", no_cds_list));
19276
}
19277
if (bad_coordinates_list != NULL) {
19278
ValNodeAddPointer (&err_list, 0, NewClickableItem (0, "%d features do not stop or start on codon boundaries", bad_coordinates_list));
19279
}
19280
return err_list;
19281
}
19282
19283
19284
static Pointer GetRegionOpts (ValNodePtr feat_list, BaseFormPtr bfp, BoolPtr cancel)
19285
{
19286
ValNodePtr err_list;
19287
WindoW w;
19288
GrouP h, nuc_prot_choice, c;
19289
DialoG bad_prot_feats = NULL;
19290
ButtoN b;
19291
ModalAcceptCancelData acd;
19292
Boolean rval = FALSE;
19293
RegionOptsPtr opts = NULL;
19294
19295
*cancel = FALSE;
19296
19297
if (feat_list == NULL) return NULL;
19298
19299
err_list = GetBadProteinConversionFeatures (feat_list);
19300
19301
w = MovableModalWindow(-20, -13, -10, -10, "Create Nucleotide or Protein Features", NULL);
19302
h = HiddenGroup (w, -1, 0, NULL);
19303
SetGroupSpacing (h, 10, 10);
19304
19305
if (err_list != NULL) {
19306
bad_prot_feats = CreateClickableListDialog (h, "Reasons", "Original Features",
19307
ScrollToDiscrepancyItem, EditDiscrepancyItem, NULL,
19308
GetDiscrepancyItemText);
19309
PointerToDialog (bad_prot_feats, err_list);
19310
}
19311
19312
nuc_prot_choice = HiddenGroup (h, 0, 2, NULL);
19313
RadioButton (nuc_prot_choice, "Create Nucleotide Features");
19314
RadioButton (nuc_prot_choice, err_list == NULL ? "Create Protein Features" : "Create Protein Features (features listed above will be skipped)");
19315
SetValue (nuc_prot_choice, err_list == NULL ? 2 : 1);
19316
19317
c = HiddenGroup (h, 2, 0, NULL);
19318
SetGroupSpacing (c, 10, 10);
19319
b = PushButton (c, "Accept", ModalAcceptButton);
19320
SetObjectExtra (b, &acd, NULL);
19321
b = PushButton (c, "Cancel", ModalCancelButton);
19322
SetObjectExtra (b, &acd, NULL);
19323
AlignObjects (ALIGN_CENTER, (HANDLE) nuc_prot_choice,
19324
(HANDLE) c,
19325
(HANDLE) bad_prot_feats,
19326
NULL);
19327
Show (w);
19328
Select (w);
19329
acd.accepted = FALSE;
19330
acd.cancelled = FALSE;
19331
while (!acd.accepted && ! acd.cancelled)
19332
{
19333
ProcessExternalEvent ();
19334
Update ();
19335
}
19336
ProcessAnEvent ();
19337
if (acd.cancelled)
19338
{
19339
*cancel = TRUE;
19340
}
19341
else
19342
{
19343
opts = (RegionOptsPtr) MemNew (sizeof (RegionOptsData));
19344
if (GetValue (nuc_prot_choice) == 2)
19345
{
19346
opts->create_prot_feats = TRUE;
19347
}
19348
else
19349
{
19350
opts->create_prot_feats = FALSE;
19351
}
19352
}
19353
Remove (w);
19354
19355
return opts;
19356
}
19357
19358
19359
static void RemoveClickableItemFeaturesFromFeatureList (ClickableItemPtr cip, ValNodePtr PNTR feat_list)
19360
{
19361
ValNodePtr vnp_i, vnp_p, vnp_r;
19362
19363
if (cip == NULL || feat_list == NULL || *feat_list == NULL) return;
19364
for (vnp_i = cip->item_list; vnp_i != NULL; vnp_i = vnp_i->next) {
19365
if (vnp_i->choice != OBJ_SEQFEAT || vnp_i->data.ptrvalue == NULL) continue;
19366
vnp_p = NULL;
19367
vnp_r = *feat_list;
19368
while (vnp_r != NULL && vnp_r->data.ptrvalue != vnp_i->data.ptrvalue) {
19369
vnp_p = vnp_r;
19370
vnp_r = vnp_r->next;
19371
}
19372
if (vnp_r != NULL) {
19373
if (vnp_p == NULL) {
19374
*feat_list = vnp_r->next;
19375
} else {
19376
vnp_p->next = vnp_r->next;
19377
}
19378
vnp_r->next = NULL;
19379
vnp_r = ValNodeFree (vnp_r);
19380
}
19381
}
19382
for (vnp_i = cip->subcategories; vnp_i != NULL; vnp_i = vnp_i->next) {
19383
RemoveClickableItemFeaturesFromFeatureList (vnp_i->data.ptrvalue, feat_list);
19384
}
19385
}
19386
19387
19388
static ValNodePtr AdjustRegionConversionFeatures (ValNodePtr feat_list, Pointer extradata, BaseFormPtr bfp, BoolPtr cancel)
19389
{
19390
RegionOptsPtr opts = (RegionOptsPtr) extradata;
19391
ValNodePtr err_list, vnp_c;
19392
19393
*cancel = FALSE;
19394
if (opts == NULL || !opts->create_prot_feats) return feat_list;
19395
19396
err_list = GetBadProteinConversionFeatures (feat_list);
19397
19398
for (vnp_c = err_list; vnp_c != NULL; vnp_c = vnp_c->next) {
19399
RemoveClickableItemFeaturesFromFeatureList (vnp_c->data.ptrvalue, &feat_list);
19400
}
19401
return feat_list;
19402
}
19403
19404
19405
static Boolean ConvertAnyToRegion (SeqFeatPtr sfp, Uint2 featdef_to, Pointer extradata)
19406
{
19407
RegionOptsPtr opts = (RegionOptsPtr) extradata;
19408
19409
if (opts == NULL || sfp == NULL) return FALSE;
19410
return ConvertToBondSiteOrRegion (sfp, 0, FEATDEF_REGION, opts->create_prot_feats);
19411
}
19412
19413
19414
static Boolean ConvertImpToImp (SeqFeatPtr sfp, Uint2 featdef_to, Pointer extradata)
19415
{
19416
ImpFeatPtr ifp;
19417
CharPtr featname;
19418
19419
if (sfp == NULL || sfp->data.choice != SEQFEAT_IMP) return FALSE;
19420
19421
ifp = (ImpFeatPtr) sfp->data.value.ptrvalue;
19422
if (NULL == ifp)
19423
return FALSE;
19424
19425
featname = GetImportFeatureName (featdef_to);
19426
ifp->key = MemFree (ifp->key);
19427
if (featname == NULL)
19428
{
19429
ifp->key = StringSave ("misc_feature");
19430
}
19431
else
19432
{
19433
ifp->key = StringSave (featname);
19434
}
19435
19436
return TRUE;
19437
}
19438
19439
19440
static void CollectFeaturesToBeConverted (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
19441
{
19442
ValNodePtr PNTR feat_list = (ValNodePtr PNTR) userdata;
19443
19444
ValNodeAddPointer (feat_list, OBJ_SEQFEAT, sfp);
19445
}
19446
19447
19448
static void MoveInferenceToOverlappingGene (SeqFeatPtr sfp)
19449
{
19450
GBQualPtr qual, qual_prev= NULL, qual_next;
19451
SeqFeatPtr gene;
19452
19453
if (sfp == NULL) return;
19454
19455
gene = GetGeneForFeature (sfp);
19456
if (gene == NULL || gene->idx.deleteme || gene == sfp) return;
19457
19458
qual = sfp->qual;
19459
while (qual != NULL) {
19460
qual_next = qual->next;
19461
if (StringCmp (qual->qual, "inference") == 0) {
19462
if (qual_prev == NULL) {
19463
sfp->qual = qual->next;
19464
} else {
19465
qual_prev->next = qual->next;
19466
}
19467
qual->next = NULL;
19468
qual->next = gene->qual;
19469
gene->qual = qual;
19470
} else {
19471
qual_prev = qual;
19472
}
19473
qual = qual_next;
19474
}
19475
}
19476
19477
19478
static Boolean NewConvertFeaturesByList (SeqEntryPtr sep, FilterSetPtr fsp, Uint1 featdef_from, FeatureSelRemConvFormPtr mrfp)
19479
{
19480
ValNodePtr feat_list = NULL, sel_feat_list = NULL, vnp;
19481
Boolean not_match = FALSE;
19482
Boolean only_pseudo = FALSE;
19483
SelStructPtr sel;
19484
SeqFeatPtr sfp;
19485
SeqMgrFeatContext fcontext;
19486
Int4 table_line_num = -1;
19487
Uint2 seqfeat_from, seqfeat_to;
19488
Pointer extradata = NULL;
19489
Boolean cancel = FALSE;
19490
ValNodePtr dup_feat_vnp = NULL;
19491
OrigFeatPtr ofp;
19492
Boolean removed_cds = FALSE;
19493
BioseqPtr protBsp;
19494
19495
OperateOnSeqEntryConstrainedObjects (sep, fsp,
19496
CollectFeaturesToBeConverted,
19497
NULL, 0, featdef_from, 0, &feat_list);
19498
sel = ObjMgrGetSelected ();
19499
while (sel != NULL) {
19500
if (sel->entityID == mrfp->input_entityID && sel->itemtype == OBJ_SEQFEAT) {
19501
sfp = SeqMgrGetDesiredFeature (sel->entityID, NULL, sel->itemID, 0, NULL, &fcontext);
19502
if (sfp != NULL) {
19503
vnp = feat_list;
19504
while (vnp != NULL && vnp->data.ptrvalue != sfp) {
19505
vnp = vnp->next;
19506
}
19507
if (vnp == NULL) {
19508
not_match = TRUE;
19509
}
19510
ValNodeAddPointer (&sel_feat_list, OBJ_SEQFEAT, sfp);
19511
}
19512
}
19513
sel = sel->next;
19514
}
19515
if (sel_feat_list != NULL) {
19516
feat_list = ValNodeFree (feat_list);
19517
if (not_match
19518
&& Message (MSG_YN,
19519
"Selected feature%s do%s not match options - apply to selected feature anyway?",
19520
sel_feat_list->next == NULL ? "" : "s",
19521
sel_feat_list->next == NULL ? "es" : "") == ANS_NO) {
19522
sel_feat_list = ValNodeFree (sel_feat_list);
19523
return FALSE;
19524
}
19525
feat_list = sel_feat_list;
19526
}
19527
19528
if (feat_list == NULL) {
19529
Message (MSG_ERROR, "No features of the specified type exist to be converted!");
19530
return FALSE;
19531
}
19532
19533
/* find line in table that applies */
19534
seqfeat_from = FindFeatFromFeatDefType (featdef_from);
19535
seqfeat_to = FindFeatFromFeatDefType (mrfp->featdef_to);
19536
19537
table_line_num = GetConvertFeatureTableLine (seqfeat_from, featdef_from, seqfeat_to, mrfp->featdef_to);
19538
if (table_line_num < 0 || ConvertFeaturesTable[table_line_num].convert_func == NULL)
19539
{
19540
Message (MSG_ERROR, "This conversion not supported - contact"
16406
19541
" sequindev for instructions.");
16407
mrfp->abort_convert = TRUE;
16408
return;
16409
}
16410
else if (fromFeat == SEQFEAT_IMP)
16411
ConvertImpToImp (sfp, mrfp->featname_to);
16412
else if (fromFeat == SEQFEAT_RNA)
16413
FeatConvertRNAToRNA (sfp, mrfp->featdef_to);
16414
else if (fromFeat == SEQFEAT_PROT)
16415
FeatConvertProtToProt (sfp, mrfp->featdef_to);
16416
16417
/* set the subtype to zero so that it will be reindexed */
16418
sfp->idx.subtype = 0;
19542
return FALSE;
19543
}
19544
19545
/* collect extra data if necessary */
19546
if (ConvertFeaturesTable[table_line_num].collect_options != NULL)
19547
{
19548
extradata = (ConvertFeaturesTable[table_line_num].collect_options) (feat_list, mrfp->bfp, &cancel);
19549
if (cancel)
19550
{
19551
feat_list = ValNodeFree (feat_list);
19552
/* free extradata */
19553
if (ConvertFeaturesTable[table_line_num].free_options != NULL)
19554
{
19555
(ConvertFeaturesTable[table_line_num].free_options) (extradata);
19556
}
19557
return FALSE;
19558
}
19559
}
19560
19561
/* adjust feature list if necessary */
19562
if (ConvertFeaturesTable[table_line_num].adjust_features != NULL)
19563
{
19564
feat_list = (ConvertFeaturesTable[table_line_num].adjust_features) (feat_list, extradata, mrfp->bfp, &cancel);
19565
if (cancel || feat_list == NULL)
19566
{
19567
feat_list = ValNodeFree (feat_list);
19568
/* free extradata */
19569
if (ConvertFeaturesTable[table_line_num].free_options != NULL)
19570
{
19571
(ConvertFeaturesTable[table_line_num].free_options) (extradata);
19572
}
19573
return FALSE;
19574
}
19575
}
19576
19577
/* process list */
19578
for (vnp = feat_list; vnp != NULL; vnp = vnp->next)
19579
{
19580
sfp = (SeqFeatPtr) vnp->data.ptrvalue;
19581
if (sfp == NULL) continue;
19582
protBsp = NULL;
19583
if (sfp->data.choice == SEQFEAT_CDREGION && !mrfp->leave_original_feature)
19584
{
19585
protBsp = BioseqFindFromSeqLoc (sfp->product);
19586
if (protBsp != NULL)
19587
{
19588
protBsp->idx.deleteme = TRUE;
19589
}
19590
removed_cds = TRUE;
19591
}
19592
19593
dup_feat_vnp = NULL;
19594
if (mrfp->leave_original_feature)
19595
{
19596
/* need a list of duplicate features that we can add to the appropriate SeqEntrys
19597
* when we are done with the conversions.
19598
*/
19599
dup_feat_vnp = AddDuplicateFeature (sfp, &(mrfp->feat_list));
19600
}
19601
19602
if (ConvertFeaturesTable[table_line_num].convert_func (sfp, mrfp->featdef_to, extradata))
19603
{
19604
/* set the subtype to zero so that it will be reindexed */
19605
sfp->idx.subtype = 0;
19606
if (mrfp->featdef_to == FEATDEF_misc_feature)
19607
{
19608
MoveInferenceToOverlappingGene (sfp);
19609
}
19610
}
19611
else if (dup_feat_vnp != NULL && dup_feat_vnp->data.ptrvalue != NULL)
19612
{
19613
/* feature wasn't removed, for whatever reason */
19614
/* remove the duplicate feature from the list to be added later */
19615
ofp = (OrigFeatPtr) dup_feat_vnp->data.ptrvalue;
19616
ofp->sfp = SeqFeatFree (ofp->sfp);
19617
ofp->sep = NULL;
19618
19619
/* don't remove protein product if feature wasn't removed */
19620
if (protBsp != NULL)
19621
{
19622
protBsp->idx.deleteme = FALSE;
19623
}
19624
}
19625
}
19626
19627
feat_list = ValNodeFree (feat_list);
19628
19629
/* do cleanup tasks */
19630
if (ConvertFeaturesTable[table_line_num].cleanup_func != NULL)
19631
{
19632
(ConvertFeaturesTable[table_line_num].cleanup_func) (mrfp->input_entityID, extradata);
19633
}
19634
19635
/* free extradata */
19636
if (ConvertFeaturesTable[table_line_num].free_options != NULL)
19637
{
19638
(ConvertFeaturesTable[table_line_num].free_options) (extradata);
19639
}
19640
19641
if (removed_cds)
19642
{
19643
DeleteMarkedObjects (mrfp->input_entityID, 0, NULL);
19644
RenormalizeNucProtSets (sep, TRUE);
19645
}
19646
19647
return TRUE;
16419
19648
}
16420
19649
19650
16421
19651
static void RemoveProteinProducts (ValNodePtr bsplist, Uint2 entityID, SeqEntryPtr sep)
16422
19652
{
16423
19653
MsgAnswer ans;
16492
19722
}
16493
19723
}
16494
19724
19725
static Boolean GetNucOrProtChoiceForConversion (ValNodePtr PNTR feat_list, BoolPtr use_prot)
19726
{
19727
ValNodePtr err_list, vnp_c;
19728
WindoW w;
19729
GrouP h, nuc_prot_choice, c;
19730
DialoG bad_prot_feats = NULL;
19731
ButtoN b;
19732
ModalAcceptCancelData acd;
19733
Boolean rval = FALSE;
19734
19735
if (feat_list == NULL || *feat_list == NULL || use_prot == NULL) return FALSE;
19736
19737
err_list = GetBadProteinConversionFeatures (*feat_list);
19738
19739
w = MovableModalWindow(-20, -13, -10, -10, "Create Nucleotide or Protein Features", NULL);
19740
h = HiddenGroup (w, -1, 0, NULL);
19741
SetGroupSpacing (h, 10, 10);
19742
19743
if (err_list != NULL) {
19744
bad_prot_feats = CreateClickableListDialog (h, "Reasons", "Original Features",
19745
ScrollToDiscrepancyItem, EditDiscrepancyItem, NULL,
19746
GetDiscrepancyItemText);
19747
PointerToDialog (bad_prot_feats, err_list);
19748
}
19749
19750
nuc_prot_choice = HiddenGroup (h, 0, 2, NULL);
19751
RadioButton (nuc_prot_choice, "Create Nucleotide Features");
19752
RadioButton (nuc_prot_choice, err_list == NULL ? "Create Protein Features" : "Create Protein Features (features listed above will be skipped)");
19753
SetValue (nuc_prot_choice, err_list == NULL ? 2 : 1);
19754
19755
c = HiddenGroup (h, 2, 0, NULL);
19756
SetGroupSpacing (c, 10, 10);
19757
b = PushButton (c, "Accept", ModalAcceptButton);
19758
SetObjectExtra (b, &acd, NULL);
19759
b = PushButton (c, "Cancel", ModalCancelButton);
19760
SetObjectExtra (b, &acd, NULL);
19761
AlignObjects (ALIGN_CENTER, (HANDLE) nuc_prot_choice,
19762
(HANDLE) c,
19763
(HANDLE) bad_prot_feats,
19764
NULL);
19765
Show (w);
19766
Select (w);
19767
acd.accepted = FALSE;
19768
acd.cancelled = FALSE;
19769
while (!acd.accepted && ! acd.cancelled)
19770
{
19771
ProcessExternalEvent ();
19772
Update ();
19773
}
19774
ProcessAnEvent ();
19775
if (acd.cancelled)
19776
{
19777
rval = FALSE;
19778
}
19779
else if (GetValue (nuc_prot_choice) == 2)
19780
{
19781
*use_prot = TRUE;
19782
if (err_list != NULL) {
19783
for (vnp_c = err_list; vnp_c != NULL; vnp_c = vnp_c->next) {
19784
RemoveClickableItemFeaturesFromFeatureList (vnp_c->data.ptrvalue, feat_list);
19785
}
19786
}
19787
rval = TRUE;
19788
} else {
19789
*use_prot = FALSE;
19790
rval = TRUE;
19791
}
19792
Remove (w);
19793
return rval;
19794
}
19795
19796
19797
19798
16495
19799
static Boolean FeatureRemoveOrConvertAction (Pointer userdata)
16496
19800
{
16497
19801
FeatureSelRemConvFormPtr mrfp;
16503
19807
RemoveFeatureData rfd;
16504
19808
OrigFeatPtr ofp;
16505
19809
SeqFeatPtr sfp;
19810
Boolean rval = TRUE;
16506
19811
16507
19812
if (userdata == NULL) return FALSE;
16508
19813
16509
19814
mrfp = (FeatureSelRemConvFormPtr) userdata;
16510
mrfp->abort_convert = FALSE;
16511
19815
window_action = GetValue (mrfp->action_choice);
16512
19816
16513
19817
fsp = (FilterSetPtr) DialogToPointer (mrfp->constraints);
16524
19828
return FALSE;
16525
19829
}
16526
19830
mrfp->featdef_to = vnp->choice;
16527
mrfp->featname_to = vnp->data.ptrvalue;
16528
19831
/* NOTE - I do not need to use ValNodeFreeData because I'm using
16529
19832
* the data.ptrvalue in mrfp->featname_to and will free it when I free
16530
19833
* mrfp.
16553
19856
switch (window_action)
16554
19857
{
16555
19858
case FEATURE_CONVERT:
16556
if ((feat_def_choice == FEATDEF_CDS || feat_def_choice == FEATDEF_GENE)
16557
&& mrfp->featdef_to == SEQFEAT_RNA)
16558
{
16559
mrfp->ask_for_transcript_id_removal = TRUE;
16560
}
16561
OperateOnSeqEntryConstrainedObjects (sep, fsp,
16562
ConvertFeatureCallback,
16563
NULL, 0, feat_def_choice, 0, mrfp);
19859
rval = NewConvertFeaturesByList (sep, fsp, feat_def_choice, mrfp);
16564
19860
break;
16565
19861
case FEATURE_REMOVE:
16566
19862
rfd.bsplist = NULL;
16607
19903
}
16608
19904
}
16609
19905
mrfp->feat_list = ValNodeFreeData (mrfp->feat_list);
19906
19907
if (mrfp->renormalize_nucprot) {
19908
RenormalizeNucProtSets (sep, TRUE);
19909
}
16610
19910
16611
19911
ObjMgrSetDirtyFlag (mrfp->input_entityID, TRUE);
16612
19912
ObjMgrSendMsg (OM_MSG_UPDATE, mrfp->input_entityID, 0, 0);
16613
19913
Update ();
16614
return TRUE;
19914
return rval;
16615
19915
}
16616
19916
16617
19917
static void FeatureRemoveOrConvert (IteM i, Int4 first_action)
16619
19919
BaseFormPtr bfp;
16620
19920
FeatureSelRemConvFormPtr mrfp;
16621
19921
WindoW w;
16622
GrouP h, k, n;
19922
GrouP h, k, g, n;
16623
19923
SeqEntryPtr sep;
16624
19924
16625
19925
#ifdef WIN_MAC
16632
19932
mrfp = (FeatureSelRemConvFormPtr) MemNew (sizeof (FeatureSelRemConvFormData));
16633
19933
if (mrfp == NULL) return;
16634
19934
19935
mrfp->bfp = bfp;
19936
16635
19937
w = FixedWindow (-50, -33, -10, -10, "Remove or Convert Features", StdCloseWindowProc);
16636
19938
SetObjectExtra (w, mrfp, CleanupFeatureSelRemConvForm);
16637
19939
mrfp->form = (ForM) w;
16661
19963
FeatureRemoveChangeNotify,
16662
19964
mrfp);
16663
19965
16664
mrfp->convert_grp = HiddenGroup (n, 2, 0, NULL);
19966
mrfp->convert_grp = HiddenGroup (n, 3, 0, NULL);
16665
19967
k = HiddenGroup (mrfp->convert_grp, 0, 2, NULL);
16666
19968
mrfp->from_prompt = StaticPrompt (k, "From", 0, dialogTextHeight, systemFont, 'l');
16667
19969
mrfp->feature_select_from = FeatureSelectionDialogEx (k, FALSE, sep,
16675
19977
mrfp);
16676
19978
AlignObjects (ALIGN_CENTER, (HANDLE) mrfp->to_prompt, (HANDLE) mrfp->feature_select_to, NULL);
16677
19979
AlignObjects (ALIGN_CENTER, (HANDLE) mrfp->remove_grp, (HANDLE) mrfp->convert_grp, NULL);
16678
mrfp->leave_original_feature_btn = CheckBox (mrfp->convert_grp, "Leave Original Feature", NULL);
19980
19981
g = HiddenGroup (mrfp->convert_grp, 0, 2, NULL);
19982
StaticPrompt (g, "Conversion Function", 0, dialogTextHeight, systemFont, 'c');
19983
SelectFont (systemFont);
19984
mrfp->help_text = DocumentPanel (g, stdCharWidth * 12, LineHeight () * (TALL_SELECTION_LIST + 1));
19985
19986
mrfp->leave_original_feature_btn = CheckBox (mrfp->convert_grp, "Leave Original Feature", FeatureRemoveChangeButton);
19987
SetObjectExtra (mrfp->leave_original_feature_btn, mrfp, NULL);
16679
19988
SetStatus (mrfp->leave_original_feature_btn, FALSE);
16680
19989
AlignObjects (ALIGN_CENTER, (HANDLE) k, (HANDLE) mrfp->leave_original_feature_btn, NULL);
16681
19990
16682
19991
mrfp->feat_list = NULL;
16683
mrfp->constraints = FilterGroup (h, TRUE, FALSE, TRUE, FALSE, "Where feature text");
19992
mrfp->constraints = FilterGroup (h, TRUE, FALSE, TRUE, FALSE, TRUE, "Where feature text");
16684
19993
mrfp->accept_cancel = AcceptCancelDialog (h, FeatureRemoveOrConvertAction, NULL, FeatureRemoveClear, FeatureRemoveClearText, (Pointer)mrfp, w);
16685
19994
AlignObjects (ALIGN_CENTER, (HANDLE) mrfp->action_choice,
16686
19995
(HANDLE) mrfp->clear_constraints_on_action_change,
16778
20087
FeatureRemoveChangeNotify,
16779
20088
mrfp);
16780
20089
16781
mrfp->constraints = FilterGroup (h, TRUE, FALSE, TRUE, FALSE, "Where feature text");
20090
mrfp->constraints = FilterGroup (h, TRUE, FALSE, TRUE, FALSE, FALSE, "Where feature text");
16782
20091
mrfp->accept_cancel = AcceptCancelDialog (h, SelectFeatureAction, NULL, FeatureRemoveClear, FeatureRemoveClearText, (Pointer)mrfp, w);
16783
20092
AlignObjects (ALIGN_CENTER, (HANDLE) mrfp->feature_select,
16784
20093
(HANDLE) mrfp->constraints,
16787
20096
Show (w);
16788
20097
}
16789
20098
20099
20100
typedef struct reverseintervalsform
20101
{
20102
FORM_MESSAGE_BLOCK
20103
DialoG feature_select;
20104
DialoG constraints;
20105
DialoG accept_cancel;
20106
20107
ValNodePtr feat_list;
20108
BaseFormPtr bfp;
20109
} ReverseIntervalsFormData, PNTR ReverseIntervalsFormPtr;
20110
20111
static void ReverseIntervalsChangeNotify (Pointer userdata)
20112
{
20113
ReverseIntervalsFormPtr fp;
20114
ValNodePtr err_list;
20115
20116
fp = (ReverseIntervalsFormPtr) userdata;
20117
if (fp == NULL) return;
20118
20119
err_list = TestDialog (fp->feature_select);
20120
20121
if (err_list == NULL)
20122
{
20123
EnableAcceptCancelDialogAccept (fp->accept_cancel);
20124
}
20125
else
20126
{
20127
DisableAcceptCancelDialogAccept (fp->accept_cancel);
20128
}
20129
ValNodeFree (err_list);
20130
}
20131
20132
static void ReverseIntervalsClearText (Pointer data)
20133
{
20134
ReverseIntervalsFormPtr mrfp;
20135
FilterSetPtr fsp;
20136
20137
mrfp = (ReverseIntervalsFormPtr) data;
20138
if (mrfp == NULL) return;
20139
20140
fsp = DialogToPointer (mrfp->constraints);
20141
FilterSetClearText (fsp);
20142
PointerToDialog (mrfp->constraints, fsp);
20143
FilterSetFree (fsp);
20144
}
20145
20146
static void ReverseIntervalsClear (Pointer data)
20147
{
20148
ReverseIntervalsFormPtr mrfp;
20149
20150
mrfp = (ReverseIntervalsFormPtr) data;
20151
if (mrfp == NULL) return;
20152
20153
PointerToDialog (mrfp->feature_select, NULL);
20154
PointerToDialog (mrfp->constraints, NULL);
20155
}
20156
20157
static void ReverseLocationIntervalOrder (SeqLocPtr slp)
20158
{
20159
SeqLocPtr subslp_list = NULL, subslp, subslp_next;
20160
PackSeqPntPtr pspp;
20161
Int4 pnt_num, swap;
20162
20163
if (slp == NULL
20164
|| slp->choice == SEQLOC_NULL
20165
|| slp->choice == SEQLOC_EMPTY
20166
|| slp->choice == SEQLOC_WHOLE
20167
|| slp->choice == SEQLOC_INT
20168
|| slp->choice == SEQLOC_PNT
20169
|| slp->choice == SEQLOC_BOND
20170
|| slp->choice == SEQLOC_FEAT) {
20171
return;
20172
}
20173
if (slp->choice == SEQLOC_MIX
20174
|| slp->choice == SEQLOC_PACKED_INT
20175
|| slp->choice == SEQLOC_EQUIV) {
20176
for (subslp = slp->data.ptrvalue;
20177
subslp != NULL;
20178
subslp = subslp_next) {
20179
subslp_next = subslp->next;
20180
subslp->next = subslp_list;
20181
subslp_list = subslp;
20182
ReverseLocationIntervalOrder (subslp);
20183
}
20184
slp->data.ptrvalue = subslp_list;
20185
} else if (slp->choice == SEQLOC_PACKED_PNT) {
20186
pspp = (PackSeqPntPtr) slp->data.ptrvalue;
20187
if (pspp != NULL) {
20188
for (pnt_num = 0; pnt_num < pspp->used / 2; pnt_num++) {
20189
swap = pspp->pnts[pnt_num];
20190
pspp->pnts[pnt_num] = pspp->pnts[pspp->used - 1 - pnt_num];
20191
pspp->pnts[pspp->used - 1 - pnt_num] = swap;
20192
}
20193
}
20194
}
20195
}
20196
20197
static void ReverseIntervalsCallback (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
20198
20199
{
20200
if (sfp == NULL || sfp->location == NULL) return;
20201
20202
ReverseLocationIntervalOrder (sfp->location);
20203
}
20204
20205
20206
static Boolean ReverseIntervalsAction (Pointer userdata)
20207
{
20208
ReverseIntervalsFormPtr mrfp;
20209
FilterSetPtr fsp;
20210
SeqEntryPtr sep;
20211
ValNodePtr feature_type_list, vnp;
20212
Uint1 feat_def_choice;
20213
20214
if (userdata == NULL) return FALSE;
20215
20216
mrfp = (ReverseIntervalsFormPtr) userdata;
20217
fsp = (FilterSetPtr) DialogToPointer (mrfp->constraints);
20218
20219
sep = GetTopSeqEntryForEntityID (mrfp->input_entityID);
20220
if (sep == NULL) return FALSE;
20221
20222
feature_type_list = (ValNodePtr) DialogToPointer (mrfp->feature_select);
20223
if (feature_type_list == NULL)
20224
{
20225
FilterSetFree (fsp);
20226
return FALSE;
20227
}
20228
20229
for (vnp = feature_type_list; vnp != NULL; vnp = vnp->next)
20230
{
20231
feat_def_choice = vnp->choice;
20232
if (feat_def_choice == 255)
20233
{
20234
feat_def_choice = 0;
20235
}
20236
OperateOnSeqEntryConstrainedObjects (sep, fsp,
20237
ReverseIntervalsCallback,
20238
NULL, 0, feat_def_choice, 0, NULL);
20239
}
20240
20241
ValNodeFree (feature_type_list);
20242
FilterSetFree (fsp);
20243
20244
ObjMgrSetDirtyFlag (mrfp->input_entityID, TRUE);
20245
ObjMgrSendMsg (OM_MSG_UPDATE, mrfp->input_entityID, 0, 0);
20246
Update ();
20247
return TRUE;
20248
}
20249
20250
extern void ReverseFeatureIntervals (IteM i)
20251
{
20252
BaseFormPtr bfp;
20253
ReverseIntervalsFormPtr fp;
20254
WindoW w;
20255
GrouP h;
20256
SeqEntryPtr sep;
20257
20258
#ifdef WIN_MAC
20259
bfp = currentFormDataPtr;
20260
#else
20261
bfp = GetObjectExtra (i);
20262
#endif
20263
if (bfp == NULL) return;
20264
20265
fp = (ReverseIntervalsFormPtr) MemNew (sizeof (ReverseIntervalsFormData));
20266
if (fp == NULL) return;
20267
20268
w = FixedWindow (-50, -33, -10, -10, "Reverse Feature Intervals", StdCloseWindowProc);
20269
SetObjectExtra (w, fp, StdCleanupFormProc);
20270
fp->form = (ForM) w;
20271
fp->input_entityID = bfp->input_entityID;
20272
sep = GetTopSeqEntryForEntityID(bfp->input_entityID);
20273
20274
h = HiddenGroup (w, -1, 0, NULL);
20275
SetGroupSpacing (h, 10, 10);
20276
20277
fp->feature_select = FeatureSelectionDialogEx (h, TRUE, sep,
20278
ReverseIntervalsChangeNotify,
20279
fp);
20280
20281
fp->constraints = FilterGroup (h, TRUE, FALSE, TRUE, FALSE, FALSE, "Where feature text");
20282
fp->accept_cancel = AcceptCancelDialog (h, ReverseIntervalsAction, NULL, ReverseIntervalsClear, ReverseIntervalsClearText, (Pointer)fp, w);
20283
AlignObjects (ALIGN_CENTER, (HANDLE) fp->feature_select,
20284
(HANDLE) fp->constraints,
20285
(HANDLE) fp->accept_cancel, NULL);
20286
20287
Show (w);
20288
}
20289
20290
20291
16790
20292
extern ParseFieldPtr ParseFieldFree (ParseFieldPtr pfp)
16791
20293
{
16792
20294
if (pfp != NULL)
16793
20295
{
16794
pfp->feature_field = ValNodeFreeData (pfp->feature_field);
16795
pfp->feature_subtype = ValNodeFreeData (pfp->feature_subtype);
20296
switch (pfp->parse_field_type) {
20297
case PARSE_FIELD_SOURCE_QUAL :
20298
case PARSE_FIELD_FEATURE_NOTE:
20299
case PARSE_FIELD_DBXREF:
20300
pfp->feature_field = ValNodeFreeData (pfp->feature_field);
20301
break;
20302
case PARSE_FIELD_DEFLINE:
20303
case PARSE_FIELD_BIOSRC_STRING:
20304
case PARSE_FIELD_GENE_FIELD:
20305
case PARSE_FIELD_RNA_FIELD:
20306
case PARSE_FIELD_CDS_COMMENT:
20307
case PARSE_FIELD_COMMENT_DESC:
20308
case PARSE_FIELD_IMPORT_QUAL:
20309
case PARSE_FIELD_PROTEIN_FIELD:
20310
pfp->feature_field = ValNodeFree (pfp->feature_field);
20311
break;
20312
default:
20313
pfp->feature_field = ValNodeFree (pfp->feature_field);
20314
}
20315
20316
if (pfp->parse_field_type == PARSE_FIELD_RNA_FIELD)
20317
{
20318
pfp->feature_subtype = ValNodeFree (pfp->feature_subtype);
20319
}
20320
else
20321
{
20322
pfp->feature_subtype = ValNodeFreeData (pfp->feature_subtype);
20323
}
16796
20324
pfp = MemFree (pfp);
16797
20325
}
16798
20326
return pfp;
16806
20334
DialoG destination_field;
16807
20335
DialoG accept_cancel;
16808
20336
ButtoN remove_from_parsed;
20337
DialoG change_case_dlg;
16809
20338
16810
20339
ParseFieldPtr dst_field_data;
16811
20340
GetSamplePtr gsp;
16812
20341
ExistingTextPtr etp;
20342
ChangeCasePtr change_case;
16813
20343
} ParseFormData, PNTR ParseFormPtr;
16814
20344
16815
20345
static void CleanupParseForm (GraphiC g, VoidPtr data)
16821
20351
{
16822
20352
mp->gsp = GetSampleFree (mp->gsp);
16823
20353
mp->etp = MemFree (mp->etp);
20354
mp->change_case = MemFree (mp->change_case);
16824
20355
}
16825
20356
StdCleanupExtraProc (g, data);
16826
20357
}
16874
20405
SEQFEAT_BIOSRC, 0,
16875
20406
Seq_descr_source);
16876
20407
break;
20408
case PARSE_FIELD_DBXREF:
20409
gsp = CheckForExistingTextInSeqEntry (sep,
20410
dst_field_data->feature_field,
20411
GetBioSourceFeatureDbxrefString,
20412
GetBioSourceDescriptorDbxrefString,
20413
ValNodeSimpleDataFree, ValNodeStringCopy,
20414
fsp,
20415
SEQFEAT_BIOSRC, 0,
20416
Seq_descr_source);
20417
break;
16877
20418
case PARSE_FIELD_GENE_FIELD:
16878
20419
gsp = CheckForExistingTextInSeqEntry (sep,
16879
20420
dst_field_data->feature_field,
16883
20424
fsp,
16884
20425
SEQFEAT_GENE, 0, 0);
16885
20426
break;
16886
case PARSE_FIELD_MRNA_FIELD:
20427
case PARSE_FIELD_RNA_FIELD:
16887
20428
gsp = CheckForExistingTextInSeqEntry (sep,
16888
20429
dst_field_data->feature_field,
16889
GetmRNAFieldString,
20430
GetRNAFieldString,
16890
20431
NULL,
16891
20432
NULL, IntValNodeCopy,
16892
20433
fsp,
16893
SEQFEAT_RNA, FEATDEF_mRNA, 0);
20434
SEQFEAT_RNA,
20435
dst_field_data->feature_subtype == NULL ? 0 : dst_field_data->feature_subtype->data.intvalue, 0);
16894
20436
break;
16895
20437
case PARSE_FIELD_CDS_COMMENT:
16896
20438
gsp = CheckForExistingTextInSeqEntry (sep,
16992
20534
return gsp;
16993
20535
}
16994
20536
16995
static void GetParseToExistingTextCallback (ParseActionPtr pap, Pointer userdata, CharPtr found_text, Int4 found_len)
16996
{
16997
ParseFormPtr mp;
16998
GetSamplePtr gsp = NULL;
16999
SeqEntryPtr sep;
17000
ValNodePtr sum_vnp;
17001
17002
mp = (ParseFormPtr) userdata;
17003
if (mp == NULL || mp->dst_field_data == NULL)
17004
{
17005
return;
17006
}
17007
17008
if (mp->dst_field_data->parse_field_type == PARSE_FIELD_SOURCE_QUAL
17009
|| mp->dst_field_data->parse_field_type == PARSE_FIELD_BIOSRC_STRING)
17010
{
17011
sep = pap->biop_sep;
17012
}
17013
else if (mp->dst_field_data->parse_field_type == PARSE_FIELD_DEFLINE)
17014
{
17015
sep = pap->title_sep;
17016
}
17017
else
17018
{
17019
sep = pap->sep;
17020
}
17021
17022
gsp = GetSampleForSeqEntry (sep, mp->input_entityID, mp->dst_field_data, NULL);
17023
17024
if (gsp == NULL)
17025
{
17026
return;
17027
}
17028
if (mp->gsp == NULL)
17029
{
17030
mp->gsp = gsp;
17031
}
17032
else
17033
{
17034
mp->gsp->num_found += gsp->num_found;
17035
if (StringCmp (mp->gsp->sample_text, gsp->sample_text) != 0)
17036
{
17037
mp->gsp->all_same = FALSE;
17038
}
17039
17040
sum_vnp = AddValNodeLists (mp->gsp->feat_dest_list, gsp->feat_dest_list);
17041
mp->gsp->feat_dest_list = ValNodeFree (mp->gsp->feat_dest_list);
17042
mp->gsp->feat_dest_list = sum_vnp;
17043
17044
sum_vnp = AddValNodeLists (mp->gsp->descr_dest_list, gsp->descr_dest_list);
17045
mp->gsp->descr_dest_list = ValNodeFree (mp->gsp->descr_dest_list);
17046
mp->gsp->descr_dest_list = sum_vnp;
17047
17048
gsp = GetSampleFree (gsp);
17049
}
17050
}
17051
17052
20537
static void
17053
20538
ParseToFeaturesOnBioseq
17054
20539
(BioseqPtr bsp,
17079
20564
prot_bsp = BioseqFindFromSeqLoc (sfp->product);
17080
20565
if (prot_bsp == NULL)
17081
20566
{
17082
SeqEdTranslateOneCDS (sfp, bsp, sfp->idx.entityID);
20567
SeqEdTranslateOneCDS (sfp, bsp, sfp->idx.entityID, Sequin_GlobalAlign2Seq);
17083
20568
SeqMgrIndexFeatures (sfp->idx.entityID, NULL);
17084
20569
prot_bsp = BioseqFindFromSeqLoc (sfp->product);
17085
20570
}
17159
20644
case PARSE_FIELD_GENE_FIELD :
17160
20645
set_string_func = SetGeneFieldString;
17161
20646
break;
17162
case PARSE_FIELD_MRNA_FIELD :
17163
set_string_func = SetmRNAFieldString;
20647
case PARSE_FIELD_RNA_FIELD :
20648
set_string_func = SetRNAFieldString;
17164
20649
break;
17165
20650
case PARSE_FIELD_CDS_COMMENT:
17166
20651
set_string_func = SetCDSComment;
17256
20741
avd.new_text [found_len] = 0;
17257
20742
avd.etp = mp->etp;
17258
20743
avd.text_to_replace = NULL;
20744
avd.where_to_replace = EditApplyFindLocation_anywhere;
17259
20745
17260
20746
switch (mp->dst_field_data->parse_field_type)
17261
20747
{
17281
20767
ApplySourceStringFeatureCallback,
17282
20768
ApplySourceStringDescriptorCallback,
17283
20769
0, 0, 0, &avd);
20770
case PARSE_FIELD_DBXREF :
20771
avd.field_list = mp->dst_field_data->feature_field;
20772
OperateOnSeqEntryConstrainedObjects (pap->biop_sep, NULL,
20773
ApplyBioSourceDbxrefFeatureCallback,
20774
ApplyBioSourceDbxrefDescriptorCallback,
20775
0, 0, 0, &avd);
20776
break;
17284
20777
case PARSE_FIELD_GENE_FIELD :
17285
20778
avd.field_list = mp->dst_field_data->feature_field;
17286
20779
ParseToFeatures (pap->sep, &avd, mp->dst_field_data->parse_field_type,
17287
20780
FEATDEF_GENE);
17288
20781
break;
17289
case PARSE_FIELD_MRNA_FIELD :
20782
case PARSE_FIELD_RNA_FIELD :
17290
20783
avd.field_list = mp->dst_field_data->feature_field;
17291
20784
ParseToFeatures (pap->sep, &avd, mp->dst_field_data->parse_field_type,
17292
FEATDEF_mRNA);
20785
mp->dst_field_data->feature_subtype == NULL ? 0 : mp->dst_field_data->feature_subtype->data.intvalue);
17293
20786
break;
17294
20787
case PARSE_FIELD_CDS_COMMENT:
17295
20788
avd.field_list = NULL;
17374
20867
NULL,
17375
20868
SEQFEAT_BIOSRC, 0, Seq_descr_source);
17376
20869
break;
20870
case PARSE_FIELD_DBXREF:
20871
gsp = CheckForExistingTextInSeqEntry (sep, dst_field_data->feature_field,
20872
GetBioSourceFeatureDbxrefString,
20873
GetBioSourceDescriptorDbxrefString,
20874
ValNodeSimpleDataFree,
20875
ValNodeStringCopy,
20876
NULL,
20877
SEQFEAT_BIOSRC, 0, Seq_descr_source);
20878
break;
17377
20879
case PARSE_FIELD_GENE_FIELD:
17378
20880
gsp = CheckForExistingTextInSeqEntry (sep, dst_field_data->feature_field,
17379
20881
GetGeneFieldString,
17381
20883
NULL, IntValNodeCopy,
17382
20884
NULL, SEQFEAT_GENE, 0, 0);
17383
20885
break;
17384
case PARSE_FIELD_MRNA_FIELD:
20886
case PARSE_FIELD_RNA_FIELD:
17385
20887
gsp = CheckForExistingTextInSeqEntry (sep, dst_field_data->feature_field,
17386
GetmRNAFieldString,
20888
GetRNAFieldString,
17387
20889
NULL,
17388
20890
NULL, IntValNodeCopy,
17389
NULL, SEQFEAT_RNA, FEATDEF_mRNA, 0);
20891
NULL, SEQFEAT_RNA, dst_field_data->feature_subtype == NULL ? 0 : dst_field_data->feature_subtype->data.intvalue, 0);
17390
20892
break;
17391
20893
case PARSE_FIELD_CDS_COMMENT:
17392
20894
gsp = CheckForExistingTextInSeqEntry (sep, NULL,
17450
20952
return gsp;
17451
20953
}
17452
20954
17453
static Boolean ParseFileToDest (ParseFormPtr mp, FilterSetPtr fsp, TextPortionPtr tp, SeqEntryPtr sep)
20955
20956
static GetSamplePtr GetFlatFileParseProteinFieldSamples (Uint2 entityID, SeqEntryPtr sep, GetSamplePtr gsp, ParseFieldPtr dst_field_data)
17454
20957
{
17455
ParseActionData pad;
17456
FILE *fp;
17457
Char path [PATH_MAX];
17458
ReadBufferData rbd;
17459
CharPtr line;
17460
CharPtr found_loc = NULL;
17461
Int4 found_len = 0;
17462
GetSamplePtr gsp;
17463
17464
if (mp == NULL || tp == NULL || sep == NULL)
17465
{
17466
return FALSE;
17467
}
17468
ResetParseActionVisitData (&pad);
17469
pad.fsp = fsp;
17470
pad.tp = tp;
17471
17472
gsp = GetDestSample (sep, mp->dst_field_data);
17473
mp->etp = GetExistingTextHandlerInfo (gsp, FALSE);
17474
gsp = GetSampleFree (gsp);
17475
if (mp->etp != NULL && mp->etp->existing_text_choice == EXISTING_TEXT_CHOICE_CANCEL)
17476
{
17477
mp->etp = MemFree (mp->etp);
17478
return FALSE;
17479
}
17480
17481
17482
if (! GetInputFileName (path, sizeof (path), "", "TEXT"))
17483
{
17484
mp->etp = MemFree (mp->etp);
17485
return FALSE;
17486
}
17487
17488
fp = FileOpen (path, "r");
17489
if (fp == NULL)
17490
{
17491
Message (MSG_ERROR, "Unable to open %s", path);
17492
mp->etp = MemFree (mp->etp);
17493
return FALSE;
17494
}
17495
17496
ResetParseActionVisitData (&pad);
17497
pad.sep = sep;
17498
pad.title_sep = sep;
17499
pad.biop_sep = sep;
17500
17501
rbd.fp = fp;
17502
rbd.current_data = NULL;
17503
line = AbstractReadFunction (&rbd);
17504
while (line != NULL)
17505
{
17506
found_loc = NULL;
17507
found_len = 0;
17508
FindTextPortionInString (line, tp, &found_loc, &found_len);
17509
17510
if (found_loc != NULL)
17511
{
17512
ParseToDest (&pad, mp, found_loc, found_len);
20958
SeqEntryPtr parent_sep, prot_sep;
20959
BioseqSetPtr bssp;
20960
GetSamplePtr new_gsp, sum_gsp;
20961
20962
if (sep == NULL) return gsp;
20963
20964
parent_sep = GetBestTopParentForData (entityID, sep->data.ptrvalue);
20965
20966
if (parent_sep != NULL && IS_Bioseq_set (parent_sep)) {
20967
bssp = (BioseqSetPtr) parent_sep->data.ptrvalue;
20968
if (bssp != NULL && bssp->_class == BioseqseqSet_class_nuc_prot && bssp->seq_set != NULL) {
20969
prot_sep = bssp->seq_set->next;
20970
while (prot_sep != NULL) {
20971
new_gsp = GetDestSample (prot_sep, dst_field_data);
20972
sum_gsp = GetSampleAdd (gsp, new_gsp);
20973
gsp = GetSampleFree (gsp);
20974
new_gsp = GetSampleFree (new_gsp);
20975
gsp = sum_gsp;
20976
sum_gsp = NULL;
20977
prot_sep = prot_sep->next;
20978
}
17513
20979
}
17514
line = AbstractReadFunction (&rbd);
17515
20980
}
17516
17517
FileClose (fp);
17518
mp->etp = MemFree (mp->etp);
17519
17520
ObjMgrSetDirtyFlag (mp->input_entityID, TRUE);
17521
ObjMgrSendMsg (OM_MSG_UPDATE, mp->input_entityID, 0, 0);
17522
ArrowCursor ();
17523
Update ();
17524
return TRUE;
20981
return gsp;
17525
20982
}
17526
20983
17527
20984
static GetSamplePtr
17577
21034
string = asn2gnbk_format (ajp, (Int4) index);
17578
21035
if (string != NULL && *string != '\0') {
17579
21036
CompressSpaces (string);
17580
FindTextPortionInString (string, pap->tp, &found_loc, &found_len);
21037
FindTextPortionXInString (string, pap->tp, &found_loc, &found_len);
17581
21038
17582
21039
if (found_loc != NULL)
17583
21040
{
17592
21049
new_gsp = GetSampleFree (new_gsp);
17593
21050
gsp = sum_gsp;
17594
21051
sum_gsp = NULL;
21052
if (mp->dst_field_data->parse_field_type == PARSE_FIELD_PROTEIN_FIELD) {
21053
/* also get samples from protein bioseqs in this nuc-prot set */
21054
gsp = GetFlatFileParseProteinFieldSamples (mp->input_entityID, pap->sep, gsp, mp->dst_field_data);
21055
}
17595
21056
}
17596
21057
}
17597
21058
MemFree (string);
17666
21127
string = asn2gnbk_format (ajp, (Int4) index);
17667
21128
if (string != NULL && *string != '\0') {
17668
21129
CompressSpaces (string);
17669
FindTextPortionInString (string, pap->tp, &found_loc, &found_len);
21130
FindTextPortionXInString (string, pap->tp, &found_loc, &found_len);
17670
21131
17671
21132
if (found_loc != NULL)
17672
21133
{
17705
21166
{
17706
21167
ParseFormPtr mp;
17707
21168
SeqEntryPtr sep;
17708
Char path [PATH_MAX];
17709
ParseActionLogData pald;
17710
21169
ParseActionData pad;
17711
21170
Boolean rval = FALSE;
17712
ParseFieldSrcPtr pfsp;
21171
ParseFieldSrcPtr pfsp;
21172
SourceQualDescPtr sqdp;
17713
21173
Boolean remove_from_parsed = FALSE;
17714
21174
17715
21175
mp = (ParseFormPtr) data;
17726
21186
17727
21187
pfsp = DialogToPointer (mp->source_field);
17728
21188
if (pfsp == NULL
17729
|| pfsp->parse_field < PARSE_FIELD_SRC_DEFLINE
21189
|| pfsp->parse_field < eParseFieldSrcDefLine
17730
21190
|| pfsp->parse_field > MAX_PARSE_FIELD
17731
|| (pfsp->parse_field == PARSE_FIELD_STRUCTURED_COMMENT && StringHasNoText (pfsp->comment_field)))
21191
|| (pfsp->parse_field == eParseFieldSrcStructuredComment && StringHasNoText (pfsp->comment_field))
21192
|| (pfsp->parse_field == eParseFieldSrcSourceQual && pfsp->sqdp == NULL))
17732
21193
{
17733
21194
pfsp = ParseFieldSrcFree (pfsp);
17734
21195
return FALSE;
17736
21197
pad.src_field = pfsp->parse_field;
17737
21198
pad.comment_field = pfsp->comment_field;
17738
21199
pfsp->comment_field = NULL;
21200
sqdp = pfsp->sqdp;
21201
pfsp->sqdp = NULL;
17739
21202
pfsp = ParseFieldSrcFree (pfsp);
17740
21203
17741
21204
pad.tp = DialogToPointer (mp->text_portion);
17743
21206
pad.biop_sep = sep;
17744
21207
pad.title_sep = sep;
17745
21208
mp->dst_field_data = DialogToPointer (mp->destination_field);
21209
21210
mp->change_case = DialogToPointer (mp->change_case_dlg);
17746
21211
17747
if (pad.src_field == PARSE_FIELD_SRC_GENBANK_FLATFILE)
21212
if (pad.src_field == eParseFieldSrcGenBankFlatFile)
17748
21213
{
17749
21214
WatchCursor ();
17750
21215
ResetParseActionVisitData (&pad);
17751
21216
17752
21217
mp->gsp = ParseFlatfileForSample (sep, &pad, mp, GENBANK_FMT, NULL);
17753
mp->etp = GetExistingTextHandlerInfo (mp->gsp, FALSE);
21218
mp->etp = GetExistingTextHandlerInfo (mp->gsp == NULL ? 0 : mp->gsp->num_found, FALSE);
17754
21219
mp->gsp = GetSampleFree (mp->gsp);
17755
if (mp->etp == NULL || mp->etp->existing_text_choice != EXISTING_TEXT_CHOICE_CANCEL)
21220
if (mp->etp == NULL || mp->etp->existing_text_choice != eExistingTextChoiceCancel)
17756
21221
{
17757
21222
ResetParseActionVisitData (&pad);
17758
21223
pad.biop_sep = sep;
17773
21238
case PARSE_FIELD_DEFLINE:
17774
21239
case PARSE_FIELD_BIOSRC_STRING:
17775
21240
case PARSE_FIELD_GENE_FIELD:
17776
case PARSE_FIELD_MRNA_FIELD:
21241
case PARSE_FIELD_RNA_FIELD:
17777
21242
case PARSE_FIELD_CDS_COMMENT:
17778
21243
case PARSE_FIELD_PROTEIN_FIELD:
17779
21244
case PARSE_FIELD_IMPORT_QUAL:
17780
21245
case PARSE_FIELD_FEATURE_NOTE:
17781
21246
case PARSE_FIELD_COMMENT_DESC:
21247
case PARSE_FIELD_DBXREF:
17782
21248
WatchCursor ();
17783
21249
Update ();
17784
21250
17786
21252
remove_from_parsed = GetStatus(mp->remove_from_parsed);
17787
21253
}
17788
21254
17789
rval = FindParseActionPairList (sep, pad.src_field, pad.comment_field, mp->dst_field_data, pad.fsp, pad.tp, remove_from_parsed);
21255
rval = FindParseActionPairList (sep, pad.src_field, sqdp, pad.comment_field, mp->dst_field_data, pad.fsp, pad.tp, remove_from_parsed, mp->change_case);
17790
21256
ObjMgrSetDirtyFlag (mp->input_entityID, TRUE);
17791
21257
ObjMgrSendMsg (OM_MSG_UPDATE, mp->input_entityID, 0, 0);
17792
21258
ArrowCursor ();
17793
21259
Update ();
17794
21260
break;
17795
21261
default:
17796
pald.data_in_log = FALSE;
17797
TmpNam (path);
17798
pald.fp = FileOpen (path, "wb");
17799
if (pald.fp != NULL)
17800
{
17801
VisitSeqEntriesForParseAction (sep, &pad, ParseActionSample, &pald, FALSE);
17802
FileClose (pald.fp);
17803
LaunchGeneralTextViewer (path, "Found Text");
17804
FileRemove (path);
17805
rval = TRUE;
17806
}
21262
Message (MSG_ERROR, "Unknown destination");
17807
21263
break;
17808
21264
}
17809
21265
}
17810
21266
17811
pad.tp = TextPortionFree (pad.tp);
21267
pad.tp = TextPortionXFree (pad.tp);
17812
21268
pad.comment_field = MemFree (pad.comment_field);
17813
21269
FilterSetFree (pad.fsp);
17814
21270
return rval;
17832
21288
static void ParseFormClearText (Pointer data)
17833
21289
{
17834
21290
ParseFormPtr mp;
17835
TextPortionPtr tp;
21291
TextPortionXPtr tp;
17836
21292
17837
21293
mp = (ParseFormPtr) data;
17838
21294
if (mp == NULL)
17880
21336
/* only allow remove_from_parsed if not parsing from flatfile or local ID */
17881
21337
pfsp = DialogToPointer (mp->source_field);
17882
21338
if (pfsp != NULL
17883
&& (pfsp->parse_field == PARSE_FIELD_SRC_GENBANK_FLATFILE
17884
|| pfsp->parse_field == PARSE_FIELD_SRC_LOCAL_ID)) {
21339
&& (pfsp->parse_field == eParseFieldSrcGenBankFlatFile
21340
|| pfsp->parse_field == eParseFieldSrcLocalID
21341
|| pfsp->parse_field == eParseFieldSrcFileID)) {
17885
21342
Disable (mp->remove_from_parsed);
17886
21343
} else {
17887
21344
Enable (mp->remove_from_parsed);
17916
21373
17917
21374
g1 = HiddenGroup (h, 2, 0, NULL);
17918
21375
StaticPrompt (g1, "Select text", 0, dialogTextHeight, systemFont, 'l');
17919
mp->text_portion = TextPortionDialog (g1);
21376
mp->text_portion = TextPortionXDialog (g1);
17920
21377
17921
21378
g2 = HiddenGroup (h, 2, 0, NULL);
17922
21379
StaticPrompt (g2, "From", 0, dialogTextHeight, systemFont, 'l');
17924
21381
17925
21382
g3 = HiddenGroup (h, 2, 0, NULL);
17926
21383
StaticPrompt (g3, "And place in", 0, dialogTextHeight, systemFont, 'l');
17927
mp->destination_field = ParseFieldDestDialog (g3, ParseChangeNotify, mp);
21384
mp->destination_field = ParseFieldDestDialogEx (g3, ParseChangeNotify, mp, FALSE, TRUE);
17928
21385
21386
mp->change_case_dlg = ChangeCaseDialog (h);
21387
17929
21388
mp->remove_from_parsed = CheckBox (h, "Remove from parsed field", NULL);
17930
21389
17931
21390
mp->accept_cancel = AcceptCancelDialog (h, ParseTextAction, NULL, ParseFormClear, ParseFormClearText, (Pointer)mp, w);
17932
21391
AlignObjects (ALIGN_CENTER, (HANDLE) g1,
17933
21392
(HANDLE) g2,
17934
21393
(HANDLE) g3,
21394
(HANDLE) mp->change_case_dlg,
17935
21395
(HANDLE) mp->remove_from_parsed,
17936
21396
(HANDLE) mp->accept_cancel,
17937
21397
NULL);
17941
21401
{
17942
21402
pfsd.parse_field = from_field;
17943
21403
pfsd.comment_field = NULL;
21404
pfsd.sqdp = NULL;
17944
21405
PointerToDialog (mp->source_field, &pfsd);
17945
21406
}
17946
21407
if (to_field > 0)
17968
21429
17969
21430
extern void ParseDefLineToSourceQual (IteM i)
17970
21431
{
17971
ParseTextItem (i, PARSE_FIELD_SRC_DEFLINE, PARSE_FIELD_SOURCE_QUAL);
21432
ParseTextItem (i, eParseFieldSrcDefLine, PARSE_FIELD_SOURCE_QUAL);
21433
}
21434
21435
extern void ParseTaxnameToSourceQual (IteM i)
21436
{
21437
ParseTextItem (i, eParseFieldSrcTaxNameAfterNomial, PARSE_FIELD_SOURCE_QUAL);
17972
21438
}
17973
21439
17974
21440
extern void ParseFlatfileToSourceQual (IteM i)
17975
21441
{
17976
ParseTextItem (i, PARSE_FIELD_SRC_GENBANK_FLATFILE, PARSE_FIELD_SOURCE_QUAL);
21442
ParseTextItem (i, eParseFieldSrcGenBankFlatFile, PARSE_FIELD_SOURCE_QUAL);
17977
21443
}
17978
21444
17979
21445
static void ParseTextToolBtn (ButtoN b, Int4 from_field, Int4 to_field)
17988
21454
17989
21455
extern void ParseLocalIDToSourceQual (ButtoN b)
17990
21456
{
17991
ParseTextToolBtn (b, PARSE_FIELD_SRC_LOCAL_ID, PARSE_FIELD_SOURCE_QUAL);
21457
ParseTextToolBtn (b, eParseFieldSrcLocalID, PARSE_FIELD_SOURCE_QUAL);
17992
21458
}
17993
21459
17994
21460
18066
21532
GrouP pseudo_action;
18067
21533
Boolean pseudo_val;
18068
21534
21535
/* for inferences */
21536
DialoG inference_dlg;
18069
21537
} FeatEdData, PNTR FeatEdPtr;
18070
21538
18071
21539
static void FeatEdChangeNotify (Pointer userdata)
18101
21569
}
18102
21570
18103
21571
err_list = TestDialog (mp->feature_select);
21572
21573
if (GetValue (mp->action_choice_grp) == FEAT_ED_INFERENCE)
21574
{
21575
ValNodeLink (&err_list, TestDialog (mp->inference_dlg));
21576
}
18104
21577
18105
21578
if (err_list == NULL)
18106
21579
{
18399
21872
18400
21873
static GrouP FeatureEditorPartialGroup (GrouP h, FeatEdPtr mp)
18401
21874
{
18402
GrouP g, k1, k2;
21875
GrouP g, g1, g2,k1, k2;
21876
PrompT p1, p2;
18403
21877
18404
21878
if (mp == NULL)
18405
21879
{
18406
21880
return NULL;
18407
21881
}
18408
21882
18409
g = HiddenGroup (h, -1, 0, NULL);
21883
g = HiddenGroup (h, 2, 0, NULL);
18410
21884
SetGroupSpacing (g, 10, 10);
18411
18412
mp->convert_choice = PopupList (g, TRUE, NULL);
18413
PopupItem (mp->convert_choice, "Do not convert location");
18414
PopupItem (mp->convert_choice, "Convert location to join");
18415
PopupItem (mp->convert_choice, "Convert location to order");
18416
PopupItem (mp->convert_choice, "Convert location to single interval");
18417
SetValue (mp->convert_choice, 1);
18418
18419
k1 = HiddenGroup (g, 2, 0, NULL);
21885
StaticPrompt (g, "", 0, dialogTextHeight, systemFont, 'l');
21886
StaticPrompt (g, "", 0, dialogTextHeight, systemFont, 'l');
21887
21888
p1 = StaticPrompt (g, "Partials:", 0, dialogTextHeight, systemFont, 'l');
21889
g1 = NormalGroup (g, 1, 0, "", programFont, NULL);
21890
k1 = HiddenGroup (g1, 2, 0, NULL);
21891
18420
21892
SetGroupSpacing (k1, 10, 10);
18421
21893
StaticPrompt (k1, "5' partial:", 0, dialogTextHeight, systemFont, 'l');
18422
21894
mp->partial5_choice = PopupList (k1, TRUE, NULL);
18430
21902
PopupItem (mp->partial5_choice, "Do not change");
18431
21903
SetValue (mp->partial5_choice, 8);
18432
21904
18433
mp->extend5_btn = CheckBox (g, "Extend to 5' end of sequence if setting 5' partial", NULL);
18434
18435
k2 = HiddenGroup (g, 2, 0, NULL);
21905
mp->extend5_btn = CheckBox (g1, "Extend to 5' end of sequence if setting 5' partial", NULL);
21906
21907
StaticPrompt (g1, "", 0, dialogTextHeight, systemFont, 'l');
21908
21909
k2 = HiddenGroup (g1, 2, 0, NULL);
18436
21910
SetGroupSpacing (k2, 10, 10);
18437
21911
StaticPrompt (k2, "3' partial:", 0, dialogTextHeight, systemFont, 'l');
18438
21912
mp->partial3_choice = PopupList (k2, TRUE, NULL);
18445
21919
PopupItem (mp->partial3_choice, "Do not change");
18446
21920
SetValue (mp->partial3_choice, 7);
18447
21921
18448
mp->extend3_btn = CheckBox (g, "Extend to 3' end of sequence if setting 3' partial", NULL);
18449
18450
AlignObjects (ALIGN_CENTER, (HANDLE) mp->convert_choice,
18451
(HANDLE) k1,
18452
(HANDLE) mp->extend5_btn,
18453
(HANDLE) k2,
18454
(HANDLE) mp->extend3_btn,
18455
NULL);
21922
mp->extend3_btn = CheckBox (g1, "Extend to 3' end of sequence if setting 3' partial", NULL);
21923
21924
p2 = StaticPrompt (g, "Join/Order/Merge:", 0, dialogTextHeight, systemFont, 'l');
21925
g2 = NormalGroup (g, 1, 0, "", programFont, NULL);
21926
mp->convert_choice = PopupList (g2, TRUE, NULL);
21927
PopupItem (mp->convert_choice, "Do not convert location");
21928
PopupItem (mp->convert_choice, "Convert location to join");
21929
PopupItem (mp->convert_choice, "Convert location to order");
21930
PopupItem (mp->convert_choice, "Convert location to single interval");
21931
SetValue (mp->convert_choice, 1);
18456
21932
18457
21933
return g;
18458
21934
}
18533
22009
18534
22010
g = HiddenGroup (h, 1, 0, NULL);
18535
22011
SetGroupSpacing (g, 10, 10);
18536
StaticPrompt (g, "Hit Accept to remove all inferences", 0, dialogTextHeight, systemFont, 'l');
22012
22013
mp->inference_dlg = CreateInferenceEditDialog (g, FeatEdChangeNotify, mp);
18537
22014
return g;
18538
22015
}
18539
22016
18584
22061
SetObjectExtra (mp->action_choice_grp, mp, NULL);
18585
22062
RadioButton (mp->action_choice_grp, "Evidence");
18586
22063
RadioButton (mp->action_choice_grp, "Exceptions");
18587
RadioButton (mp->action_choice_grp, "Partials");
22064
RadioButton (mp->action_choice_grp, "Location");
18588
22065
RadioButton (mp->action_choice_grp, "Strands");
18589
22066
RadioButton (mp->action_choice_grp, "Citations");
18590
22067
RadioButton (mp->action_choice_grp, "Experiment");
18640
22117
sfp->pseudo = mp->pseudo_val;
18641
22118
}
18642
22119
22120
22121
static Boolean DoesInferenceMatchCategory (CharPtr inf_cat, CharPtr match_cat)
22122
{
22123
if (StringHasNoText (inf_cat)) return FALSE;
22124
22125
if (StringHasNoText (match_cat)
22126
|| StringICmp (match_cat, "ANY") == 0
22127
|| StringICmp (inf_cat, match_cat) == 0)
22128
{
22129
return TRUE;
22130
}
22131
else
22132
{
22133
return FALSE;
22134
}
22135
22136
}
22137
22138
#define AECR_APPLY 1
22139
#define AECR_EDIT 2
22140
#define AECR_CONVERT 3
22141
#define AECR_SWAP 4
22142
#define AECR_PARSE 5
22143
#define AECR_REMOVE 6
22144
#define NUM_AECR 6
22145
22146
static void
22147
AddEditApplyDataToApplyValue
22148
(Int4 action_choice,
22149
EditApplyPtr edit_apply,
22150
ApplyValuePtr avp);
22151
22152
22153
static void DoInferenceFeatureProc (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
22154
{
22155
InferenceEditPtr iep;
22156
GBQualPtr gbqual, gbqual_last = NULL, gbqual_next;
22157
CharPtr new_val;
22158
InferenceParsePtr ipp;
22159
Boolean changed;
22160
ApplyValueData avd;
22161
22162
iep = (InferenceEditPtr) userdata;
22163
22164
if (iep == NULL || sfp == NULL) return;
22165
22166
/* apply requested changes */
22167
gbqual = sfp->qual;
22168
while (gbqual != NULL)
22169
{
22170
gbqual_next = gbqual->next;
22171
if (StringCmp (gbqual->qual, "inference") == 0)
22172
{
22173
if (iep->action == eInferenceRemove)
22174
{
22175
if (gbqual_last == NULL)
22176
{
22177
sfp->qual = gbqual->next;
22178
}
22179
else
22180
{
22181
gbqual_last->next = gbqual->next;
22182
}
22183
gbqual->next = NULL;
22184
GBQualFree (gbqual);
22185
}
22186
else
22187
{
22188
/* perform editing here */
22189
ipp = ParseInferenceText (gbqual->val);
22190
changed = FALSE;
22191
if (ipp != NULL)
22192
{
22193
switch (iep->action)
22194
{
22195
case eInferenceEditCategory:
22196
if (DoesInferenceMatchCategory(ipp->category, iep->category_from))
22197
{
22198
ipp->category = MemFree (ipp->category);
22199
ipp->category = StringSave (iep->category_to);
22200
changed = TRUE;
22201
}
22202
break;
22203
case eInferenceApplyCategoryFields:
22204
case eInferenceEditCategoryFields:
22205
if (iep->field_edit != NULL
22206
&& iep->field_edit->edit_apply != NULL
22207
&& DoesInferenceMatchCategory (ipp->category, iep->field_edit->field_category))
22208
{
22209
avd.where_to_replace = EditApplyFindLocation_anywhere;
22210
avd.field_list = NULL;
22211
avd.etp = NULL;
22212
AddEditApplyDataToApplyValue (iep->action == eInferenceApplyCategoryFields ? AECR_APPLY : AECR_EDIT,
22213
iep->field_edit->edit_apply, &avd);
22214
if (iep->field_edit->field_choice == 0)
22215
{
22216
ipp->first_field = HandleApplyValue (ipp->first_field, &avd);
22217
}
22218
else
22219
{
22220
ipp->second_field = HandleApplyValue (ipp->second_field, &avd);
22221
}
22222
avd.text_to_replace = MemFree (avd.text_to_replace);
22223
avd.new_text = MemFree (avd.new_text);
22224
changed = TRUE;
22225
}
22226
break;
22227
default:
22228
break;
22229
}
22230
if (changed)
22231
{
22232
new_val = InferenceTextFromStruct (ipp);
22233
gbqual->val = MemFree (gbqual->val);
22234
gbqual->val = new_val;
22235
}
22236
}
22237
gbqual_last = gbqual;
22238
}
22239
}
22240
else
22241
{
22242
gbqual_last = gbqual;
22243
}
22244
gbqual = gbqual_next;
22245
}
22246
22247
22248
22249
}
22250
18643
22251
static void DoEvidenceFeatureProc (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
18644
22252
{
18645
22253
FeatEdPtr mp;
18676
22284
sfp->except_text = NULL;
18677
22285
if (mp->do_move_to_comment)
18678
22286
{
18679
etd.existing_text_choice = EXISTING_TEXT_CHOICE_APPEND_SEMI;
22287
etd.existing_text_choice = eExistingTextChoiceAppendSemi;
18680
22288
sfp->comment = HandleExistingText (sfp->comment, old_explanation, &etd);
18681
22289
old_explanation = NULL;
18682
22290
}
19223
22831
GetSamplePtr gsp;
19224
22832
MsgAnswer ans;
19225
22833
Boolean also_remove_evidence = FALSE;
22834
InferenceEditPtr iep;
19226
22835
19227
22836
avd.etp = NULL;
19228
22837
avd.field_list = NULL;
19229
22838
avd.text_to_replace = NULL;
19230
22839
avd.new_text = NULL;
22840
avd.where_to_replace = EditApplyFindLocation_anywhere;
19231
22841
19232
22842
if (action_choice == FEAT_ED_EXPERIMENT)
19233
22843
{
19244
22854
gsp = GetGBQualExistingText (sep, feature_type_list,
19245
22855
avd.field_list,
19246
22856
fsp);
19247
avd.etp = GetExistingTextHandlerInfo (gsp, FALSE);
22857
avd.etp = GetExistingTextHandlerInfo (gsp == NULL ? 0 : gsp->num_found, FALSE);
19248
22858
gsp = GetSampleFree (gsp);
19249
22859
if (avd.etp != NULL
19250
&& avd.etp->existing_text_choice == EXISTING_TEXT_CHOICE_CANCEL)
22860
&& avd.etp->existing_text_choice == eExistingTextChoiceCancel)
19251
22861
{
19252
22862
avd.etp = MemFree (avd.etp);
19253
22863
avd.field_list = ValNodeFree (avd.field_list);
19257
22867
}
19258
22868
else if (action_choice == FEAT_ED_INFERENCE)
19259
22869
{
19260
avd.field_list = ValNodeNew (NULL);
19261
avd.field_list->data.intvalue = QUAL_EVIDENCE;
19262
avd.new_text = NULL;
19263
/* get handling for existing text */
19264
gsp = GetGBQualExistingText (sep, feature_type_list,
19265
avd.field_list,
19266
fsp);
19267
if (gsp->num_found > 0)
22870
iep = DialogToPointer (mp->inference_dlg);
22871
if (iep->action == eInferenceRemove)
19268
22872
{
19269
ans = Message (MSG_YNC, "There are evidence qualifiers on your features, which are displayed as inference qualifiers in the flat file. Would you like to remove them as well?");
19270
if (ans == ANS_CANCEL)
19271
{
19272
gsp = GetSampleFree (gsp);
19273
avd.field_list = ValNodeFree (avd.field_list);
19274
return;
19275
}
19276
else if (ans == ANS_YES)
19277
{
19278
also_remove_evidence = TRUE;
19279
}
22873
avd.field_list = ValNodeNew (NULL);
22874
avd.field_list->data.intvalue = QUAL_EVIDENCE;
22875
avd.new_text = NULL;
22876
/* get handling for existing text */
22877
gsp = GetGBQualExistingText (sep, feature_type_list,
22878
avd.field_list,
22879
fsp);
22880
if (gsp->num_found > 0)
22881
{
22882
ans = Message (MSG_YNC, "There are evidence qualifiers on your features, which are displayed as inference qualifiers in the flat file. Would you like to remove them as well?");
22883
if (ans == ANS_CANCEL)
22884
{
22885
gsp = GetSampleFree (gsp);
22886
avd.field_list = ValNodeFree (avd.field_list);
22887
iep = InferenceEditFree (iep);
22888
return;
22889
}
22890
else if (ans == ANS_YES)
22891
{
22892
also_remove_evidence = TRUE;
22893
}
22894
}
22895
gsp = GetSampleFree (gsp);
19280
22896
}
19281
gsp = GetSampleFree (gsp);
22897
iep = InferenceEditFree (iep);
19282
22898
}
19283
22899
19284
22900
for (vnp = feature_type_list; vnp != NULL; vnp = vnp->next)
19371
22987
19372
22988
break;
19373
22989
case FEAT_ED_INFERENCE:
19374
OperateOnSeqEntryConstrainedObjects (sep, fsp, RemoveInference,
19375
NULL, 0, feat_def_choice, 0, &avd);
22990
iep = DialogToPointer (mp->inference_dlg);
22991
OperateOnSeqEntryConstrainedObjects (sep, fsp, DoInferenceFeatureProc,
22992
NULL, 0, feat_def_choice, 0, iep);
22993
iep = InferenceEditFree (iep);
19376
22994
if (also_remove_evidence)
19377
22995
{
19378
22996
mp->evidence_val = 0;
19458
23076
19459
23077
g = FeatureEditorActionGroup (h, mp, first_action);
19460
23078
19461
mp->constraints = FilterGroup (h, TRUE, FALSE, TRUE, FALSE, "Where feature text");
23079
mp->constraints = FilterGroup (h, TRUE, FALSE, TRUE, FALSE, FALSE, "Where feature text");
19462
23080
19463
23081
mp->accept_cancel = AcceptCancelDialog (h, FeatureEditorAction, NULL,
19464
23082
FeatEdClear,
19541
23159
return NULL;
19542
23160
}
19543
23161
19544
static CharPtr GetCDSGeneProtFieldName (ValNodePtr vnp)
23162
extern CharPtr GetCDSGeneProtFieldName (ValNodePtr vnp)
19545
23163
{
19546
23164
CharPtr PNTR field_name_list = NULL;
19547
23165
Int4 num_fields = 0;
19665
23283
return NULL;
19666
23284
}
19667
23285
23286
typedef struct buildcdset2
23287
{
23288
ValNodePtr cds_list;
23289
ValNodePtr mrna_list;
23290
ValNodePtr gene_list;
23291
} BuildCDSet2Data, PNTR BuildCDSet2Ptr;
23292
23293
static void BuildCDSet2Callback (SeqFeatPtr sfp, Pointer userdata)
23294
{
23295
BuildCDSet2Ptr b;
23296
23297
if (sfp == NULL || sfp->idx.deleteme || userdata == NULL) return;
23298
b = (BuildCDSet2Ptr) userdata;
23299
if (sfp->data.choice == SEQFEAT_CDREGION)
23300
{
23301
ValNodeAddPointer (&(b->cds_list), OBJ_SEQFEAT, sfp);
23302
}
23303
else if (sfp->data.choice == SEQFEAT_GENE)
23304
{
23305
ValNodeAddPointer (&(b->gene_list), OBJ_SEQFEAT, sfp);
23306
}
23307
else if (sfp->idx.subtype == FEATDEF_mRNA)
23308
{
23309
ValNodeAddPointer (&(b->mrna_list), OBJ_SEQFEAT, sfp);
23310
}
23311
else if (SeqMgrGetGeneXref (sfp) != NULL)
23312
{
23313
ValNodeAddPointer (&(b->gene_list), OBJ_SEQFEAT, sfp);
23314
}
23315
}
23316
23317
23318
static void UnmarkFeatureList (ValNodePtr list)
23319
{
23320
SeqFeatPtr sfp;
23321
23322
while (list != NULL)
23323
{
23324
sfp = list->data.ptrvalue;
23325
if (sfp != NULL)
23326
{
23327
sfp->idx.deleteme = FALSE;
23328
}
23329
list = list->next;
23330
}
23331
}
23332
23333
23334
static SeqFeatPtr GetGeneForCDSetFeature (SeqFeatPtr sfp)
23335
{
23336
GeneRefPtr grp;
23337
SeqFeatPtr gene = NULL;
23338
SeqMgrFeatContext fcontext;
23339
23340
grp = SeqMgrGetGeneXref (sfp);
23341
if (grp == NULL)
23342
{
23343
gene = SeqMgrGetOverlappingGene (sfp->location, &fcontext);
23344
}
23345
else if (!SeqMgrGeneIsSuppressed (grp))
23346
{
23347
if (!StringHasNoText (grp->locus_tag))
23348
{
23349
gene = SeqMgrGetGeneByLocusTag (BioseqFindFromSeqLoc (sfp->location), grp->locus_tag, &fcontext);
23350
}
23351
}
23352
return gene;
23353
}
23354
23355
23356
static CDSetPtr BuildCDSetFromCodingRegion (SeqFeatPtr cds, BoolPtr indexing_needed)
23357
{
23358
SeqMgrFeatContext fcontext;
23359
SeqFeatPtr gene = NULL, mrna, prot;
23360
BioseqPtr protbsp;
23361
CDSetPtr cdsp;
23362
ProtRefPtr prp;
23363
23364
if (cds == NULL || cds->data.choice != SEQFEAT_CDREGION) return NULL;
23365
23366
cdsp = (CDSetPtr) MemNew (sizeof (CDSetData));
23367
ValNodeAddPointer (&(cdsp->cds_list), 0, cds);
23368
23369
gene = GetGeneForCDSetFeature (cds);
23370
if (gene != NULL)
23371
{
23372
ValNodeAddPointer (&(cdsp->gene_list), 0, gene);
23373
/* mark gene, so that we'll know it isn't lonely */
23374
gene->idx.deleteme = TRUE;
23375
}
23376
23377
mrna = SeqMgrGetOverlappingmRNA (cds->location, &fcontext);
23378
if (mrna != NULL)
23379
{
23380
ValNodeAddPointer (&(cdsp->mrna_list), 0, mrna);
23381
/* mark mrna, so that we'll know it's already in a set */
23382
mrna->idx.deleteme = TRUE;
23383
}
23384
23385
if (cds->product != NULL)
23386
{
23387
protbsp = BioseqFindFromSeqLoc (cds->product);
23388
if (protbsp != NULL)
23389
{
23390
prot = SeqMgrGetNextFeature (protbsp, NULL, SEQFEAT_PROT, FEATDEF_PROT, &fcontext);
23391
/* if there is no full-length protein feature, make one */
23392
if (prot == NULL)
23393
{
23394
prp = ProtRefNew ();
23395
prot = CreateNewFeatureOnBioseq (protbsp, SEQFEAT_PROT, NULL);
23396
if (prot != NULL)
23397
{
23398
prot->data.value.ptrvalue = prp;
23399
if (indexing_needed != NULL)
23400
{
23401
*indexing_needed = TRUE;
23402
}
23403
}
23404
}
23405
if (prot != NULL)
23406
{
23407
ValNodeAddPointer (&(cdsp->prot_list), 0, prot);
23408
}
23409
23410
/* also add in mat_peptides from protein feature */
23411
prot = SeqMgrGetNextFeature (protbsp, NULL, SEQFEAT_PROT, FEATDEF_mat_peptide_aa, &fcontext);
23412
while (prot != NULL)
23413
{
23414
ValNodeAddPointer (&(cdsp->prot_list), 0, prot);
23415
prot = SeqMgrGetNextFeature (protbsp, prot, SEQFEAT_PROT, FEATDEF_mat_peptide_aa, &fcontext);
23416
}
23417
}
23418
}
23419
return cdsp;
23420
}
23421
23422
23423
static CDSetPtr BuildCDSetFrommRNA (SeqFeatPtr mrna)
23424
{
23425
SeqFeatPtr gene;
23426
CDSetPtr cdsp;
23427
23428
if (mrna == NULL || mrna->idx.deleteme || mrna->idx.subtype != FEATDEF_mRNA) return NULL;
23429
23430
cdsp = (CDSetPtr) MemNew (sizeof (CDSetData));
23431
ValNodeAddPointer (&(cdsp->mrna_list), 0, mrna);
23432
23433
gene = GetGeneForCDSetFeature (mrna);
23434
if (gene != NULL)
23435
{
23436
ValNodeAddPointer (&(cdsp->gene_list), 0, gene);
23437
/* mark gene, so that we'll know it isn't lonely */
23438
gene->idx.deleteme = TRUE;
23439
}
23440
23441
return cdsp;
23442
}
23443
23444
23445
static Boolean DoesCDSetMatchConstraint (CDSetPtr cdsp, ChoiceConstraintPtr ccp);
23446
23447
static ValNodePtr BuildCDSet2List (Uint2 entityID, ChoiceConstraintPtr ccp)
23448
{
23449
SeqEntryPtr sep;
23450
BuildCDSet2Data b;
23451
CDSetPtr cdsp;
23452
ValNodePtr vnp, vnp_next, vnp_prev;
23453
ValNodePtr cdset_list = NULL;
23454
SeqFeatPtr cds, gene, mrna;
23455
Boolean need_indexing = FALSE;
23456
23457
sep = GetTopSeqEntryForEntityID (entityID);
23458
23459
b.cds_list = NULL;
23460
b.gene_list = NULL;
23461
b.mrna_list = NULL;
23462
23463
VisitFeaturesInSep (sep, &b, BuildCDSet2Callback);
23464
23465
/* build cdsets that have coding regions */
23466
for (vnp = b.cds_list; vnp != NULL; vnp = vnp->next)
23467
{
23468
cds = (SeqFeatPtr) vnp->data.ptrvalue;
23469
if (cds == NULL) continue;
23470
cdsp = BuildCDSetFromCodingRegion (cds, &need_indexing);
23471
if (cdsp != NULL)
23472
{
23473
ValNodeAddPointer (&cdset_list, 0, cdsp);
23474
}
23475
}
23476
if (need_indexing)
23477
{
23478
/* indexing because we have created full-length protein features */
23479
SeqMgrIndexFeatures (entityID, NULL);
23480
}
23481
23482
/* build cdsets for mrna features that don't have coding regions */
23483
for (vnp = b.mrna_list; vnp != NULL; vnp = vnp->next)
23484
{
23485
mrna = (SeqFeatPtr) vnp->data.ptrvalue;
23486
if (mrna == NULL || mrna->idx.deleteme) continue;
23487
cdsp = BuildCDSetFrommRNA (mrna);
23488
if (cdsp != NULL)
23489
{
23490
ValNodeAddPointer (&cdset_list, 0, cdsp);
23491
}
23492
}
23493
23494
/* build cdsets for lonely genes / features with gene xrefs that are not coding regions or mrnas */
23495
for (vnp = b.gene_list; vnp != NULL; vnp = vnp->next)
23496
{
23497
gene = (SeqFeatPtr) vnp->data.ptrvalue;
23498
if (gene == NULL || gene->idx.deleteme) continue;
23499
cdsp = (CDSetPtr) MemNew (sizeof (CDSetData));
23500
ValNodeAddPointer (&(cdsp->gene_list), 0, gene);
23501
ValNodeAddPointer (&cdset_list, 0, cdsp);
23502
}
23503
23504
/* now unmark features */
23505
UnmarkFeatureList (b.cds_list);
23506
UnmarkFeatureList (b.mrna_list);
23507
UnmarkFeatureList (b.gene_list);
23508
23509
b.cds_list = ValNodeFree (b.cds_list);
23510
b.mrna_list = ValNodeFree (b.mrna_list);
23511
b.gene_list = ValNodeFree (b.gene_list);
23512
23513
/* now remove sets that don't match our choice constraint */
23514
vnp_prev = NULL;
23515
for (vnp = cdset_list; vnp != NULL; vnp = vnp_next)
23516
{
23517
vnp_next = vnp->next;
23518
if (!DoesCDSetMatchConstraint (vnp->data.ptrvalue, ccp))
23519
{
23520
if (vnp_prev == NULL)
23521
{
23522
cdset_list = vnp->next;
23523
}
23524
else
23525
{
23526
vnp_prev->next = vnp->next;
23527
}
23528
vnp->next = NULL;
23529
FreeCDSetList (vnp);
23530
}
23531
else
23532
{
23533
vnp_prev = vnp;
23534
}
23535
}
23536
23537
return cdset_list;
23538
}
23539
19668
23540
typedef struct buildcdset
19669
23541
{
19670
23542
ValNodePtr cdset_list;
19671
ValNodePtr lonely_gene_list;
23543
ValNodePtr lonely_gene_list;
19672
23544
} BuildCDSetData, PNTR BuildCDSetPtr;
19673
23545
19674
23546
static void BuildCDSSetCallback (SeqFeatPtr sfp, Pointer userdata)
19731
23603
{
19732
23604
cds = sfp;
19733
23605
mrna = SeqMgrGetOverlappingmRNA (sfp->location, &fcontext);
19734
if (mrna != NULL)
19735
{
23606
if (mrna != NULL)
23607
{
19736
23608
mrna_gene = SeqMgrGetOverlappingGene (mrna->location, &fcontext);
19737
if (mrna_gene == gene)
19738
{
23609
if (mrna_gene == gene)
23610
{
19739
23611
vnp = AlreadyInCDSList (bp->cdset_list, mrna);
19740
23612
if (vnp != NULL && vnp->data.ptrvalue != NULL)
19741
23613
{
19744
23616
if (AlreadyInList (cdsp->gene_list, gene))
19745
23617
{
19746
23618
gene = NULL;
19747
}
19748
}
23619
}
23620
}
19749
23621
}
19750
23622
}
19751
23623
}
19790
23662
if (prot != NULL)
19791
23663
{
19792
23664
prot->data.value.ptrvalue = prp;
19793
SeqMgrIndexFeatures (protbsp->idx.entityID, NULL);
23665
if (SeqMgrFeaturesAreIndexed (protbsp->idx.entityID) == 0) {
23666
SeqMgrIndexFeatures (protbsp->idx.entityID, NULL);
23667
}
19794
23668
}
19795
23669
}
19796
23670
if (prot != NULL && ! AlreadyInList (cdsp->prot_list, prot))
19846
23720
return str;
19847
23721
}
19848
23722
19849
static void SetCDSetField (CDSetPtr cdsp, ValNodePtr vnp, CharPtr new_text, ExistingTextPtr etp)
23723
static Boolean SetCDSetField (CDSetPtr cdsp, ValNodePtr vnp, ApplyValuePtr avp, FilterSetPtr fsp)
19850
23724
{
19851
23725
ValNodePtr sfp_vnp;
19852
CharPtr str = NULL;
19853
19854
if (cdsp == NULL || vnp == NULL)
19855
{
19856
return;
19857
}
19858
19859
for (sfp_vnp = cdsp->cds_list; sfp_vnp != NULL && str == NULL; sfp_vnp = sfp_vnp->next)
19860
{
19861
SetCDSGeneProtField (sfp_vnp->data.ptrvalue, vnp, new_text, etp);
19862
}
19863
for (sfp_vnp = cdsp->gene_list; sfp_vnp != NULL && str == NULL; sfp_vnp = sfp_vnp->next)
19864
{
19865
SetCDSGeneProtField (sfp_vnp->data.ptrvalue, vnp, new_text, etp);
19866
}
19867
for (sfp_vnp = cdsp->prot_list; sfp_vnp != NULL && str == NULL; sfp_vnp = sfp_vnp->next)
19868
{
19869
SetCDSGeneProtField (sfp_vnp->data.ptrvalue, vnp, new_text, etp);
19870
}
19871
for (sfp_vnp = cdsp->mrna_list; sfp_vnp != NULL && str == NULL; sfp_vnp = sfp_vnp->next)
19872
{
19873
SetCDSGeneProtField (sfp_vnp->data.ptrvalue, vnp, new_text, etp);
19874
}
23726
Boolean rval = FALSE;
23727
23728
if (cdsp == NULL || vnp == NULL || avp == NULL)
23729
{
23730
return FALSE;
23731
}
23732
23733
for (sfp_vnp = cdsp->cds_list; sfp_vnp != NULL ; sfp_vnp = sfp_vnp->next)
23734
{
23735
rval |= SetCDSGeneProtField (sfp_vnp->data.ptrvalue, vnp, avp, fsp);
23736
}
23737
for (sfp_vnp = cdsp->gene_list; sfp_vnp != NULL; sfp_vnp = sfp_vnp->next)
23738
{
23739
if (sfp_vnp->choice == 0) /* don't set again if already set */
23740
{
23741
rval |= SetCDSGeneProtField (sfp_vnp->data.ptrvalue, vnp, avp, fsp);
23742
}
23743
}
23744
for (sfp_vnp = cdsp->prot_list; sfp_vnp != NULL; sfp_vnp = sfp_vnp->next)
23745
{
23746
rval |= SetCDSGeneProtField (sfp_vnp->data.ptrvalue, vnp, avp, fsp);
23747
}
23748
for (sfp_vnp = cdsp->mrna_list; sfp_vnp != NULL; sfp_vnp = sfp_vnp->next)
23749
{
23750
rval |= SetCDSGeneProtField (sfp_vnp->data.ptrvalue, vnp, avp, fsp);
23751
}
23752
return rval;
19875
23753
}
19876
23754
19877
static void RemoveCDSetField (CDSetPtr cdsp, ValNodePtr vnp)
23755
static void RemoveCDSetField (CDSetPtr cdsp, ValNodePtr vnp, FilterSetPtr fsp)
19878
23756
{
19879
23757
ValNodePtr sfp_vnp;
19880
23758
CharPtr str = NULL;
19886
23764
19887
23765
for (sfp_vnp = cdsp->cds_list; sfp_vnp != NULL && str == NULL; sfp_vnp = sfp_vnp->next)
19888
23766
{
19889
RemoveCDSGeneProtField (sfp_vnp->data.ptrvalue, vnp);
23767
RemoveCDSGeneProtField (sfp_vnp->data.ptrvalue, vnp, fsp);
19890
23768
}
19891
23769
for (sfp_vnp = cdsp->gene_list; sfp_vnp != NULL && str == NULL; sfp_vnp = sfp_vnp->next)
19892
23770
{
19893
RemoveCDSGeneProtField (sfp_vnp->data.ptrvalue, vnp);
23771
RemoveCDSGeneProtField (sfp_vnp->data.ptrvalue, vnp, fsp);
19894
23772
}
19895
23773
for (sfp_vnp = cdsp->prot_list; sfp_vnp != NULL && str == NULL; sfp_vnp = sfp_vnp->next)
19896
23774
{
19897
RemoveCDSGeneProtField (sfp_vnp->data.ptrvalue, vnp);
23775
RemoveCDSGeneProtField (sfp_vnp->data.ptrvalue, vnp, fsp);
19898
23776
}
19899
23777
for (sfp_vnp = cdsp->mrna_list; sfp_vnp != NULL && str == NULL; sfp_vnp = sfp_vnp->next)
19900
23778
{
19901
RemoveCDSGeneProtField (sfp_vnp->data.ptrvalue, vnp);
23779
RemoveCDSGeneProtField (sfp_vnp->data.ptrvalue, vnp, fsp);
19902
23780
}
19903
23781
}
19904
23782
19967
23845
return FALSE;
19968
23846
}
19969
23847
23848
static Boolean DoCDSFieldsMatch (CDSetPtr cdsp, ValNodePtr qual_choice, ValNodePtr qual_choice_match)
23849
{
23850
CharPtr str1, str2;
23851
Int4 field_choice, field_choice2;
23852
ValNode field_vn, field_vn2;
23853
Boolean does_match = FALSE;
23854
23855
if (qual_choice == NULL && qual_choice_match == NULL)
23856
{
23857
/* both are wildcards */
23858
field_vn.next = NULL;
23859
field_vn.choice = 0;
23860
field_vn2.next = NULL;
23861
field_vn2.choice = 0;
23862
23863
for (field_choice = 1;
23864
! does_match && field_choice < num_gene_fields + num_mrna_fields + num_protein_fields;
23865
field_choice++)
23866
{
23867
field_vn.data.intvalue = field_choice;
23868
str1 = GetCDSetField (cdsp, &field_vn);
23869
if (!StringHasNoText (str1)) {
23870
for (field_choice2 = field_choice + 1;
23871
! does_match && field_choice2 < 1 + num_gene_fields + num_mrna_fields + num_protein_fields;
23872
field_choice2++)
23873
{
23874
field_vn2.data.intvalue = field_choice2;
23875
str2 = GetCDSetField (cdsp, &field_vn2);
23876
if (StringCmp (str1, str2) == 0)
23877
{
23878
does_match = TRUE;
23879
}
23880
str2 = MemFree (str2);
23881
}
23882
}
23883
str1 = MemFree (str1);
23884
}
23885
}
23886
else if (qual_choice == NULL || qual_choice_match == NULL)
23887
{
23888
/* one is a wildcard */
23889
/* make sure it is the first one */
23890
if (qual_choice_match == NULL)
23891
{
23892
qual_choice_match = qual_choice;
23893
qual_choice = NULL;
23894
}
23895
field_vn.next = NULL;
23896
field_vn.choice = 0;
23897
str2 = GetCDSetField (cdsp, qual_choice_match);
23898
if (!StringHasNoText (str2)) {
23899
for (field_choice = 1;
23900
! does_match && field_choice < num_gene_fields + num_mrna_fields + num_protein_fields;
23901
field_choice++)
23902
{
23903
if (field_choice != qual_choice_match->data.intvalue) {
23904
/* don't compare something to itself */
23905
field_vn.data.intvalue = field_choice;
23906
str1 = GetCDSetField (cdsp, &field_vn);
23907
if (StringCmp (str1, str2) == 0)
23908
{
23909
does_match = TRUE;
23910
}
23911
str1 = MemFree (str1);
23912
}
23913
}
23914
}
23915
str2 = MemFree (str2);
23916
} else {
23917
str1 = GetCDSetField (cdsp, qual_choice);
23918
str2 = GetCDSetField (cdsp, qual_choice_match);
23919
if (!StringHasNoText (str1) && StringCmp (str1, str2) == 0)
23920
{
23921
does_match = TRUE;
23922
}
23923
str1 = MemFree (str1);
23924
str2 = MemFree (str2);
23925
}
23926
return does_match;
23927
}
23928
23929
19970
23930
static Boolean DoesCDSetMatchConstraint (CDSetPtr cdsp, ChoiceConstraintPtr ccp)
19971
23931
{
19972
23932
Boolean does_match = FALSE;
19973
23933
CharPtr str;
19974
23934
Int4 field_choice;
19975
23935
ValNode field_vn;
23936
ValNodePtr sfp_vnp;
19976
23937
19977
23938
if (cdsp == NULL)
19978
23939
{
20010
23971
{
20011
23972
field_vn.data.intvalue = field_choice;
20012
23973
str = GetCDSetField (cdsp, &field_vn);
20013
does_match = DoesStringMatchConstraint (str, ccp->string_constraint);
23974
does_match = DoesStringMatchConstraintX (str, ccp->string_constraint);
20014
23975
MemFree (str);
20015
23976
}
23977
if (ccp->string_constraint != NULL && ccp->string_constraint->not_present)
23978
{
23979
does_match = ! does_match;
23980
}
20016
23981
}
23982
else if (IsCDSetMatPeptideQualChoice(ccp->qual_choice))
23983
{
23984
/* if we're matching protein fields, we need to look at all of them */
23985
for (sfp_vnp = cdsp->prot_list; sfp_vnp != NULL && !does_match; sfp_vnp = sfp_vnp->next)
23986
{
23987
str = GetCDSGeneProtField (sfp_vnp->data.ptrvalue, ccp->qual_choice, NULL);
23988
does_match = DoesStringMatchConstraintX (str, ccp->string_constraint);
23989
if (ccp->string_constraint != NULL && ccp->string_constraint->not_present)
23990
{
23991
does_match = ! does_match;
23992
}
23993
MemFree (str);
23994
}
23995
}
20017
23996
else
20018
23997
{
20019
23998
str = GetCDSetField (cdsp, ccp->qual_choice);
20020
does_match = DoesStringMatchConstraint (str, ccp->string_constraint);
23999
does_match = DoesStringMatchConstraintX (str, ccp->string_constraint);
20021
24000
MemFree (str);
20022
}
20023
if (ccp->string_constraint != NULL && ccp->string_constraint->not_present)
20024
{
20025
does_match = ! does_match;
20026
}
24001
if (ccp->string_constraint != NULL && ccp->string_constraint->not_present)
24002
{
24003
does_match = ! does_match;
24004
}
24005
}
24006
}
24007
else if (ccp->constraint_type == CHOICE_CONSTRAINT_MATCH)
24008
{
24009
does_match = DoCDSFieldsMatch (cdsp, ccp->qual_choice, ccp->qual_choice_match);
20027
24010
}
20028
24011
else if (ccp->constraint_type == CHOICE_CONSTRAINT_PSEUDO)
20029
24012
{
20053
24036
bd.lonely_gene_list = NULL;
20054
24037
20055
24038
VisitFeaturesInSep (sep, &bd, BuildCDSSetCallback);
20056
24039
20057
24040
for (vnp = bd.lonely_gene_list; vnp != NULL; vnp = vnp->next)
20058
24041
{
20059
24042
/* only create sets for lonely genes if they have not been added to other sets */
20097
24080
return bd.cdset_list;
20098
24081
}
20099
24082
20100
static SeqFeatPtr BuildOneNewCDSGeneProtFeature (CDSetPtr cdsp, Uint1 choice)
24083
24084
static SeqLocPtr GetNewFeatureLocation(ValNodePtr feat_list, Uint2 choice, Uint2 choice_from)
24085
{
24086
ValNodePtr vnp;
24087
SeqFeatPtr sfp;
24088
BioseqPtr bsp = NULL;
24089
SeqLocPtr slp = NULL;
24090
24091
for (vnp = feat_list; vnp != NULL && slp == NULL; vnp = vnp->next)
24092
{
24093
sfp = vnp->data.ptrvalue;
24094
if (sfp != NULL)
24095
{
24096
if (choice == FEATDEF_PROT || choice == FEATDEF_mat_peptide_aa)
24097
{
24098
bsp = BioseqFindFromSeqLoc (sfp->product);
24099
slp = SeqLocWholeNew (bsp);
24100
}
24101
else
24102
{
24103
if (choice_from == sfp->idx.subtype || (sfp->idx.subtype == FEATDEF_CDS && (choice_from == FEATDEF_PROT || choice_from == FEATDEF_mat_peptide_aa)))
24104
{
24105
slp = (SeqLocPtr) AsnIoMemCopy (sfp->location, (AsnReadFunc) SeqLocAsnRead, (AsnWriteFunc) SeqLocAsnWrite);
24106
}
24107
else
24108
{
24109
bsp = BioseqFindFromSeqLoc (sfp->location);
24110
slp = SeqLocWholeNew (bsp);
24111
}
24112
}
24113
}
24114
}
24115
return slp;
24116
}
24117
24118
24119
static SeqFeatPtr BuildOneNewCDSGeneProtFeature (CDSetPtr cdsp, Uint2 choice, Uint2 choice_from)
20101
24120
{
20102
24121
BioseqPtr bsp = NULL;
20103
SeqLocPtr slp = NULL, slp_tmp;
20104
ValNodePtr vnp;
24122
SeqLocPtr slp = NULL, slp_tmp, slp_sum;
20105
24123
SeqFeatPtr sfp = NULL;
20106
24124
RnaRefPtr rrp;
24125
ProtRefPtr prp;
20107
24126
20108
24127
if (cdsp == NULL)
20109
24128
{
20110
24129
return NULL;
20111
24130
}
20112
24131
20113
/* get location from CDS features */
20114
for (vnp = cdsp->cds_list; vnp != NULL; vnp = vnp->next)
20115
{
20116
sfp = vnp->data.ptrvalue;
20117
if (sfp != NULL)
20118
{
20119
if (choice == SEQFEAT_PROT)
20120
{
20121
if (bsp == NULL)
20122
{
20123
bsp = BioseqFindFromSeqLoc (sfp->product);
20124
}
20125
}
20126
else
20127
{
20128
if (bsp == NULL)
20129
{
20130
bsp = BioseqFindFromSeqLoc (sfp->location);
20131
}
20132
if (bsp != NULL)
20133
{
20134
slp_tmp = SeqLocMerge (bsp, sfp->location, slp, TRUE, FALSE, FALSE);
20135
slp = SeqLocFree (slp);
20136
slp = slp_tmp;
20137
slp_tmp = NULL;
20138
}
20139
}
20140
}
20141
}
20142
20143
/* get location from mRNA features */
20144
for (vnp = cdsp->mrna_list; vnp != NULL; vnp = vnp->next)
20145
{
20146
sfp = vnp->data.ptrvalue;
20147
if (sfp != NULL)
20148
{
20149
if (choice == SEQFEAT_PROT)
20150
{
20151
if (bsp == NULL)
20152
{
20153
bsp = BioseqFindFromSeqLoc (sfp->product);
20154
}
20155
}
20156
else
20157
{
20158
if (bsp == NULL)
20159
{
20160
bsp = BioseqFindFromSeqLoc (sfp->location);
20161
}
20162
if (bsp != NULL)
20163
{
20164
slp_tmp = SeqLocMerge (bsp, sfp->location, slp, TRUE, FALSE, FALSE);
20165
slp = SeqLocFree (slp);
20166
slp = slp_tmp;
20167
slp_tmp = NULL;
20168
}
20169
}
20170
}
20171
}
20172
20173
if (choice == SEQFEAT_PROT)
20174
{
20175
if (bsp != NULL)
20176
{
20177
slp = SeqLocWholeNew (bsp);
20178
}
24132
if (choice == FEATDEF_PROT || choice == FEATDEF_mat_peptide_aa)
24133
{
24134
slp = GetNewFeatureLocation(cdsp->cds_list, choice, choice_from);
20179
24135
}
20180
24136
else
20181
24137
{
24138
/* get location from CDS features */
24139
if (choice_from == 0 || choice_from == FEATDEF_CDS || choice_from == FEATDEF_PROT || choice_from == FEATDEF_mat_peptide_aa)
24140
{
24141
slp = GetNewFeatureLocation(cdsp->cds_list, choice, choice_from);
24142
}
24143
24144
/* get location from mRNA features */
24145
if ((choice_from == 0 && slp == NULL) || choice_from == FEATDEF_mRNA)
24146
{
24147
slp_tmp = GetNewFeatureLocation(cdsp->mrna_list, choice, choice_from);
24148
if (slp == NULL)
24149
{
24150
slp = slp_tmp;
24151
}
24152
else
24153
{
24154
bsp = BioseqFindFromSeqLoc (sfp->location);
24155
if (bsp != NULL)
24156
{
24157
slp_sum = SeqLocMerge (bsp, slp_tmp, slp, TRUE, FALSE, FALSE);
24158
slp = SeqLocFree (slp);
24159
slp_tmp = SeqLocFree (slp_tmp);
24160
slp = slp_sum;
24161
slp_sum = NULL;
24162
}
24163
}
24164
}
24165
20182
24166
/* get location from gene features */
20183
for (vnp = cdsp->gene_list; vnp != NULL; vnp = vnp->next)
20184
{
20185
sfp = vnp->data.ptrvalue;
20186
if (sfp != NULL)
20187
{
20188
if (bsp == NULL)
20189
{
20190
bsp = BioseqFindFromSeqLoc (sfp->location);
20191
}
24167
if ((choice_from == 0 && slp == NULL) || choice_from == FEATDEF_GENE)
24168
{
24169
slp_tmp = GetNewFeatureLocation(cdsp->gene_list, choice, choice_from);
24170
if (slp == NULL)
24171
{
24172
slp = slp_tmp;
24173
}
24174
else
24175
{
24176
bsp = BioseqFindFromSeqLoc (sfp->location);
20192
24177
if (bsp != NULL)
20193
24178
{
20194
slp_tmp = SeqLocMerge (bsp, sfp->location, slp, TRUE, FALSE, FALSE);
24179
slp_sum = SeqLocMerge (bsp, slp_tmp, slp, TRUE, FALSE, FALSE);
20195
24180
slp = SeqLocFree (slp);
20196
slp = slp_tmp;
20197
slp_tmp = NULL;
24181
slp_tmp = SeqLocFree (slp_tmp);
24182
slp = slp_sum;
24183
slp_sum = NULL;
20198
24184
}
20199
24185
}
20200
24186
}
20201
}
20202
20203
/* for now, cover the entire sequence */
20204
slp = SeqLocFree (slp);
20205
slp = SeqLocWholeNew (bsp);
20206
24187
}
24188
24189
bsp = BioseqFindFromSeqLoc (slp);
20207
24190
if (bsp != NULL && slp != NULL)
20208
24191
{
20209
sfp = CreateNewFeatureOnBioseq (bsp, choice, slp);
20210
if (choice == SEQFEAT_RNA)
24192
sfp = CreateNewFeatureOnBioseq (bsp, FindFeatFromFeatDefType(choice), slp);
24193
switch (choice)
20211
24194
{
20212
rrp = RnaRefNew ();
20213
rrp->type = 2;
20214
sfp->data.value.ptrvalue = rrp;
24195
case FEATDEF_mRNA:
24196
rrp = RnaRefNew ();
24197
rrp->type = 2;
24198
sfp->data.value.ptrvalue = rrp;
24199
break;
24200
case FEATDEF_GENE:
24201
sfp->data.value.ptrvalue = GeneRefNew();
24202
break;
24203
case FEATDEF_CDS:
24204
sfp->data.value.ptrvalue = CdRegionNew();
24205
break;
24206
case FEATDEF_PROT:
24207
case FEATDEF_mat_peptide_aa:
24208
prp = ProtRefNew();
24209
if (choice == FEATDEF_mat_peptide_aa)
24210
{
24211
prp->processed = 2;
24212
}
24213
sfp->data.value.ptrvalue = prp;
24214
break;
20215
24215
}
20216
24216
}
20217
24217
return sfp;
20218
24218
}
20219
24219
20220
static void BuildNewCDSGeneProtFeature (CDSetPtr cdsp, ValNodePtr vnp)
24220
static SeqFeatPtr BuildNewCDSGeneProtFeature (CDSetPtr cdsp, ValNodePtr vnp, ValNodePtr field_from)
20221
24221
{
20222
SeqFeatPtr new_sfp;
24222
SeqFeatPtr new_sfp = NULL, sfp;
24223
Uint2 choice_to, choice_from;
24224
ValNodePtr v;
24225
Boolean found;
20223
24226
20224
24227
if (cdsp == NULL || vnp == NULL)
20225
24228
{
20226
return;
20227
}
20228
if (vnp->data.intvalue == 1)
20229
{
20230
/* for now, don't build anything but genes */
20231
#if 0
20232
if (cdsp->cds_list == NULL)
20233
{
20234
/* add new CDS */
20235
new_sfp = BuildOneNewCDSGeneProtFeature (cdsp, SEQFEAT_CDREGION);
20236
if (new_sfp != NULL)
20237
{
20238
ValNodeAddPointer (&(cdsp->cds_list), 0, new_sfp);
20239
}
20240
}
20241
#endif
20242
}
20243
else if (vnp->data.intvalue <= 1 + num_gene_fields)
20244
{
20245
if (cdsp->gene_list == NULL)
20246
{
20247
/* add new gene */
20248
new_sfp = BuildOneNewCDSGeneProtFeature (cdsp, SEQFEAT_GENE);
20249
if (new_sfp != NULL)
20250
{
20251
ValNodeAddPointer (&(cdsp->gene_list), 0, new_sfp);
20252
}
20253
}
20254
}
20255
else if (vnp->data.intvalue <= 1 + num_gene_fields + num_mrna_fields)
20256
{
20257
/* for now, don't build anything but genes */
20258
#if 0
20259
if (cdsp->mrna_list == NULL)
20260
{
20261
/* add new mrna */
20262
new_sfp = BuildOneNewCDSGeneProtFeature (cdsp, SEQFEAT_RNA);
20263
if (new_sfp != NULL)
20264
{
20265
ValNodeAddPointer (&(cdsp->mrna_list), 0, new_sfp);
20266
}
20267
}
20268
#endif
20269
}
20270
else if (vnp->data.intvalue <= 1 + num_gene_fields + num_mrna_fields + num_protein_fields)
20271
{
20272
/* for now, don't build anything but genes */
20273
#if 0
20274
if (cdsp->prot_list == NULL)
20275
{
20276
/* add new prot */
20277
new_sfp = BuildOneNewCDSGeneProtFeature (cdsp, SEQFEAT_PROT);
20278
if (new_sfp != NULL)
20279
{
20280
ValNodeAddPointer (&(cdsp->prot_list), 0, new_sfp);
20281
}
20282
}
20283
#endif
20284
}
20285
}
20286
20287
static void BuildGeneForSegSet (BioseqSetPtr segset)
24229
return NULL;
24230
}
24231
24232
choice_to = FeatDefTypeFromFieldList (vnp);
24233
choice_from = FeatDefTypeFromFieldList (field_from);
24234
24235
switch (choice_to)
24236
{
24237
case FEATDEF_CDS:
24238
if (choice_from != 0 && cdsp->cds_list == NULL)
24239
{
24240
/* add new CDS */
24241
new_sfp = BuildOneNewCDSGeneProtFeature (cdsp, choice_to, choice_from);
24242
if (new_sfp != NULL)
24243
{
24244
ValNodeAddPointer (&(cdsp->cds_list), 0, new_sfp);
24245
}
24246
}
24247
break;
24248
case FEATDEF_GENE:
24249
if ((choice_from != 0 || vnp->data.intvalue - 1 == GENEFIELD_LOCUS) && cdsp->gene_list == NULL)
24250
{
24251
/* add new gene */
24252
new_sfp = BuildOneNewCDSGeneProtFeature (cdsp, choice_to, choice_from);
24253
if (new_sfp != NULL)
24254
{
24255
ValNodeAddPointer (&(cdsp->gene_list), 0, new_sfp);
24256
}
24257
}
24258
break;
24259
case FEATDEF_mRNA:
24260
if (choice_from != 0 && cdsp->mrna_list == NULL)
24261
{
24262
/* add new mrna */
24263
new_sfp = BuildOneNewCDSGeneProtFeature (cdsp, choice_to, choice_from);
24264
if (new_sfp != NULL)
24265
{
24266
ValNodeAddPointer (&(cdsp->mrna_list), 0, new_sfp);
24267
}
24268
}
24269
break;
24270
case FEATDEF_PROT:
24271
case FEATDEF_mat_peptide_aa:
24272
if (choice_from != 0 && cdsp->cds_list != NULL)
24273
{
24274
found = FALSE;
24275
for (v = cdsp->prot_list; v != NULL && !found; v = v->next)
24276
{
24277
sfp = (SeqFeatPtr) v->data.ptrvalue;
24278
if (sfp != NULL && sfp->idx.subtype == choice_to)
24279
{
24280
found = FALSE;
24281
}
24282
}
24283
if (!found)
24284
{
24285
new_sfp = BuildOneNewCDSGeneProtFeature (cdsp, choice_to, choice_from);
24286
if (new_sfp != NULL)
24287
{
24288
/* set subtype so other functions will work */
24289
new_sfp->idx.subtype = choice_to;
24290
ValNodeAddPointer (&(cdsp->mrna_list), 0, new_sfp);
24291
}
24292
}
24293
}
24294
break;
24295
}
24296
return new_sfp;
24297
}
24298
24299
static Boolean CDSetOnBioseq (CDSetPtr cdsp, BioseqPtr bsp)
24300
{
24301
SeqFeatPtr sfp;
24302
Boolean is_on_bioseq = FALSE;
24303
ValNodePtr sfp_vnp;
24304
24305
if (cdsp == NULL || bsp == NULL) return FALSE;
24306
24307
for (sfp_vnp = cdsp->cds_list; sfp_vnp != NULL && !is_on_bioseq; sfp_vnp = sfp_vnp->next)
24308
{
24309
sfp = sfp_vnp->data.ptrvalue;
24310
if (sfp != NULL && BioseqFindFromSeqLoc (sfp->location) == bsp) {
24311
is_on_bioseq = TRUE;
24312
}
24313
}
24314
for (sfp_vnp = cdsp->gene_list; sfp_vnp != NULL && !is_on_bioseq; sfp_vnp = sfp_vnp->next)
24315
{
24316
sfp = sfp_vnp->data.ptrvalue;
24317
if (sfp != NULL && BioseqFindFromSeqLoc (sfp->location) == bsp) {
24318
is_on_bioseq = TRUE;
24319
}
24320
}
24321
for (sfp_vnp = cdsp->mrna_list; sfp_vnp != NULL && !is_on_bioseq; sfp_vnp = sfp_vnp->next)
24322
{
24323
sfp = sfp_vnp->data.ptrvalue;
24324
if (sfp != NULL && BioseqFindFromSeqLoc (sfp->location) == bsp) {
24325
is_on_bioseq = TRUE;
24326
}
24327
}
24328
return is_on_bioseq;
24329
}
24330
24331
static Boolean ValNodeDataAlreadyInValNodeList (ValNodePtr list, ValNodePtr findme)
24332
{
24333
if (findme == NULL) return FALSE;
24334
while (list != NULL)
24335
{
24336
if (list->data.ptrvalue == findme->data.ptrvalue)
24337
{
24338
return TRUE;
24339
}
24340
list = list->next;
24341
}
24342
return FALSE;
24343
}
24344
24345
static void BuildGeneForSegSet (BioseqSetPtr segset, ValNodePtr PNTR cdset_list, Boolean lonely_ok)
20288
24346
{
20289
24347
SeqEntryPtr this_sep, master_sep = NULL;
20290
24348
BioseqSetPtr part_set = NULL;
20291
24349
SeqLocPtr slp = NULL, slp_new, slp_last = NULL;
20292
24350
SeqFeatPtr sfp;
20293
24351
SeqMgrFeatContext context;
24352
ValNodePtr vnp, add_gene_to = NULL;
24353
Boolean on_part;
24354
CDSetPtr cdsp;
20294
24355
20295
24356
if (segset == NULL || segset->seq_set == NULL)
20296
24357
{
20333
24394
{
20334
24395
return;
20335
24396
}
20336
20337
this_sep = part_set->seq_set;
20338
while (this_sep != NULL)
24397
24398
/* no other genes anywhere in segmented set. Any cdsets? */
24399
for (vnp = *cdset_list; vnp != NULL; vnp = vnp->next)
20339
24400
{
20340
if (IS_Bioseq (this_sep))
20341
{
20342
slp_new = SeqLocWholeNew (this_sep->data.ptrvalue);
20343
if (slp_new != NULL)
20344
{
20345
if (slp_last == NULL)
20346
{
20347
slp = slp_new;
20348
}
20349
else
20350
{
20351
slp_last = ValNodeNew (slp);
20352
slp_last->choice = SEQLOC_NULL;
20353
slp_last->next = slp_new;
20354
}
20355
slp_last = slp_new;
20356
}
20357
}
20358
this_sep = this_sep->next;
20359
}
20360
slp_new = ValNodeNew (NULL);
20361
slp_new->choice = SEQLOC_MIX;
20362
slp_new->data.ptrvalue = slp;
20363
sfp = CreateNewFeature (master_sep, NULL, SEQFEAT_GENE, NULL);
20364
sfp->location = SeqLocFree (sfp->location);
20365
sfp->location = slp_new;
20366
sfp->data.value.ptrvalue = GeneRefNew ();
20367
}
20368
}
20369
20370
static void BuildNewGenes (SeqEntryPtr sep)
24401
cdsp = (CDSetPtr) vnp->data.ptrvalue;
24402
if (CDSetOnBioseq(cdsp, master_sep->data.ptrvalue)
24403
&& !ValNodeDataAlreadyInValNodeList(add_gene_to, vnp))
24404
{
24405
ValNodeAddPointer (&add_gene_to, 0, cdsp);
24406
}
24407
else
24408
{
24409
on_part = FALSE;
24410
for (this_sep = part_set->seq_set; this_sep != NULL && !on_part; this_sep = this_sep->next)
24411
{
24412
if (CDSetOnBioseq(cdsp, this_sep->data.ptrvalue)
24413
&& !ValNodeDataAlreadyInValNodeList(add_gene_to, vnp))
24414
{
24415
ValNodeAddPointer (&add_gene_to, 0, cdsp);
24416
on_part = TRUE;
24417
}
24418
}
24419
}
24420
}
24421
24422
if (add_gene_to != NULL || lonely_ok) {
24423
/* create gene */
24424
this_sep = part_set->seq_set;
24425
while (this_sep != NULL)
24426
{
24427
if (IS_Bioseq (this_sep))
24428
{
24429
slp_new = SeqLocWholeNew (this_sep->data.ptrvalue);
24430
if (slp_new != NULL)
24431
{
24432
if (slp_last == NULL)
24433
{
24434
slp = slp_new;
24435
}
24436
else
24437
{
24438
slp_last = ValNodeNew (slp);
24439
slp_last->choice = SEQLOC_NULL;
24440
slp_last->next = slp_new;
24441
}
24442
slp_last = slp_new;
24443
}
24444
}
24445
this_sep = this_sep->next;
24446
}
24447
slp_new = ValNodeNew (NULL);
24448
slp_new->choice = SEQLOC_MIX;
24449
slp_new->data.ptrvalue = slp;
24450
sfp = CreateNewFeature (master_sep, NULL, SEQFEAT_GENE, NULL);
24451
sfp->location = SeqLocFree (sfp->location);
24452
sfp->location = slp_new;
24453
sfp->data.value.ptrvalue = GeneRefNew ();
24454
24455
/* add to sets */
24456
if (add_gene_to == NULL)
24457
{
24458
cdsp = (CDSetPtr) MemNew (sizeof (CDSetData));
24459
MemSet (cdsp, 0, sizeof (CDSetData));
24460
ValNodeAddPointer (&(cdsp->gene_list), 0, sfp);
24461
ValNodeAddPointer (cdset_list, 0, cdsp);
24462
}
24463
else
24464
{
24465
for (vnp = add_gene_to; vnp != NULL; vnp = vnp->next)
24466
{
24467
cdsp = (CDSetPtr) vnp->data.ptrvalue;
24468
ValNodeAddPointer (&(cdsp->gene_list), 0, sfp);
24469
}
24470
}
24471
}
24472
add_gene_to = ValNodeFree (add_gene_to);
24473
}
24474
}
24475
24476
static Boolean LoneGeneOkWithFilter (FilterSetPtr fsp)
24477
{
24478
if (fsp == NULL || fsp->cgp == NULL
24479
|| fsp->cgp->constraint_type == CHOICE_CONSTRAINT_ANY
24480
|| (fsp->cgp->constraint_type == CHOICE_CONSTRAINT_QUAL_PRESENT
24481
&& fsp->cgp->qual_choice == NULL))
24482
{
24483
return TRUE;
24484
}
24485
else
24486
{
24487
return FALSE;
24488
}
24489
}
24490
24491
static void BuildNewGenes (SeqEntryPtr sep, ValNodePtr PNTR cdset_list, Boolean lonely_ok)
20371
24492
{
20372
24493
BioseqSetPtr bssp = NULL;
20373
24494
BioseqPtr bsp = NULL;
20374
24495
SeqFeatPtr sfp;
20375
24496
SeqMgrFeatContext context;
20376
24497
SeqLocPtr slp = NULL;
24498
ValNodePtr vnp;
24499
CDSetPtr cdsp;
24500
ValNodePtr add_gene_to;
20377
24501
20378
24502
if (sep == NULL)
20379
24503
{
20388
24512
sfp = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_GENE, FEATDEF_GENE, &context);
20389
24513
if (sfp == NULL)
20390
24514
{
20391
slp = SeqLocWholeNew (bsp);
20392
sfp = CreateNewFeatureOnBioseq (bsp, SEQFEAT_GENE, slp);
20393
sfp->data.value.ptrvalue = GeneRefNew();
24515
/* are there any sets already on this Bioseq? */
24516
add_gene_to = NULL;
24517
for (vnp = *cdset_list; vnp != NULL; vnp = vnp->next)
24518
{
24519
cdsp = (CDSetPtr) vnp->data.ptrvalue;
24520
if (CDSetOnBioseq(cdsp, bsp))
24521
{
24522
if (cdsp->gene_list == NULL)
24523
{
24524
ValNodeAddPointer (&add_gene_to, 0, cdsp);
24525
}
24526
}
24527
}
24528
if (add_gene_to != NULL || lonely_ok)
24529
{
24530
slp = SeqLocWholeNew (bsp);
24531
sfp = CreateNewFeatureOnBioseq (bsp, SEQFEAT_GENE, slp);
24532
sfp->data.value.ptrvalue = GeneRefNew();
24533
if (add_gene_to == NULL)
24534
{
24535
cdsp = (CDSetPtr) MemNew (sizeof (CDSetData));
24536
MemSet (cdsp, 0, sizeof (CDSetData));
24537
ValNodeAddPointer (&(cdsp->gene_list), 0, sfp);
24538
ValNodeAddPointer (cdset_list, 0, cdsp);
24539
}
24540
else
24541
{
24542
for (vnp = add_gene_to; vnp != NULL; vnp = vnp->next)
24543
{
24544
cdsp = (CDSetPtr) vnp->data.ptrvalue;
24545
ValNodeAddPointer (&(cdsp->gene_list), 0, sfp);
24546
}
24547
}
24548
}
24549
add_gene_to = ValNodeFree (add_gene_to);
20394
24550
}
20395
24551
}
20396
24552
}
20399
24555
bssp = (BioseqSetPtr) sep->data.ptrvalue;
20400
24556
if (bssp->_class == BioseqseqSet_class_segset)
20401
24557
{
20402
BuildGeneForSegSet (bssp);
24558
BuildGeneForSegSet (bssp, cdset_list, lonely_ok);
20403
24559
}
20404
24560
else
20405
24561
{
20406
BuildNewGenes (bssp->seq_set);
24562
BuildNewGenes (bssp->seq_set, cdset_list, lonely_ok);
20407
24563
}
20408
24564
}
20409
BuildNewGenes (sep->next);
24565
BuildNewGenes (sep->next, cdset_list, lonely_ok);
20410
24566
}
20411
24567
20412
24568
typedef Boolean (*Nlm_TestAECRChoiceProc) PROTO((Pointer));
20415
24571
typedef DialoG (*Nlm_FieldListDlgProc) PROTO ((GrouP, Boolean, Nlm_ChangeNotifyProc, Pointer));
20416
24572
typedef DialoG (*Nlm_SubtypeListDlgProc) PROTO ((GrouP, Boolean, SeqEntryPtr, Nlm_ChangeNotifyProc, Pointer));
20417
24573
20418
#define AECR_APPLY 1
20419
#define AECR_EDIT 2
20420
#define AECR_CONVERT 3
20421
#define AECR_SWAP 4
20422
#define AECR_PARSE 5
20423
#define AECR_REMOVE 6
20424
#define NUM_AECR 6
20425
20426
24574
#define AECR_VIB_MSG_SET_DEFAULT (NUM_VIB_MSG + 1)
20427
24575
#define AECR_VIB_MSG_CLEAR_TEXT (NUM_VIB_MSG + 2)
20428
24576
#define AECR_VIB_MSG_AUTOPOPULATE (NUM_VIB_MSG + 3)
20636
24784
Boolean source_constraint,
20637
24785
Boolean location_constraint,
20638
24786
Boolean cds_gene_prot_constraint,
24787
Boolean id_list_constraint,
20639
24788
CharPtr string_constraint_label,
20640
24789
Nlm_AcceptActnProc accept_actn,
20641
24790
Nlm_CancelActnProc cancel_actn,
20673
24822
SetObjectExtra (w, mp, NULL);
20674
24823
mp->form = (ForM) w;
20675
24824
mp->input_entityID = bfp->input_entityID;
24825
24826
#ifndef WIN_MAC
24827
CreateStandardEditMenu (w);
24828
#endif
20676
24829
20677
24830
n = HiddenGroup (w, -1, 0, NULL);
20678
24831
SetGroupSpacing (n, 10, 10);
20741
24894
(HANDLE) NULL);
20742
24895
mp->constraints = FilterGroup (n, string_constraint, source_constraint,
20743
24896
location_constraint, cds_gene_prot_constraint,
24897
id_list_constraint,
20744
24898
string_constraint_label);
20745
24899
20746
24900
}
20806
24960
}
20807
24961
20808
24962
20809
typedef struct editapply
20810
{
20811
CharPtr find_txt;
20812
CharPtr repl_txt;
20813
CharPtr apply_txt;
20814
} EditApplyData, PNTR EditApplyPtr;
20815
20816
static EditApplyPtr EditApplyFree (EditApplyPtr eap)
20817
{
20818
if (eap != NULL)
20819
{
20820
eap->find_txt = MemFree (eap->find_txt);
20821
eap->repl_txt = MemFree (eap->repl_txt);
20822
eap->apply_txt = MemFree (eap->apply_txt);
20823
eap = MemFree (eap);
20824
}
20825
return eap;
20826
}
20827
20828
typedef struct EditApplydlg
20829
{
20830
DIALOG_MESSAGE_BLOCK
20831
TexT find_txt;
20832
TexT repl_txt;
20833
TexT apply_txt;
20834
Int4 action_choice;
20835
} EditApplyDlgData, PNTR EditApplyDlgPtr;
20836
20837
static void ResetEditApplyDlg (EditApplyDlgPtr dlg)
20838
{
20839
if (dlg != NULL)
20840
{
20841
if (dlg->find_txt != NULL)
20842
{
20843
SetTitle (dlg->find_txt, "");
20844
}
20845
if (dlg->repl_txt != NULL)
20846
{
20847
SetTitle (dlg->repl_txt, "");
20848
}
20849
if (dlg->apply_txt != NULL)
20850
{
20851
SetTitle (dlg->apply_txt, "");
20852
}
20853
}
20854
}
20855
20856
static void EditApplyToDialog (DialoG d, Pointer userdata)
20857
{
20858
EditApplyDlgPtr dlg;
20859
EditApplyPtr data;
20860
20861
dlg = (EditApplyDlgPtr) GetObjectExtra (d);
20862
if (dlg == NULL)
20863
{
20864
return;
20865
}
20866
20867
ResetEditApplyDlg (dlg);
20868
data = (EditApplyPtr) userdata;
20869
if (data != NULL)
20870
{
20871
if (dlg->find_txt != NULL && !StringHasNoText (data->find_txt))
20872
{
20873
SetTitle (dlg->find_txt, data->find_txt);
20874
}
20875
if (dlg->repl_txt != NULL && !StringHasNoText (data->repl_txt))
20876
{
20877
SetTitle (dlg->repl_txt, data->repl_txt);
20878
}
20879
if (dlg->apply_txt != NULL && !StringHasNoText (data->apply_txt))
20880
{
20881
SetTitle (dlg->apply_txt, data->apply_txt);
20882
}
20883
}
20884
}
20885
20886
static Pointer DialogToEditApply (DialoG d)
20887
{
20888
EditApplyDlgPtr dlg;
20889
EditApplyPtr data;
20890
20891
dlg = (EditApplyDlgPtr) GetObjectExtra (d);
20892
if (dlg == NULL)
20893
{
20894
return NULL;
20895
}
20896
20897
data = (EditApplyPtr) MemNew (sizeof (EditApplyData));
20898
if (data != NULL)
20899
{
20900
if (dlg->find_txt != NULL)
20901
{
20902
data->find_txt = JustSaveStringFromText (dlg->find_txt);
20903
}
20904
if (dlg->repl_txt != NULL)
20905
{
20906
data->repl_txt = JustSaveStringFromText (dlg->repl_txt);
20907
}
20908
if (dlg->apply_txt != NULL)
20909
{
20910
data->apply_txt = JustSaveStringFromText (dlg->apply_txt);
20911
}
20912
}
20913
return data;
20914
}
20915
20916
static void EditApplyMessage (DialoG d, Int2 mssg)
20917
20918
{
20919
EditApplyDlgPtr dlg;
20920
20921
dlg = (EditApplyDlgPtr) GetObjectExtra (d);
20922
if (dlg != NULL) {
20923
switch (mssg)
20924
{
20925
case VIB_MSG_INIT :
20926
/* reset list */
20927
ResetEditApplyDlg (dlg);
20928
break;
20929
case VIB_MSG_ENTER :
20930
if (dlg->find_txt != NULL)
20931
{
20932
Select (dlg->find_txt);
20933
}
20934
else if (dlg->apply_txt != NULL)
20935
{
20936
Select (dlg->apply_txt);
20937
}
20938
break;
20939
case AECR_VIB_MSG_SET_DEFAULT :
20940
ResetEditApplyDlg (dlg);
20941
break;
20942
case AECR_VIB_MSG_CLEAR_TEXT :
20943
ResetEditApplyDlg (dlg);
20944
break;
20945
default :
20946
break;
20947
}
20948
}
20949
}
20950
20951
static ValNodePtr TestEditApply (DialoG d)
20952
{
20953
EditApplyDlgPtr dlg;
20954
ValNodePtr total_err_list = NULL;
20955
20956
dlg = (EditApplyDlgPtr) GetObjectExtra (d);
20957
if (dlg == NULL)
20958
{
20959
return FALSE;
20960
}
20961
20962
if (dlg->action_choice == AECR_APPLY)
20963
{
20964
if (TextHasNoText (dlg->apply_txt))
20965
{
20966
ValNodeAddPointer (&total_err_list, 0, "apply text");
20967
}
20968
}
20969
else if (dlg->action_choice == AECR_EDIT)
20970
{
20971
if (TextHasNoText (dlg->find_txt))
20972
{
20973
ValNodeAddPointer (&total_err_list, 0, "find text");
20974
}
20975
}
20976
return total_err_list;
20977
}
20978
20979
static void EditApplyDialogCopy (ButtoN b)
20980
{
20981
EditApplyDlgPtr dlg;
20982
CharPtr str = NULL;
20983
20984
dlg = (EditApplyDlgPtr) GetObjectExtra (b);
20985
if (dlg == NULL)
20986
{
20987
return;
20988
}
20989
str = JustSaveStringFromText (dlg->find_txt);
20990
SetTitle (dlg->repl_txt, str);
20991
str = MemFree (str);
20992
}
20993
20994
static DialoG EditApplyDialog
20995
(GrouP h,
20996
Int4 action_choice,
20997
CharPtr apply_label,
20998
Nlm_ChangeNotifyProc change_notify,
20999
Pointer change_userdata)
21000
{
21001
EditApplyDlgPtr dlg;
21002
GrouP p;
21003
ButtoN b;
21004
21005
dlg = (EditApplyDlgPtr) MemNew (sizeof (EditApplyDlgData));
21006
if (dlg == NULL)
21007
{
21008
return NULL;
21009
}
21010
21011
p = HiddenGroup (h, 3, 0, NULL);
21012
SetGroupSpacing (p, 10, 10);
21013
SetObjectExtra (p, dlg, StdCleanupExtraProc);
21014
21015
dlg->dialog = (DialoG) p;
21016
dlg->todialog = EditApplyToDialog;
21017
dlg->fromdialog = DialogToEditApply;
21018
dlg->dialogmessage = EditApplyMessage;
21019
dlg->testdialog = TestEditApply;
21020
dlg->action_choice = action_choice;
21021
21022
if (action_choice == AECR_APPLY)
21023
{
21024
StaticPrompt (p, apply_label, 0, dialogTextHeight, systemFont, 'r');
21025
dlg->apply_txt = DialogText (p, "", 20, ApplyEditConvertRemoveTextChange);
21026
SetObjectExtra (dlg->apply_txt, change_userdata, NULL);
21027
}
21028
else if (action_choice == AECR_EDIT)
21029
{
21030
StaticPrompt (p, "Find", 0, dialogTextHeight, systemFont, 'r');
21031
dlg->find_txt = DialogText (p, "", 18, ApplyEditConvertRemoveTextChange);
21032
SetObjectExtra (dlg->find_txt, change_userdata, NULL);
21033
b = PushButton (p, "Copy", EditApplyDialogCopy);
21034
SetObjectExtra (b, dlg, NULL);
21035
Hide (b);
21036
StaticPrompt (p, "Replace", 0, dialogTextHeight, systemFont, 'r');
21037
dlg->repl_txt = DialogText (p, "", 18, ApplyEditConvertRemoveTextChange);
21038
SetObjectExtra (dlg->repl_txt, change_userdata, NULL);
21039
b = PushButton (p, "Copy", EditApplyDialogCopy);
21040
SetObjectExtra (b, dlg, NULL);
21041
}
21042
return (DialoG) p;
21043
}
21044
21045
24963
typedef struct conversionconflict
21046
24964
{
21047
24965
ConvertFieldPtr cfp;
21206
25124
{
21207
25125
avp->text_to_replace = NULL;
21208
25126
avp->new_text = NULL;
25127
avp->where_to_replace = EditApplyFindLocation_anywhere;
25128
21209
25129
return;
21210
25130
}
21211
25131
21213
25133
{
21214
25134
avp->text_to_replace = StringSave (edit_apply->find_txt);
21215
25135
avp->new_text = StringSave (edit_apply->repl_txt);
25136
avp->where_to_replace = edit_apply->find_location;
21216
25137
}
21217
25138
else if (action_choice == AECR_APPLY)
21218
25139
{
21219
25140
avp->new_text = StringSave (edit_apply->apply_txt);
21220
25141
avp->text_to_replace = NULL;
25142
avp->where_to_replace = EditApplyFindLocation_anywhere;
21221
25143
}
21222
25144
else
21223
25145
{
21224
25146
avp->text_to_replace = NULL;
21225
25147
avp->new_text = NULL;
25148
avp->where_to_replace = EditApplyFindLocation_anywhere;
21226
25149
}
21227
25150
}
21228
25151
25152
#define AECR_DATA_BLOCK \
25153
ValNodePtr field_list; \
25154
ValNodePtr field_list_to; \
25155
ValNodePtr subtype_list; \
25156
Boolean leave_on_original; \
25157
Boolean strip_name_from_text; \
25158
EditApplyPtr edit_apply; \
25159
TextPortionXPtr text_portion; \
25160
Boolean remove_parsed; \
25161
FreeValNodeProc free_field_vn_proc; \
25162
FreeValNodeProc free_subtype_vn_proc;
25163
21229
25164
typedef struct simpleaecr
21230
25165
{
21231
ValNodePtr field_list;
21232
ValNodePtr field_list_to;
21233
ValNodePtr subtype_list;
21234
Boolean leave_on_original;
21235
Boolean strip_name_from_text;
21236
EditApplyPtr edit_apply;
21237
TextPortionPtr text_portion;
21238
Boolean remove_parsed;
21239
FreeValNodeProc free_field_vn_proc;
21240
FreeValNodeProc free_subtype_vn_proc;
25166
AECR_DATA_BLOCK
21241
25167
} SimpleAECRData, PNTR SimpleAECRPtr;
21242
25168
21243
static SimpleAECRPtr SimpleAECRFree (SimpleAECRPtr sp)
25169
static void AECRDataBlockFreeContents (SimpleAECRPtr sp)
21244
25170
{
21245
25171
if (sp != NULL)
21246
25172
{
21248
25174
sp->field_list_to = ValNodeFuncFree (sp->field_list_to, sp->free_field_vn_proc);
21249
25175
sp->subtype_list = ValNodeFuncFree (sp->subtype_list, sp->free_subtype_vn_proc);
21250
25176
sp->edit_apply = EditApplyFree (sp->edit_apply);
21251
sp->text_portion = TextPortionFree(sp->text_portion);
25177
sp->text_portion = TextPortionXFree(sp->text_portion);
25178
}
25179
}
25180
25181
static SimpleAECRPtr SimpleAECRFree (SimpleAECRPtr sp)
25182
{
25183
if (sp != NULL)
25184
{
25185
AECRDataBlockFreeContents (sp);
21252
25186
sp = MemFree (sp);
21253
25187
}
21254
25188
return sp;
21257
25191
/* This function is used to autopopulate the new_text and find fields */
21258
25192
typedef CharPtr (*GetAutoPopulateTextFunc) PROTO ((ValNodePtr, ValNodePtr, Uint2));
21259
25193
21260
typedef struct simpleecrdlg
25194
#define AECR_BLOCK \
25195
DIALOG_MESSAGE_BLOCK \
25196
DialoG field_list; \
25197
DialoG field_list_to; \
25198
DialoG subtype_list; \
25199
ButtoN leave_on_original; \
25200
ButtoN strip_name_from_text; \
25201
DialoG edit_apply; \
25202
DialoG text_portion; \
25203
ButtoN remove_parsed; \
25204
Int4 action_choice; \
25205
/* These are necessary to produce the SimpleAECR structure for output */ \
25206
FreeValNodeProc free_field_vn_proc; \
25207
FreeValNodeProc free_subtype_vn_proc; \
25208
/* These are used for autopopulating text fields */ \
25209
GetAutoPopulateTextFunc get_autopopulate_text; \
25210
Nlm_ChangeNotifyProc change_notify; \
25211
Pointer change_userdata; \
25212
Uint2 entityID;
25213
25214
typedef struct simpleaecrdlg
21261
25215
{
21262
DIALOG_MESSAGE_BLOCK
21263
DialoG field_list;
21264
DialoG field_list_to;
21265
DialoG subtype_list;
21266
ButtoN leave_on_original;
21267
ButtoN strip_name_from_text;
21268
DialoG edit_apply;
21269
DialoG text_portion;
21270
ButtoN remove_parsed;
21271
Int4 action_choice;
21272
/* These are necessary to produce the SimpleAECR structure for output */
21273
FreeValNodeProc free_field_vn_proc;
21274
FreeValNodeProc free_subtype_vn_proc;
21275
21276
/* These are used for autopopulating text fields */
21277
GetAutoPopulateTextFunc get_autopopulate_text;
21278
Nlm_ChangeNotifyProc change_notify;
21279
Pointer change_userdata;
21280
Uint2 entityID;
25216
AECR_BLOCK
21281
25217
} SimpleAECRDlgData, PNTR SimpleAECRDlgPtr;
21282
25218
21283
25219
static void ClearTextSimpleAECRDlg (SimpleAECRDlgPtr dlg)
21508
25444
return total_err_list;
21509
25445
}
21510
25446
25447
static void SimpleAECRButtonChange (ButtoN b)
25448
{
25449
SimpleAECRDlgPtr dlg;
25450
25451
dlg = (SimpleAECRDlgPtr) GetObjectExtra (b);
25452
if (dlg == NULL) return;
25453
25454
if (dlg->change_notify != NULL)
25455
{
25456
(dlg->change_notify) (dlg->change_userdata);
25457
}
25458
}
25459
21511
25460
static DialoG SimpleAECRDialogEx
21512
25461
(GrouP h,
21513
25462
Int4 action_choice,
21582
25531
change_userdata);
21583
25532
if (action_choice == AECR_CONVERT && is_text)
21584
25533
{
21585
dlg->leave_on_original = CheckBox (p, "Leave on original", NULL);
25534
dlg->leave_on_original = CheckBox (p, "Leave on original", SimpleAECRButtonChange);
25535
SetObjectExtra (dlg->leave_on_original, dlg, NULL);
21586
25536
}
21587
25537
if (strip_name)
21588
25538
{
21589
dlg->strip_name_from_text = CheckBox (p, "Strip name from text", NULL);
25539
dlg->strip_name_from_text = CheckBox (p, "Strip name from text", SimpleAECRButtonChange);
25540
SetObjectExtra (dlg->strip_name_from_text, dlg, NULL);
21590
25541
}
21591
25542
}
21592
25543
else
21628
25579
21629
25580
if (is_text && (action_choice == AECR_APPLY || action_choice == AECR_EDIT))
21630
25581
{
21631
dlg->edit_apply = EditApplyDialog (p, action_choice, "New Text",
25582
dlg->edit_apply = EditApplyDialog (p,
25583
action_choice == AECR_APPLY ? eEditApplyChoice_Apply : eEditApplyChoice_Edit,
25584
"New Text", NULL,
21632
25585
change_notify, change_userdata);
21633
25586
dlg->text_portion = NULL;
21634
25587
dlg->remove_parsed = NULL;
21637
25590
{
21638
25591
dlg->edit_apply = NULL;
21639
25592
if (is_text) {
21640
dlg->text_portion = TextPortionDialog(p);
25593
dlg->text_portion = TextPortionXDialog(p);
21641
25594
}
21642
dlg->remove_parsed = CheckBox (p, "Remove from parsed field", NULL);
25595
dlg->remove_parsed = CheckBox (p, "Remove from parsed field", SimpleAECRButtonChange);
25596
SetObjectExtra (dlg->remove_parsed, dlg, NULL);
21643
25597
}
21644
25598
else
21645
25599
{
21719
25673
return rval;
21720
25674
}
21721
25675
25676
typedef struct cdsgeneprotaecrdlg
25677
{
25678
AECR_BLOCK
25679
ButtoN also_mrna;
25680
} CDSGeneProtAECRDlgData, PNTR CDSGeneProtAECRDlgPtr;
25681
25682
typedef struct cdsgeneprotaecr
25683
{
25684
AECR_DATA_BLOCK
25685
Boolean also_mrna;
25686
} CDSGeneProtAECRData, PNTR CDSGeneProtAECRPtr;
25687
25688
25689
static CDSGeneProtAECRPtr CDSGeneProtAECRFree (CDSGeneProtAECRPtr sp)
25690
{
25691
if (sp != NULL)
25692
{
25693
AECRDataBlockFreeContents ((SimpleAECRPtr) sp);
25694
sp = MemFree (sp);
25695
}
25696
return sp;
25697
}
25698
25699
25700
static void PointerToCDSGeneProtAECRDialog (DialoG d, Pointer userdata)
25701
{
25702
CDSGeneProtAECRDlgPtr dlg;
25703
CDSGeneProtAECRPtr data;
25704
25705
dlg = (CDSGeneProtAECRDlgPtr) GetObjectExtra (d);
25706
if (dlg == NULL) return;
25707
data = (CDSGeneProtAECRPtr) userdata;
25708
SimpleAECRToDialog (d, userdata);
25709
if (data != NULL)
25710
{
25711
SetStatus (dlg->also_mrna, data->also_mrna);
25712
}
25713
25714
}
25715
25716
25717
static Boolean ShowingProteinName (CDSGeneProtAECRDlgPtr dlg)
25718
{
25719
ValNodePtr vnp_from, vnp_to;
25720
Int4 protein_name_field_num = 2 + num_gene_fields + num_mrna_fields;
25721
Boolean rval = FALSE;
25722
25723
if (dlg == NULL) return FALSE;
25724
25725
vnp_from = DialogToPointer (dlg->field_list);
25726
vnp_to = DialogToPointer (dlg->field_list_to);
25727
25728
if ((vnp_from != NULL && vnp_from->data.intvalue == protein_name_field_num)
25729
|| (vnp_to != NULL && vnp_to->data.intvalue == protein_name_field_num))
25730
{
25731
rval = TRUE;
25732
}
25733
vnp_from = ValNodeFree (vnp_from);
25734
vnp_to = ValNodeFree (vnp_to);
25735
25736
return rval;
25737
}
25738
25739
25740
static Pointer CDSGeneProtAECRDialogToPointer (DialoG d)
25741
{
25742
CDSGeneProtAECRDlgPtr dlg;
25743
SimpleAECRPtr subset;
25744
CDSGeneProtAECRPtr data = NULL;
25745
25746
dlg = (CDSGeneProtAECRDlgPtr) GetObjectExtra (d);
25747
if (dlg == NULL) return NULL;
25748
25749
subset = DialogToSimpleAECR (d);
25750
if (subset != NULL)
25751
{
25752
data = (CDSGeneProtAECRPtr) MemNew (sizeof (CDSGeneProtAECRData));
25753
MemCpy (data, subset, sizeof (SimpleAECRData));
25754
MemSet (subset, 0, sizeof (SimpleAECRData));
25755
subset = MemFree (subset);
25756
if (ShowingProteinName (dlg))
25757
{
25758
data->also_mrna = GetStatus (dlg->also_mrna);
25759
}
25760
else
25761
{
25762
data->also_mrna = FALSE;
25763
}
25764
}
25765
return data;
25766
}
25767
25768
25769
static void CDSGeneProtAECRDialogChange (Pointer data)
25770
{
25771
CDSGeneProtAECRDlgPtr dlg;
25772
25773
dlg = (CDSGeneProtAECRDlgPtr) data;
25774
if (dlg == NULL) return;
25775
25776
if (ShowingProteinName (dlg))
25777
{
25778
Show (dlg->also_mrna);
25779
}
25780
else
25781
{
25782
Hide (dlg->also_mrna);
25783
}
25784
25785
SimpleAECRDialogChangeNotify (dlg);
25786
}
25787
25788
21722
25789
static DialoG CDSGeneProtAECRDialog
21723
25790
(GrouP h,
21724
25791
Int4 action_choice,
21726
25793
Pointer change_userdata,
21727
25794
Uint2 entityID)
21728
25795
{
21729
return SimpleAECRDialog (h, action_choice, change_notify, change_userdata,
21730
NULL, NULL,
21731
CDSGeneProtFieldSelectionDialog, NULL,
21732
CDSGeneProtAutopopulate,
21733
"Field", NULL, TRUE, entityID);
25796
CDSGeneProtAECRDlgPtr dlg;
25797
GrouP p, g1;
25798
SeqEntryPtr sep;
25799
25800
dlg = (CDSGeneProtAECRDlgPtr) MemNew (sizeof (CDSGeneProtAECRDlgData));
25801
if (dlg == NULL)
25802
{
25803
return NULL;
25804
}
25805
25806
p = HiddenGroup (h, -1, 0, NULL);
25807
SetObjectExtra (p, dlg, StdCleanupExtraProc);
25808
SetGroupSpacing (p, 10, 10);
25809
25810
dlg->dialog = (DialoG) p;
25811
dlg->todialog = PointerToCDSGeneProtAECRDialog;
25812
dlg->fromdialog = CDSGeneProtAECRDialogToPointer;
25813
dlg->dialogmessage = SimpleAECRMessage;
25814
dlg->testdialog = TestSimpleAECR;
25815
dlg->action_choice = action_choice;
25816
dlg->free_field_vn_proc = NULL;
25817
dlg->free_subtype_vn_proc = NULL;
25818
dlg->change_notify = change_notify;
25819
dlg->change_userdata = change_userdata;
25820
dlg->get_autopopulate_text = CDSGeneProtAutopopulate;
25821
dlg->entityID = entityID;
25822
dlg->strip_name_from_text = NULL;
25823
25824
dlg->subtype_list = NULL;
25825
25826
sep = GetTopSeqEntryForEntityID(entityID);
25827
25828
if (action_choice == AECR_CONVERT || action_choice == AECR_SWAP || action_choice == AECR_PARSE)
25829
{
25830
g1 = HiddenGroup (p, 2, 0, NULL);
25831
StaticPrompt (g1, "From", 0, dialogTextHeight, systemFont, 'l');
25832
StaticPrompt (g1, "To", 0, dialogTextHeight, systemFont, 'l');
25833
25834
dlg->field_list = CDSGeneProtFieldSelectionDialog (g1, FALSE,
25835
CDSGeneProtAECRDialogChange,
25836
dlg);
25837
dlg->field_list_to = CDSGeneProtFieldSelectionDialog (g1, FALSE,
25838
CDSGeneProtAECRDialogChange,
25839
dlg);
25840
if (action_choice == AECR_CONVERT)
25841
{
25842
dlg->leave_on_original = CheckBox (p, "Leave on original", NULL);
25843
}
25844
}
25845
else
25846
{
25847
g1 = HiddenGroup (p, 1, 0, NULL);
25848
StaticPrompt (g1, "Field", 0, dialogTextHeight, systemFont, 'l');
25849
if (action_choice == AECR_REMOVE)
25850
{
25851
dlg->field_list = CDSGeneProtFieldSelectionDialog (g1, TRUE,
25852
CDSGeneProtAECRDialogChange,
25853
dlg);
25854
}
25855
else
25856
{
25857
dlg->field_list = CDSGeneProtFieldSelectionDialog (g1, FALSE,
25858
CDSGeneProtAECRDialogChange,
25859
dlg);
25860
}
25861
}
25862
25863
if (action_choice == AECR_APPLY || action_choice == AECR_EDIT)
25864
{
25865
dlg->edit_apply = EditApplyDialog (p,
25866
action_choice == AECR_APPLY ? eEditApplyChoice_Apply : eEditApplyChoice_Edit,
25867
"New Text", NULL,
25868
change_notify, change_userdata);
25869
dlg->text_portion = NULL;
25870
dlg->remove_parsed = NULL;
25871
}
25872
else if (action_choice == AECR_PARSE)
25873
{
25874
dlg->edit_apply = NULL;
25875
dlg->text_portion = TextPortionXDialog(p);
25876
dlg->remove_parsed = CheckBox (p, "Remove from parsed field", NULL);
25877
}
25878
else
25879
{
25880
dlg->edit_apply = NULL;
25881
dlg->text_portion = NULL;
25882
dlg->remove_parsed = NULL;
25883
}
25884
25885
dlg->also_mrna = CheckBox (p, "Make mRNA product match CDS protein name", NULL);
25886
25887
if (action_choice == AECR_CONVERT)
25888
{
25889
AlignObjects (ALIGN_CENTER, (HANDLE) g1, (HANDLE) dlg->leave_on_original, (HANDLE) dlg->also_mrna, NULL);
25890
}
25891
else if (action_choice == AECR_SWAP)
25892
{
25893
AlignObjects (ALIGN_CENTER, (HANDLE) g1, (HANDLE) dlg->strip_name_from_text, (HANDLE) dlg->also_mrna, NULL);
25894
}
25895
else if (action_choice == AECR_PARSE)
25896
{
25897
AlignObjects (ALIGN_CENTER, (HANDLE) g1, (HANDLE) dlg->text_portion, (HANDLE) dlg->remove_parsed, (HANDLE) dlg->also_mrna, NULL);
25898
}
25899
else
25900
{
25901
AlignObjects (ALIGN_CENTER, (HANDLE) g1, (HANDLE) dlg->edit_apply, (HANDLE) dlg->also_mrna, NULL);
25902
}
25903
return (DialoG) p;
25904
}
25905
25906
static Boolean AreFilterAndFieldBothForMatPeptide (FilterSetPtr fsp, ValNodePtr field_list)
25907
{
25908
if (fsp != NULL && fsp->cgp == NULL
25909
&& IsCDSetMatPeptideQualChoice(fsp->cgp->qual_choice)
25910
&& IsCDSetMatPeptideQualChoice(field_list))
25911
{
25912
return TRUE;
25913
}
25914
else
25915
{
25916
return FALSE;
25917
}
25918
}
25919
25920
static void AddStringToSample (CharPtr str, GetSamplePtr gsp)
25921
{
25922
if (gsp == NULL) return;
25923
25924
if (str != NULL)
25925
{
25926
gsp->num_found ++;
25927
}
25928
if (gsp->sample_text == NULL)
25929
{
25930
gsp->sample_text = StringSave (str);
25931
}
25932
else
25933
{
25934
if (StringCmp (str, gsp->sample_text) != 0)
25935
{
25936
gsp->all_same = FALSE;
25937
}
25938
}
21734
25939
}
21735
25940
21736
25941
static GetSamplePtr
21737
25942
GetCDSGeneProtAECRSample
21738
25943
(ValNodePtr cdset_list,
21739
25944
ValNodePtr field_list,
21740
ValNodePtr field_list_to)
25945
ValNodePtr field_list_to,
25946
FilterSetPtr fsp)
21741
25947
{
21742
25948
GetSamplePtr gsp;
21743
ValNodePtr cdset_vnp;
25949
ValNodePtr cdset_vnp, sfp_vnp;
21744
25950
CharPtr str;
21745
25951
CDSetPtr cdsp;
25952
21746
25953
gsp = (GetSamplePtr) MemNew (sizeof (GetSampleData));
21747
25954
if (gsp == NULL)
21748
25955
{
21752
25959
gsp->copy_vn_proc = IntValNodeCopy;
21753
25960
for (cdset_vnp = cdset_list; cdset_vnp != NULL; cdset_vnp = cdset_vnp->next)
21754
25961
{
21755
str = GetCDSetField (cdset_vnp->data.ptrvalue, field_list);
21756
if (str != NULL && field_list_to != NULL)
21757
{
21758
str = MemFree (str);
21759
str = GetCDSetField (cdset_vnp->data.ptrvalue, field_list_to);
21760
}
21761
if (str != NULL)
21762
{
21763
gsp->num_found ++;
21764
}
21765
if (gsp->sample_text == NULL)
21766
{
21767
gsp->sample_text = str;
21768
}
21769
else
21770
{
21771
if (StringCmp (str, gsp->sample_text) != 0)
21772
{
21773
gsp->all_same = FALSE;
21774
}
25962
cdsp = (CDSetPtr) cdset_vnp->data.ptrvalue;
25963
if (IsCDSetMatPeptideQualChoice(field_list) || IsCDSetMatPeptideQualChoice(field_list_to))
25964
{
25965
/* need to look at all mat_peptide features */
25966
for (sfp_vnp = cdsp->prot_list; sfp_vnp != NULL; sfp_vnp = sfp_vnp->next)
25967
{
25968
if (fsp != NULL && fsp->cgp != NULL && DoesConstraintDisqualifyFeature (sfp_vnp->data.ptrvalue, fsp->cgp))
25969
{
25970
/* this feature will be skipped in the action, so it should not be included in the sample */
25971
}
25972
else
25973
{
25974
str = GetCDSGeneProtField (sfp_vnp->data.ptrvalue, field_list, fsp);
25975
if (str != NULL && field_list_to != NULL)
25976
{
25977
str = GetCDSGeneProtField (sfp_vnp->data.ptrvalue, field_list_to, fsp);
25978
}
25979
AddStringToSample (str, gsp);
25980
str = MemFree (str);
25981
}
25982
}
25983
} else {
25984
str = GetCDSetField (cdsp, field_list);
25985
if (str != NULL && field_list_to != NULL)
25986
{
25987
str = MemFree (str);
25988
str = GetCDSetField (cdset_vnp->data.ptrvalue, field_list_to);
25989
}
25990
AddStringToSample (str, gsp);
21775
25991
str = MemFree (str);
21776
25992
}
21777
25993
}
21778
25994
return gsp;
21779
25995
}
21780
25996
25997
static Boolean FeatureTypeMissingFromCDSet (CDSetPtr cdsp, Uint2 choice)
25998
{
25999
ValNodePtr vnp;
26000
SeqFeatPtr sfp;
26001
Boolean is_missing = TRUE;
26002
26003
if (cdsp == NULL) return TRUE;
26004
switch (choice)
26005
{
26006
case FEATDEF_CDS:
26007
if (cdsp->cds_list != NULL)
26008
{
26009
is_missing = FALSE;
26010
}
26011
break;
26012
case FEATDEF_GENE:
26013
if (cdsp->gene_list != NULL)
26014
{
26015
is_missing = FALSE;
26016
}
26017
break;
26018
case FEATDEF_mRNA:
26019
if (cdsp->mrna_list != NULL)
26020
{
26021
is_missing = FALSE;
26022
}
26023
break;
26024
case FEATDEF_PROT:
26025
case FEATDEF_mat_peptide_aa:
26026
for (vnp = cdsp->prot_list; vnp != NULL; vnp = vnp->next)
26027
{
26028
sfp = (SeqFeatPtr) vnp->data.ptrvalue;
26029
if (sfp != NULL && sfp->idx.subtype == choice)
26030
{
26031
is_missing = FALSE;
26032
}
26033
}
26034
break;
26035
}
26036
return is_missing;
26037
}
26038
26039
static Int4
26040
CountMissingFeatures
26041
(ValNodePtr cdset_list,
26042
ValNodePtr field_list,
26043
ValNodePtr field_list_to,
26044
FilterSetPtr fsp)
26045
{
26046
ValNodePtr cdset_vnp, sfp_vnp;
26047
CharPtr str;
26048
CDSetPtr cdsp;
26049
Uint2 choice_from, choice_to;
26050
Int4 num_missing = 0;
26051
26052
choice_from = FeatDefTypeFromFieldList (field_list);
26053
choice_to = FeatDefTypeFromFieldList (field_list_to);
26054
26055
if (choice_from == 0 || choice_to == 0 || choice_from == choice_to)
26056
{
26057
return 0;
26058
}
26059
26060
for (cdset_vnp = cdset_list; cdset_vnp != NULL; cdset_vnp = cdset_vnp->next)
26061
{
26062
cdsp = (CDSetPtr) cdset_vnp->data.ptrvalue;
26063
26064
if (choice_from == FEATDEF_mat_peptide_aa)
26065
{
26066
/* need to look at all mat_peptide features */
26067
for (sfp_vnp = cdsp->prot_list; sfp_vnp != NULL; sfp_vnp = sfp_vnp->next)
26068
{
26069
if (fsp != NULL && fsp->cgp != NULL && DoesConstraintDisqualifyFeature (sfp_vnp->data.ptrvalue, fsp->cgp))
26070
{
26071
/* this feature will be skipped in the action, so it doesn't count towards missing sets */
26072
}
26073
else
26074
{
26075
str = GetCDSGeneProtField (sfp_vnp->data.ptrvalue, field_list, fsp);
26076
if (str != NULL)
26077
{
26078
if (FeatureTypeMissingFromCDSet (cdsp, choice_to))
26079
{
26080
num_missing++;
26081
}
26082
}
26083
str = MemFree (str);
26084
}
26085
}
26086
} else {
26087
str = GetCDSetField (cdsp, field_list);
26088
if (str != NULL)
26089
{
26090
if (FeatureTypeMissingFromCDSet (cdsp, choice_to))
26091
{
26092
num_missing++;
26093
}
26094
}
26095
str = MemFree (str);
26096
}
26097
}
26098
return num_missing;
26099
}
26100
26101
26102
/* things get tricksy when we're dealing with mat_peptides, because there
26103
* can be more than one of them in the CDS-mRNA-Gene-Prot group.
26104
*/
26105
26106
static Boolean CDSGeneProtApplyToAllThatMatchFilter
26107
(CharPtr str_src,
26108
CDSetPtr cdsp,
26109
ValNodePtr field_list_to,
26110
FilterSetPtr fsp,
26111
ExistingTextPtr etp)
26112
{
26113
ApplyValueData avd;
26114
26115
avd.where_to_replace = EditApplyFindLocation_anywhere;
26116
26117
/* build gene if we're applying to gene but gene doesn't already exist */
26118
BuildNewCDSGeneProtFeature (cdsp, field_list_to, NULL);
26119
avd.field_list = NULL;
26120
avd.new_text = str_src;
26121
avd.text_to_replace = NULL;
26122
avd.etp = etp;
26123
26124
return SetCDSetField (cdsp, field_list_to, &avd, fsp);
26125
}
26126
26127
static Boolean CDSGeneProtApplyToOneFeature
26128
(CharPtr str_src,
26129
SeqFeatPtr sfp,
26130
ValNodePtr field_list_to,
26131
FilterSetPtr fsp,
26132
ExistingTextPtr etp)
26133
{
26134
ApplyValueData avd;
26135
26136
avd.where_to_replace = EditApplyFindLocation_anywhere;
26137
26138
avd.field_list = NULL;
26139
avd.new_text = str_src;
26140
avd.text_to_replace = NULL;
26141
avd.etp = etp;
26142
26143
return SetCDSGeneProtField (sfp, field_list_to, &avd, fsp);
26144
}
26145
26146
26147
static void CopyProteinNameTomRNAName (CDSetPtr cdsp)
26148
{
26149
Int4 protein_name_field_num = 2 + num_gene_fields + num_mrna_fields;
26150
Int4 mrna_product_field_num = 2 + num_gene_fields;
26151
ValNode vn_src, vn_dst;
26152
ApplyValueData avd;
26153
26154
vn_src.data.intvalue = protein_name_field_num;
26155
vn_src.next = NULL;
26156
vn_src.choice = 0;
26157
26158
vn_dst.data.intvalue = mrna_product_field_num;
26159
vn_dst.next = NULL;
26160
vn_dst.choice = 0;
26161
26162
avd.new_text = GetCDSetField (cdsp, &vn_src);
26163
avd.etp = NULL;
26164
avd.field_list = NULL;
26165
avd.text_to_replace = NULL;
26166
avd.where_to_replace = EditApplyFindLocation_anywhere;
26167
SetCDSetField (cdsp, &vn_dst, &avd, NULL);
26168
}
26169
26170
static void CDSGeneProtConvert
26171
(CDSetPtr cdsp,
26172
CDSGeneProtAECRPtr sp,
26173
FilterSetPtr fsp,
26174
ExistingTextPtr etp,
26175
Boolean build_missing)
26176
{
26177
CharPtr str_src = NULL;
26178
CharPtr str_dst = NULL;
26179
ValNodePtr sfp_vnp;
26180
SeqFeatPtr sfp;
26181
Boolean able_to_apply = FALSE;
26182
Boolean change_made = FALSE;
26183
26184
if (IsCDSetMatPeptideQualChoice(sp->field_list))
26185
{
26186
for (sfp_vnp = cdsp->prot_list; sfp_vnp != NULL; sfp_vnp = sfp_vnp->next)
26187
{
26188
sfp = sfp_vnp->data.ptrvalue;
26189
able_to_apply = FALSE;
26190
if (fsp == NULL || !DoesConstraintDisqualifyFeature(sfp, fsp->cgp)) {
26191
str_src = GetCDSGeneProtField (sfp_vnp->data.ptrvalue, sp->field_list, NULL);
26192
if (str_src != NULL)
26193
{
26194
if (IsCDSetMatPeptideQualChoice (sp->field_list_to))
26195
{
26196
CDSGeneProtApplyToOneFeature (str_src, sfp, sp->field_list_to, fsp, etp);
26197
change_made = TRUE;
26198
}
26199
else
26200
{
26201
if (build_missing)
26202
{
26203
BuildNewCDSGeneProtFeature (cdsp, sp->field_list_to, sp->field_list);
26204
}
26205
able_to_apply = CDSGeneProtApplyToAllThatMatchFilter (str_src, cdsp, sp->field_list_to, fsp, etp);
26206
if (able_to_apply)
26207
{
26208
change_made = TRUE;
26209
}
26210
}
26211
if (!sp->leave_on_original && able_to_apply)
26212
{
26213
sp->field_list->choice = 1;
26214
RemoveCDSGeneProtField (sfp, sp->field_list, fsp);
26215
change_made = TRUE;
26216
}
26217
}
26218
}
26219
}
26220
}
26221
else
26222
{
26223
str_src = GetCDSetField (cdsp, sp->field_list);
26224
if (str_src != NULL)
26225
{
26226
if (build_missing)
26227
{
26228
BuildNewCDSGeneProtFeature (cdsp, sp->field_list_to, sp->field_list);
26229
}
26230
able_to_apply = CDSGeneProtApplyToAllThatMatchFilter (str_src, cdsp, sp->field_list_to, fsp, etp);
26231
if (!sp->leave_on_original && able_to_apply)
26232
{
26233
sp->field_list->choice = 1;
26234
RemoveCDSetField (cdsp, sp->field_list, fsp);
26235
}
26236
if (able_to_apply)
26237
{
26238
change_made = TRUE;
26239
}
26240
}
26241
}
26242
if (sp->also_mrna && change_made)
26243
{
26244
CopyProteinNameTomRNAName (cdsp);
26245
}
26246
26247
}
26248
26249
static void CDSGeneProtSwap
26250
(CDSetPtr cdsp,
26251
CDSGeneProtAECRPtr sp,
26252
FilterSetPtr fsp,
26253
ExistingTextPtr etp,
26254
Boolean build_missing)
26255
{
26256
CharPtr str_src = NULL;
26257
CharPtr str_dst = NULL;
26258
ValNodePtr sfp_vnp_src, sfp_vnp_dst, vnp_swap;
26259
SeqFeatPtr sfp_src, sfp_dst;
26260
ApplyValueData avd;
26261
Uint2 choice_to, choice_from;
26262
Boolean change_made = FALSE;
26263
26264
avd.where_to_replace = EditApplyFindLocation_anywhere;
26265
26266
choice_from = FeatDefTypeFromFieldList (sp->field_list);
26267
choice_to = FeatDefTypeFromFieldList (sp->field_list_to);
26268
26269
if (choice_from == FEATDEF_mat_peptide_aa || choice_to == FEATDEF_mat_peptide_aa)
26270
{
26271
/* make sure mat_peptide qual if in field_list */
26272
if (!IsCDSetMatPeptideQualChoice(sp->field_list))
26273
{
26274
vnp_swap = sp->field_list;
26275
sp->field_list = sp->field_list_to;
26276
sp->field_list_to = vnp_swap;
26277
}
26278
for (sfp_vnp_src = cdsp->prot_list; sfp_vnp_src != NULL; sfp_vnp_src = sfp_vnp_src->next)
26279
{
26280
sfp_src = sfp_vnp_src->data.ptrvalue;
26281
if (fsp == NULL || !DoesConstraintDisqualifyFeature(sfp_src, fsp->cgp))
26282
{
26283
str_src = GetCDSGeneProtField (sfp_src, sp->field_list, NULL);
26284
if (IsCDSetMatPeptideQualChoice(sp->field_list_to))
26285
{
26286
for (sfp_vnp_dst = cdsp->prot_list; sfp_vnp_dst != NULL; sfp_vnp_dst = sfp_vnp_dst->next)
26287
{
26288
sfp_dst = sfp_vnp_dst->data.ptrvalue;
26289
if (fsp == NULL || !DoesConstraintDisqualifyFeature(sfp_dst, fsp->cgp))
26290
{
26291
str_dst = GetCDSGeneProtField (sfp_dst, sp->field_list_to, NULL);
26292
if (!StringHasNoText (str_src) || !StringHasNoText (str_dst))
26293
{
26294
if (build_missing)
26295
{
26296
BuildNewCDSGeneProtFeature (cdsp, sp->field_list, sp->field_list_to);
26297
BuildNewCDSGeneProtFeature (cdsp, sp->field_list_to, sp->field_list);
26298
}
26299
if (!FeatureTypeMissingFromCDSet(cdsp, choice_from)
26300
&& !FeatureTypeMissingFromCDSet(cdsp, choice_to))
26301
{
26302
avd.etp = NULL;
26303
avd.text_to_replace = NULL;
26304
avd.new_text = StringSave (str_src);
26305
avd.field_list = NULL;
26306
SetCDSGeneProtField (sfp_dst, sp->field_list_to, &avd, fsp);
26307
avd.new_text = StringSave (str_dst);
26308
SetCDSGeneProtField (sfp_src, sp->field_list, &avd, fsp);
26309
change_made = TRUE;
26310
}
26311
}
26312
str_dst = MemFree (str_dst);
26313
}
26314
}
26315
}
26316
else
26317
{
26318
str_dst = GetCDSetField (cdsp, sp->field_list_to);
26319
if (!StringHasNoText (str_src) || !StringHasNoText (str_dst))
26320
{
26321
if (build_missing)
26322
{
26323
BuildNewCDSGeneProtFeature (cdsp, sp->field_list, sp->field_list_to);
26324
BuildNewCDSGeneProtFeature (cdsp, sp->field_list_to, sp->field_list);
26325
}
26326
if (!FeatureTypeMissingFromCDSet(cdsp, choice_from)
26327
&& !FeatureTypeMissingFromCDSet(cdsp, choice_to))
26328
{
26329
avd.etp = NULL;
26330
avd.text_to_replace = NULL;
26331
avd.new_text = StringSave (str_src);
26332
avd.field_list = NULL;
26333
SetCDSetField (cdsp, sp->field_list_to, &avd, fsp);
26334
avd.new_text = StringSave (str_dst);
26335
SetCDSGeneProtField (sfp_src, sp->field_list, &avd, fsp);
26336
change_made = TRUE;
26337
}
26338
}
26339
str_dst = MemFree (str_dst);
26340
}
26341
str_src = MemFree (str_src);
26342
}
26343
}
26344
}
26345
else
26346
{
26347
str_src = GetCDSetField (cdsp, sp->field_list);
26348
str_dst = GetCDSetField (cdsp, sp->field_list_to);
26349
if (!StringHasNoText (str_src) || !StringHasNoText (str_dst))
26350
{
26351
if (build_missing)
26352
{
26353
BuildNewCDSGeneProtFeature (cdsp, sp->field_list, sp->field_list_to);
26354
BuildNewCDSGeneProtFeature (cdsp, sp->field_list_to, sp->field_list);
26355
}
26356
if (!FeatureTypeMissingFromCDSet(cdsp, choice_from)
26357
&& !FeatureTypeMissingFromCDSet(cdsp, choice_to))
26358
{
26359
avd.etp = NULL;
26360
avd.text_to_replace = NULL;
26361
avd.new_text = str_src;
26362
avd.field_list = NULL;
26363
SetCDSetField (cdsp, sp->field_list_to, &avd, fsp);
26364
avd.new_text = str_dst;
26365
SetCDSetField (cdsp, sp->field_list, &avd, fsp);
26366
change_made = TRUE;
26367
}
26368
}
26369
}
26370
if (change_made && sp->also_mrna)
26371
{
26372
CopyProteinNameTomRNAName (cdsp);
26373
}
26374
}
26375
26376
26377
static void CDSGeneProtParse
26378
(CDSetPtr cdsp,
26379
CDSGeneProtAECRPtr sp,
26380
FilterSetPtr fsp,
26381
ExistingTextPtr etp,
26382
Boolean build_missing)
26383
{
26384
CharPtr str_src = NULL;
26385
CharPtr str_dst = NULL;
26386
ValNodePtr sfp_vnp;
26387
SeqFeatPtr sfp;
26388
ApplyValueData avd;
26389
Boolean able_to_apply;
26390
Boolean change_made = FALSE;
26391
26392
avd.where_to_replace = EditApplyFindLocation_anywhere;
26393
26394
if (IsCDSetMatPeptideQualChoice(sp->field_list))
26395
{
26396
for (sfp_vnp = cdsp->prot_list; sfp_vnp != NULL; sfp_vnp = sfp_vnp->next)
26397
{
26398
sfp = sfp_vnp->data.ptrvalue;
26399
if (fsp == NULL || !DoesConstraintDisqualifyFeature(sfp, fsp->cgp))
26400
{
26401
str_src = GetCDSGeneProtField (sfp, sp->field_list, NULL);
26402
str_dst = str_src;
26403
str_src = ReplaceStringForParse(str_src, sp->text_portion);
26404
if (!sp->remove_parsed) {
26405
str_dst = MemFree (str_dst);
26406
}
26407
26408
if (str_src != NULL) {
26409
if (build_missing)
26410
{
26411
BuildNewCDSGeneProtFeature (cdsp, sp->field_list_to, sp->field_list);
26412
}
26413
able_to_apply = FALSE;
26414
if (IsCDSetMatPeptideQualChoice (sp->field_list_to))
26415
{
26416
able_to_apply = CDSGeneProtApplyToOneFeature (str_src, sfp, sp->field_list_to, fsp, etp);
26417
}
26418
else
26419
{
26420
able_to_apply = CDSGeneProtApplyToAllThatMatchFilter (str_src, cdsp, sp->field_list_to, fsp, etp);
26421
}
26422
if (sp->remove_parsed && able_to_apply) {
26423
CDSGeneProtApplyToOneFeature (str_dst, sfp, sp->field_list, fsp, NULL);
26424
}
26425
if (able_to_apply)
26426
{
26427
change_made = TRUE;
26428
}
26429
str_src = MemFree (str_src);
26430
}
26431
str_dst = MemFree (str_dst);
26432
}
26433
}
26434
}
26435
else
26436
{
26437
str_src = GetCDSetField (cdsp, sp->field_list);
26438
str_dst = str_src;
26439
str_src = ReplaceStringForParse(str_src, sp->text_portion);
26440
if (!sp->remove_parsed) {
26441
str_dst = MemFree (str_dst);
26442
}
26443
if (str_src != NULL) {
26444
if (build_missing)
26445
{
26446
BuildNewCDSGeneProtFeature (cdsp, sp->field_list_to, sp->field_list);
26447
}
26448
able_to_apply = CDSGeneProtApplyToAllThatMatchFilter (str_src, cdsp, sp->field_list_to, fsp, etp);
26449
if (sp->remove_parsed && able_to_apply) {
26450
CDSGeneProtApplyToAllThatMatchFilter (str_dst, cdsp, sp->field_list, fsp, NULL);
26451
}
26452
if (able_to_apply)
26453
{
26454
change_made = TRUE;
26455
}
26456
str_src = MemFree (str_src);
26457
}
26458
str_dst = MemFree (str_dst);
26459
}
26460
26461
if (sp->also_mrna && change_made)
26462
{
26463
CopyProteinNameTomRNAName (cdsp);
26464
}
26465
}
26466
26467
static void CDSGeneProtEdit
26468
(CDSetPtr cdsp,
26469
CDSGeneProtAECRPtr sp,
26470
FilterSetPtr fsp,
26471
ExistingTextPtr etp)
26472
{
26473
ApplyValueData avd;
26474
26475
avd.where_to_replace = EditApplyFindLocation_anywhere;
26476
26477
avd.field_list = sp->field_list;
26478
avd.etp = NULL;
26479
AddEditApplyDataToApplyValue (AECR_EDIT, sp->edit_apply, &avd);
26480
SetCDSetField (cdsp, sp->field_list, &avd, fsp);
26481
avd.text_to_replace = MemFree (avd.text_to_replace);
26482
avd.new_text = MemFree (avd.new_text);
26483
if (sp->also_mrna)
26484
{
26485
CopyProteinNameTomRNAName (cdsp);
26486
}
26487
}
26488
26489
static ValNodePtr CollectCDSetList (Uint2 entityID, FilterSetPtr fsp)
26490
{
26491
ValNodePtr cdset_list;
26492
26493
/* need to create a list of sets */
26494
#if 1
26495
cdset_list = BuildCDSet2List (entityID, fsp == NULL || fsp->cgp == NULL ? NULL : fsp->cgp);
26496
26497
#else
26498
if (fsp == NULL || fsp->cgp == NULL)
26499
{
26500
/* if we are applying to mat_peptides AND the constraint involved mat_peptides,
26501
* create all sets and we'll filter out later.
26502
*/
26503
cdset_list = BuildCDSetList (entityID, NULL);
26504
}
26505
else
26506
{
26507
cdset_list = BuildCDSetList (entityID, fsp->cgp);
26508
}
26509
#endif
26510
return cdset_list;
26511
}
26512
26513
26514
static void MarkAlreadyEditedGenes (CDSetPtr cdsp, ValNodePtr cdset_list)
26515
{
26516
ValNodePtr gene_vnp, list_vnp, genecheck_vnp;
26517
CDSetPtr check_cdsp;
26518
26519
if (cdsp == NULL || cdset_list == NULL || cdsp->gene_list == NULL) return;
26520
26521
for (gene_vnp = cdsp->gene_list; gene_vnp != NULL; gene_vnp = gene_vnp->next)
26522
{
26523
if (gene_vnp->choice > 0) continue;
26524
for (list_vnp = cdset_list; list_vnp != NULL; list_vnp = list_vnp->next)
26525
{
26526
check_cdsp = (CDSetPtr) list_vnp->data.ptrvalue;
26527
if (check_cdsp != NULL)
26528
{
26529
for (genecheck_vnp = check_cdsp->gene_list; genecheck_vnp != NULL; genecheck_vnp = genecheck_vnp->next)
26530
{
26531
if (genecheck_vnp->data.ptrvalue == gene_vnp->data.ptrvalue)
26532
{
26533
genecheck_vnp->choice = 1;
26534
}
26535
}
26536
}
26537
}
26538
}
26539
}
26540
26541
21781
26542
static Boolean CDSGeneProtAECRAction (Pointer userdata)
21782
26543
{
21783
26544
ApplyEditConvertRemovePtr ap;
21784
SimpleAECRPtr sp;
26545
CDSGeneProtAECRPtr sp;
21785
26546
Int4 action_choice;
21786
26547
SeqEntryPtr sep;
21787
ApplyValueData avd;
21788
26548
FilterSetPtr fsp;
21789
26549
GetSamplePtr gsp = NULL;
21790
26550
Boolean rval = TRUE;
21791
26551
ValNodePtr cdset_list, cdset_vnp;
21792
26552
ExistingTextPtr etp = NULL;
21793
CharPtr str_src, str_dst;
26553
Int4 num_missing;
26554
Boolean build_missing = FALSE;
26555
MsgAnswer ans;
21794
26556
21795
26557
ap = (ApplyEditConvertRemovePtr) userdata;
21796
26558
if (ap == NULL)
21813
26575
{
21814
26576
return FALSE;
21815
26577
}
21816
sp = (SimpleAECRPtr) DialogToPointer (ap->aecr_pages[action_choice - 1]);
26578
sp = (CDSGeneProtAECRPtr) DialogToPointer (ap->aecr_pages[action_choice - 1]);
21817
26579
21818
26580
sep = GetTopSeqEntryForEntityID (ap->input_entityID);
21819
26581
if (sp->field_list == NULL
21820
26582
|| ((action_choice == AECR_CONVERT || action_choice == AECR_SWAP)
21821
26583
&& sp->field_list == NULL))
21822
26584
{
21823
sp = SimpleAECRFree (sp);
26585
sp = CDSGeneProtAECRFree (sp);
21824
26586
ArrowCursor ();
21825
26587
Update ();
21826
26588
return FALSE;
21829
26591
fsp = (FilterSetPtr) DialogToPointer (ap->constraints);
21830
26592
21831
26593
/* need to create a list of sets */
21832
if (fsp == NULL)
21833
{
21834
cdset_list = BuildCDSetList (ap->input_entityID, NULL);
21835
}
21836
else
21837
{
21838
cdset_list = BuildCDSetList (ap->input_entityID, fsp->cgp);
21839
}
26594
cdset_list = CollectCDSetList (ap->input_entityID, fsp);
21840
26595
21841
26596
/* find existing text and how to handle it */
21842
26597
if (action_choice == AECR_CONVERT || action_choice == AECR_APPLY || action_choice == AECR_PARSE)
21843
26598
{
21844
gsp = GetCDSGeneProtAECRSample (cdset_list, sp->field_list, sp->field_list_to);
21845
etp = GetExistingTextHandlerInfo (gsp, FALSE);
26599
gsp = GetCDSGeneProtAECRSample (cdset_list, sp->field_list, sp->field_list_to, fsp);
26600
etp = GetExistingTextHandlerInfo (gsp == NULL ? 0 : gsp->num_found, FALSE);
21846
26601
gsp = GetSampleFree (gsp);
21847
if (etp != NULL && etp->existing_text_choice == EXISTING_TEXT_CHOICE_CANCEL)
26602
if (etp != NULL && etp->existing_text_choice == eExistingTextChoiceCancel)
21848
26603
{
21849
26604
rval = FALSE;
21850
26605
}
21851
26606
}
21852
26607
26608
num_missing = CountMissingFeatures (cdset_list, sp->field_list, sp->field_list_to, fsp);
26609
if (action_choice == AECR_SWAP)
26610
{
26611
num_missing += CountMissingFeatures (cdset_list, sp->field_list_to, sp->field_list, fsp);
26612
}
26613
if (num_missing > 0)
26614
{
26615
ans = Message (MSG_YNC, "There are %d fields where the feature to which the field should be applied does not exist. Do you want to create these features?", num_missing);
26616
if (ans == ANS_CANCEL)
26617
{
26618
rval = FALSE;
26619
} else if (ans == ANS_YES) {
26620
build_missing = TRUE;
26621
}
26622
}
21853
26623
21854
26624
if (rval)
21855
26625
{
21856
/* if we are applying gene fields, we need to make sure every sequence has a gene
26626
/* if we are applying gene locus, we need to make sure every sequence has a gene
21857
26627
* and we need to recollect the cdset_list
21858
26628
*/
21859
26629
if ((action_choice == AECR_APPLY || action_choice == AECR_PARSE)
21860
26630
&& sp->field_list != NULL
21861
&& sp->field_list->data.intvalue > 1
21862
&& sp->field_list->data.intvalue <= 1 + num_gene_fields)
26631
&& sp->field_list->data.intvalue == 1 + GENEFIELD_LOCUS)
21863
26632
{
21864
BuildNewGenes (sep);
21865
FreeCDSetList (cdset_list);
21866
if (fsp == NULL)
21867
{
21868
cdset_list = BuildCDSetList (ap->input_entityID, NULL);
21869
}
21870
else
21871
{
21872
cdset_list = BuildCDSetList (ap->input_entityID, fsp->cgp);
21873
}
26633
BuildNewGenes (sep, &cdset_list, LoneGeneOkWithFilter(fsp));
21874
26634
}
21875
26635
21876
26636
for (cdset_vnp = cdset_list; cdset_vnp != NULL; cdset_vnp = cdset_vnp->next)
21877
26637
{
21878
26638
if (action_choice == AECR_CONVERT)
21879
26639
{
21880
str_src = GetCDSetField (cdset_vnp->data.ptrvalue, sp->field_list);
21881
if (str_src != NULL)
21882
{
21883
BuildNewCDSGeneProtFeature (cdset_vnp->data.ptrvalue, sp->field_list_to);
21884
SetCDSetField (cdset_vnp->data.ptrvalue, sp->field_list_to, str_src, etp);
21885
if (!sp->leave_on_original)
21886
{
21887
sp->field_list->choice = 1;
21888
RemoveCDSetField (cdset_vnp->data.ptrvalue, sp->field_list);
21889
}
21890
}
26640
CDSGeneProtConvert (cdset_vnp->data.ptrvalue, sp, fsp, etp, build_missing);
21891
26641
}
21892
26642
else if (action_choice == AECR_SWAP)
21893
26643
{
21894
str_src = GetCDSetField (cdset_vnp->data.ptrvalue, sp->field_list);
21895
str_dst = GetCDSetField (cdset_vnp->data.ptrvalue, sp->field_list_to);
21896
if (!StringHasNoText (str_src) || !StringHasNoText (str_dst))
21897
{
21898
BuildNewCDSGeneProtFeature (cdset_vnp->data.ptrvalue, sp->field_list);
21899
BuildNewCDSGeneProtFeature (cdset_vnp->data.ptrvalue, sp->field_list_to);
21900
SetCDSetField (cdset_vnp->data.ptrvalue, sp->field_list_to, str_src, NULL);
21901
SetCDSetField (cdset_vnp->data.ptrvalue, sp->field_list, str_dst, NULL);
21902
}
26644
CDSGeneProtSwap (cdset_vnp->data.ptrvalue, sp, fsp, etp, build_missing);
21903
26645
}
21904
26646
else if (action_choice == AECR_PARSE)
21905
26647
{
21906
str_src = GetCDSetField (cdset_vnp->data.ptrvalue, sp->field_list);
21907
str_dst = str_src;
21908
str_src = ReplaceStringForParse(str_src, sp->text_portion);
21909
if (!sp->remove_parsed) {
21910
str_dst = MemFree (str_dst);
21911
}
21912
if (str_src != NULL) {
21913
BuildNewCDSGeneProtFeature (cdset_vnp->data.ptrvalue, sp->field_list_to);
21914
if (sp->remove_parsed) {
21915
BuildNewCDSGeneProtFeature (cdset_vnp->data.ptrvalue, sp->field_list);
21916
}
21917
SetCDSetField (cdset_vnp->data.ptrvalue, sp->field_list_to, str_src, etp);
21918
if (sp->remove_parsed) {
21919
SetCDSetField (cdset_vnp->data.ptrvalue, sp->field_list, str_dst, NULL);
21920
}
21921
str_src = MemFree (str_src);
21922
}
21923
str_dst = MemFree (str_dst);
26648
CDSGeneProtParse (cdset_vnp->data.ptrvalue, sp, fsp, etp, build_missing);
21924
26649
}
21925
26650
else if (action_choice == AECR_APPLY)
21926
26651
{
21927
/* for now, this is taken care of by BuildNewGenes */
21928
/* BuildNewCDSGeneProtFeature (cdset_vnp->data.ptrvalue, sp->field_list); */
21929
SetCDSetField (cdset_vnp->data.ptrvalue, sp->field_list, sp->edit_apply->apply_txt, etp);
26652
CDSGeneProtApplyToAllThatMatchFilter (sp->edit_apply->apply_txt, cdset_vnp->data.ptrvalue, sp->field_list, fsp, etp);
21930
26653
}
21931
26654
else if (action_choice == AECR_REMOVE)
21932
26655
{
21933
26656
sp->field_list->choice = 1;
21934
RemoveCDSetField (cdset_vnp->data.ptrvalue, sp->field_list);
26657
RemoveCDSetField (cdset_vnp->data.ptrvalue, sp->field_list, fsp);
26658
if (sp->also_mrna)
26659
{
26660
CopyProteinNameTomRNAName (cdset_vnp->data.ptrvalue);
26661
}
21935
26662
}
21936
26663
else if (action_choice == AECR_EDIT)
21937
26664
{
21938
str_src = GetCDSetField (cdset_vnp->data.ptrvalue, sp->field_list);
21939
avd.field_list = sp->field_list;
21940
avd.etp = NULL;
21941
AddEditApplyDataToApplyValue (AECR_EDIT, sp->edit_apply, &avd);
21942
str_src = HandleApplyValue (str_src, &avd);
21943
SetCDSetField (cdset_vnp->data.ptrvalue, sp->field_list, str_src, NULL);
21944
avd.text_to_replace = MemFree (avd.text_to_replace);
21945
avd.new_text = MemFree (avd.new_text);
26665
CDSGeneProtEdit (cdset_vnp->data.ptrvalue, sp, fsp, etp);
26666
}
26667
if (((action_choice == AECR_APPLY || action_choice == AECR_EDIT) && IsCDSetGeneQualChoice (sp->field_list))
26668
|| ((action_choice == AECR_PARSE || action_choice == AECR_CONVERT) && IsCDSetGeneQualChoice (sp->field_list_to))
26669
|| (action_choice == AECR_SWAP && (IsCDSetGeneQualChoice (sp->field_list) || IsCDSetGeneQualChoice (sp->field_list_to))))
26670
{
26671
MarkAlreadyEditedGenes (cdset_vnp->data.ptrvalue, cdset_vnp->next);
21946
26672
}
21947
26673
}
21948
26674
}
21949
26675
FilterSetFree (fsp);
21950
sp = SimpleAECRFree (sp);
26676
sp = CDSGeneProtAECRFree (sp);
21951
26677
FreeCDSetList (cdset_list);
21952
26678
21953
26679
if (rval)
21972
26698
"CDS-Gene-Prot-mRNA",
21973
26699
CDSGeneProtAECRDialog,
21974
26700
TRUE, GetCDSGeneProtSample,
21975
FALSE, FALSE, FALSE, TRUE, NULL,
26701
FALSE, FALSE, FALSE, TRUE, FALSE, NULL,
21976
26702
CDSGeneProtAECRAction, NULL, NULL,
21977
26703
CheckFeaturesForPresample);
21978
26704
}
22025
26751
SimpleAECRPtr origin;
22026
26752
SimpleAECRPtr strings;
22027
26753
26754
TaxnameOptionsPtr taxname_options;
22028
26755
} SourceQualAECRData, PNTR SourceQualAECRPtr;
22029
26756
22030
26757
static SourceQualAECRPtr SourceQualAECRFree (SourceQualAECRPtr sp)
22032
26759
if (sp != NULL)
22033
26760
{
22034
26761
sp->source_qual = SimpleAECRFree (sp->source_qual);
26762
sp->taxname_options = MemFree (sp->taxname_options);
22035
26763
sp = MemFree (sp);
22036
26764
}
22037
26765
return sp;
22046
26774
DialoG location;
22047
26775
DialoG origin;
22048
26776
DialoG strings;
26777
26778
DialoG taxname_options;
22049
26779
22050
26780
Int4 action_choice;
22051
26781
Nlm_ChangeNotifyProc change_notify;
22053
26783
22054
26784
} SourceQualAECRDlgData, PNTR SourceQualAECRDlgPtr;
22055
26785
26786
26787
static Boolean AreTaxNameOptionsRelevant (Int4 action_choice, SimpleAECRPtr sp)
26788
{
26789
Boolean relevant = FALSE;
26790
if (sp == NULL) return FALSE;
26791
26792
switch (action_choice)
26793
{
26794
case AECR_APPLY:
26795
case AECR_EDIT:
26796
case AECR_REMOVE:
26797
if (sp->field_list != NULL && sp->field_list->choice == 1)
26798
{
26799
relevant = TRUE;
26800
}
26801
break;
26802
case AECR_SWAP:
26803
if ((sp->field_list != NULL && sp->field_list->choice == 1)
26804
|| (sp->field_list_to != NULL && sp->field_list_to->choice == 1))
26805
{
26806
relevant = TRUE;
26807
}
26808
break;
26809
case AECR_CONVERT:
26810
if ((sp->field_list != NULL && sp->field_list->choice == 1 && !sp->leave_on_original)
26811
|| (sp->field_list_to != NULL && sp->field_list_to->choice == 1))
26812
{
26813
relevant = TRUE;
26814
}
26815
break;
26816
case AECR_PARSE:
26817
if ((sp->field_list != NULL && sp->field_list->choice == 1 && sp->remove_parsed)
26818
|| (sp->field_list_to != NULL && sp->field_list_to->choice == 1))
26819
{
26820
relevant = TRUE;
26821
}
26822
break;
26823
default:
26824
relevant = FALSE;
26825
break;
26826
}
26827
return relevant;
26828
}
26829
22056
26830
static void ChangeQualKind (GrouP g)
22057
26831
{
22058
26832
SourceQualAECRDlgPtr dlg;
22059
26833
Int4 qual_kind;
26834
SimpleAECRPtr sp;
22060
26835
22061
26836
dlg = (SourceQualAECRDlgPtr) GetObjectExtra (g);
22062
26837
if (dlg == NULL)
22068
26843
Hide (dlg->location);
22069
26844
Hide (dlg->origin);
22070
26845
Hide (dlg->strings);
26846
Hide (dlg->taxname_options);
22071
26847
qual_kind = GetValue (dlg->qual_kind);
22072
26848
switch (qual_kind)
22073
26849
{
22082
26858
break;
22083
26859
case QUALKIND_STRINGS :
22084
26860
Show (dlg->strings);
26861
Show (dlg->taxname_options);
26862
sp = DialogToPointer (dlg->strings);
26863
if (AreTaxNameOptionsRelevant (dlg->action_choice, sp))
26864
{
26865
Enable (dlg->taxname_options);
26866
}
26867
else
26868
{
26869
Disable (dlg->taxname_options);
26870
}
26871
sp = SimpleAECRFree (sp);
22085
26872
break;
22086
26873
}
22087
26874
if (dlg->change_notify != NULL)
22102
26889
PointerToDialog (dlg->origin, NULL);
22103
26890
PointerToDialog (dlg->strings, NULL);
22104
26891
ChangeQualKind (dlg->qual_kind);
26892
PointerToDialog (dlg->taxname_options, NULL);
22105
26893
}
22106
26894
22107
26895
static void ClearTextSourceQualAECRDlg (SourceQualAECRDlgPtr dlg)
22147
26935
&& (dlg->action_choice == AECR_EDIT || dlg->action_choice == AECR_SWAP))
22148
26936
{
22149
26937
SetValue (dlg->qual_kind, QUALKIND_STRINGS);
26938
PointerToDialog (dlg->taxname_options, data->taxname_options);
22150
26939
}
22151
26940
else if (data->qual_kind > QUALKIND_ORIGIN)
22152
26941
{
22173
26962
data = (SourceQualAECRPtr) MemNew (sizeof (SourceQualAECRData));
22174
26963
if (data != NULL)
22175
26964
{
26965
data->taxname_options = NULL;
22176
26966
data->qual_kind = GetValue (dlg->qual_kind);
22177
26967
switch (data->qual_kind)
22178
26968
{
22187
26977
break;
22188
26978
case QUALKIND_STRINGS :
22189
26979
data->strings = DialogToPointer (dlg->strings);
26980
if (AreTaxNameOptionsRelevant (dlg->action_choice, data->strings))
26981
{
26982
data->taxname_options = DialogToPointer (dlg->taxname_options);
26983
}
22190
26984
break;
22191
26985
}
22192
26986
22216
27010
SendMessageToDialog (dlg->location, AECR_VIB_MSG_SET_DEFAULT);
22217
27011
SendMessageToDialog (dlg->origin, AECR_VIB_MSG_SET_DEFAULT);
22218
27012
SendMessageToDialog (dlg->strings, AECR_VIB_MSG_SET_DEFAULT);
27013
PointerToDialog (dlg->taxname_options, NULL);
22219
27014
ChangeQualKind (dlg->qual_kind);
22220
27015
break;
22221
27016
case AECR_VIB_MSG_CLEAR_TEXT :
22230
27025
static ValNodePtr TestSourceQualAECR (DialoG d)
22231
27026
{
22232
27027
SourceQualAECRDlgPtr dlg;
22233
ValNodePtr err_list = NULL;
22234
27028
ValNodePtr total_err_list = NULL;
22235
27029
Int4 qual_kind;
22236
27030
22517
27311
dlg);
22518
27312
22519
27313
g2 = HiddenGroup (p, 0, 0, NULL);
22520
dlg->edit_apply = EditApplyDialog (g2, AECR_APPLY, "New Text",
27314
dlg->edit_apply = EditApplyDialog (g2, eEditApplyChoice_Apply, "New Text", NULL,
22521
27315
change_notify, change_userdata);
22522
27316
22523
27317
dlg->true_false = PopupList (g2, TRUE, NULL);
22643
27437
return (DialoG) p;
22644
27438
}
22645
27439
27440
27441
static void ChangeTaxonomyStrings (Pointer data)
27442
{
27443
SourceQualAECRDlgPtr dlg;
27444
SimpleAECRPtr sp;
27445
27446
dlg = (SourceQualAECRDlgPtr) data;
27447
if (dlg == NULL) return;
27448
27449
if (GetValue (dlg->qual_kind) == QUALKIND_STRINGS)
27450
{
27451
sp = DialogToPointer (dlg->strings);
27452
if (AreTaxNameOptionsRelevant (dlg->action_choice, sp))
27453
{
27454
Enable (dlg->taxname_options);
27455
}
27456
else
27457
{
27458
Disable (dlg->taxname_options);
27459
}
27460
sp = SimpleAECRFree (sp);
27461
}
27462
if (dlg->change_notify != NULL)
27463
{
27464
(dlg->change_notify)(dlg->change_userdata);
27465
}
27466
27467
}
27468
22646
27469
static DialoG SourceQualAECRDialog
22647
27470
(GrouP h,
22648
27471
Int4 action_choice,
22726
27549
}
22727
27550
22728
27551
/* Taxonomy Strings dialog */
22729
dlg->strings = SimpleAECRDialog (g1, action_choice, change_notify, change_userdata,
27552
dlg->strings = SimpleAECRDialog (g1, action_choice, ChangeTaxonomyStrings, dlg,
22730
27553
ValNodeSimpleDataFree, NULL,
22731
27554
SourceStringSelectionDialog, NULL, NULL,
22732
27555
"Taxonomy", NULL, TRUE, entityID);
22765
27588
SourceOriginSelectionDialog, NULL, NULL,
22766
27589
"Origin", NULL, FALSE, entityID);
22767
27590
}
27591
27592
dlg->taxname_options = TaxnameOptionsDialog (p, change_notify, change_userdata);
27593
27594
Disable (dlg->taxname_options);
22768
27595
22769
27596
AlignObjects (ALIGN_CENTER, (HANDLE) dlg->source_qual,
22770
27597
(HANDLE) dlg->location,
22774
27601
22775
27602
AlignObjects (ALIGN_CENTER, (HANDLE) dlg->qual_kind,
22776
27603
(HANDLE) g1,
27604
(HANDLE) dlg->taxname_options,
22777
27605
NULL);
22778
27606
22779
27607
ChangeQualKind (dlg->qual_kind);
22780
27608
return (DialoG) p;
22781
27609
}
22782
27610
22783
typedef struct multiqual
22784
{
22785
Boolean multi_found;
22786
SourceQualDescPtr sqdp;
22787
FilterSetPtr fsp;
22788
} MultiQualData, PNTR MultiQualPtr;
22789
27611
22790
static void CheckForMultipleQuals (BioSourcePtr biop, Pointer userdata)
27612
static Boolean BioSourceHasMultipleQuals (BioSourcePtr biop, SourceQualDescPtr sqdp, FilterSetPtr fsp)
22791
27613
{
22792
MultiQualPtr mqp;
27614
OrgModPtr mod;
27615
SubSourcePtr ssp;
22793
27616
Boolean found_one = FALSE;
22794
OrgModPtr mod;
22795
SubSourcePtr ssp;
22796
22797
if (biop == NULL || userdata == NULL)
22798
{
22799
return;
22800
}
22801
22802
mqp = (MultiQualPtr) userdata;
22803
if (mqp->sqdp == NULL || mqp->multi_found) return;
22804
22805
if (mqp->sqdp->isOrgMod)
27617
27618
if (biop == NULL || sqdp == NULL) return FALSE;
27619
27620
if (sqdp->isOrgMod)
22806
27621
{
22807
27622
if (biop->org != NULL && biop->org->orgname != NULL)
22808
27623
{
22809
27624
mod = biop->org->orgname->mod;
22810
while (mod != NULL && !mqp->multi_found)
27625
while (mod != NULL)
22811
27626
{
22812
if (mod->subtype == mqp->sqdp->subtype
27627
if (mod->subtype == sqdp->subtype
22813
27628
&& !StringHasNoText (mod->subname)
22814
&& OrgModSpecialMatch (mod, mqp->fsp))
27629
&& OrgModSpecialMatch (mod, fsp))
22815
27630
{
22816
27631
if (found_one) {
22817
mqp->multi_found = TRUE;
27632
return TRUE;
22818
27633
} else {
22819
27634
found_one = TRUE;
22820
27635
}
22826
27641
else
22827
27642
{
22828
27643
ssp = biop->subtype;
22829
while (ssp != NULL && !mqp->multi_found)
27644
while (ssp != NULL)
22830
27645
{
22831
if (ssp->subtype == mqp->sqdp->subtype
27646
if (ssp->subtype == sqdp->subtype
22832
27647
&& !StringHasNoText (ssp->name)
22833
&& SubSrcSpecialMatch (ssp, mqp->fsp))
27648
&& SubSrcSpecialMatch (ssp, fsp))
22834
27649
{
22835
27650
if (found_one) {
22836
mqp->multi_found = TRUE;
27651
return TRUE;
22837
27652
} else {
22838
27653
found_one = TRUE;
22839
27654
}
22841
27656
ssp = ssp->next;
22842
27657
}
22843
27658
}
27659
return FALSE;
27660
}
27661
27662
static Boolean CheckBioSrcListForMultipleQuals (ValNodePtr biosrc_list, SourceQualDescPtr sqdp, FilterSetPtr fsp)
27663
{
27664
ValNodePtr vnp;
27665
SeqFeatPtr sfp;
27666
SeqDescrPtr sdp;
27667
Boolean has_multiple = FALSE;
27668
27669
if (sqdp == NULL) return FALSE;
27670
27671
for (vnp = biosrc_list; vnp != NULL && !has_multiple; vnp = vnp->next)
27672
{
27673
if (vnp->data.ptrvalue == NULL) continue;
27674
if (vnp->choice == OBJ_SEQFEAT)
27675
{
27676
sfp = (SeqFeatPtr) vnp->data.ptrvalue;
27677
if (sfp->data.choice == SEQFEAT_BIOSRC)
27678
{
27679
has_multiple = BioSourceHasMultipleQuals ((BioSourcePtr)sfp->data.value.ptrvalue, sqdp, fsp);
27680
}
27681
}
27682
else if (vnp->choice == OBJ_SEQDESC)
27683
{
27684
sdp = (SeqDescrPtr) vnp->data.ptrvalue;
27685
if (sdp->choice == Seq_descr_source)
27686
{
27687
has_multiple = BioSourceHasMultipleQuals ((BioSourcePtr)sdp->data.ptrvalue, sqdp, fsp);
27688
}
27689
}
27690
}
27691
return has_multiple;
27692
}
27693
27694
27695
typedef struct taxnameoptionsdlg
27696
{
27697
DIALOG_MESSAGE_BLOCK
27698
ButtoN remove_taxref;
27699
ButtoN remove_common;
27700
ButtoN remove_old_name;
27701
Nlm_ChangeNotifyProc change_notify;
27702
Pointer change_userdata;
27703
} TaxnameOptionsDlgData, PNTR TaxnameOptionsDlgPtr;
27704
27705
static void TaxnameOptionsToDialog (DialoG d, Pointer data)
27706
{
27707
TaxnameOptionsDlgPtr dlg;
27708
TaxnameOptionsPtr top;
27709
27710
dlg = (TaxnameOptionsDlgPtr) GetObjectExtra (d);
27711
if (dlg == NULL) return;
27712
27713
top = (TaxnameOptionsPtr) data;
27714
if (top == NULL)
27715
{
27716
SetStatus (dlg->remove_taxref, TRUE);
27717
SetStatus (dlg->remove_common, TRUE);
27718
SetStatus (dlg->remove_old_name, TRUE);
27719
}
27720
else
27721
{
27722
SetStatus (dlg->remove_taxref, top->remove_taxref);
27723
SetStatus (dlg->remove_common, top->remove_common);
27724
SetStatus (dlg->remove_old_name, top->remove_old_name);
27725
}
27726
if (dlg->change_notify != NULL)
27727
{
27728
(dlg->change_notify) (dlg->change_userdata);
27729
}
27730
}
27731
27732
static Pointer TaxnameOptionsFromDialog (DialoG d)
27733
{
27734
TaxnameOptionsDlgPtr dlg;
27735
TaxnameOptionsPtr top;
27736
27737
dlg = (TaxnameOptionsDlgPtr) GetObjectExtra (d);
27738
if (dlg == NULL) return NULL;
27739
27740
top = (TaxnameOptionsPtr) MemNew (sizeof (TaxnameOptionsData));
27741
top->remove_taxref = GetStatus (dlg->remove_taxref);
27742
top->remove_common = GetStatus (dlg->remove_common);
27743
top->remove_old_name = GetStatus (dlg->remove_old_name);
27744
return top;
27745
}
27746
27747
27748
static void ChangeTaxnameOptions (ButtoN b)
27749
{
27750
TaxnameOptionsDlgPtr dlg;
27751
27752
dlg = (TaxnameOptionsDlgPtr) GetObjectExtra (b);
27753
if (dlg != NULL && dlg->change_notify != NULL)
27754
{
27755
(dlg->change_notify) (dlg->change_userdata);
27756
}
27757
}
27758
27759
27760
extern DialoG TaxnameOptionsDialog (GrouP h, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata)
27761
{
27762
TaxnameOptionsDlgPtr dlg;
27763
GrouP p;
27764
27765
dlg = (TaxnameOptionsDlgPtr) MemNew (sizeof (TaxnameOptionsDlgData));
27766
if (dlg == NULL)
27767
{
27768
return NULL;
27769
}
27770
27771
p = HiddenGroup (h, 3, 0, NULL);
27772
SetObjectExtra (p, dlg, StdCleanupExtraProc);
27773
SetGroupSpacing (p, 10, 10);
27774
27775
dlg->dialog = (DialoG) p;
27776
dlg->todialog = TaxnameOptionsToDialog;
27777
dlg->fromdialog = TaxnameOptionsFromDialog;
27778
dlg->change_notify = change_notify;
27779
dlg->change_userdata = change_userdata;
27780
27781
dlg->remove_taxref = CheckBox (p, "Remove taxonomy xref", ChangeTaxnameOptions);
27782
SetObjectExtra (dlg->remove_taxref, dlg, NULL);
27783
SetStatus (dlg->remove_taxref, TRUE);
27784
dlg->remove_common = CheckBox (p, "Remove GenBank common name", ChangeTaxnameOptions);
27785
SetObjectExtra (dlg->remove_common, dlg, NULL);
27786
SetStatus (dlg->remove_common, TRUE);
27787
dlg->remove_old_name = CheckBox (p, "Remove old_name qualifier", ChangeTaxnameOptions);
27788
SetObjectExtra (dlg->remove_old_name, dlg, NULL);
27789
SetStatus (dlg->remove_old_name, TRUE);
27790
return (DialoG) p;
27791
}
27792
27793
extern void ApplyTaxnameOptionsToBioSource (BioSourcePtr biop, TaxnameOptionsPtr top)
27794
{
27795
if (biop == NULL || top == NULL) return;
27796
27797
if (top->remove_taxref)
27798
{
27799
RemoveTaxRef (biop->org);
27800
}
27801
if (top->remove_old_name)
27802
{
27803
RemoveOldName (biop->org);
27804
}
27805
if (top->remove_common)
27806
{
27807
if (biop->org != NULL)
27808
{
27809
biop->org->common = MemFree (biop->org->common);
27810
}
27811
}
27812
}
27813
27814
static void HandleTaxnameOptionsFeature (SeqFeatPtr sfp, TaxnameOptionsPtr top)
27815
{
27816
if (sfp == NULL || sfp->data.choice != SEQFEAT_BIOSRC || top == NULL)
27817
{
27818
return;
27819
}
27820
ApplyTaxnameOptionsToBioSource (sfp->data.value.ptrvalue, top);
27821
}
27822
27823
static void HandleTaxnameOptionsDescriptorCallback (SeqDescrPtr sdp, TaxnameOptionsPtr top)
27824
{
27825
if (sdp == NULL || sdp->choice != Seq_descr_source || top == NULL)
27826
{
27827
return;
27828
}
27829
ApplyTaxnameOptionsToBioSource (sdp->data.ptrvalue, top);
27830
}
27831
27832
27833
static void HandleTaxnameOptionsForBioSourceList (ValNodePtr biosrc_list, TaxnameOptionsPtr top)
27834
{
27835
ValNodePtr vnp;
27836
27837
if (top == NULL) return;
27838
for (vnp = biosrc_list; vnp != NULL; vnp = vnp->next)
27839
{
27840
if (vnp->choice == OBJ_SEQFEAT)
27841
{
27842
HandleTaxnameOptionsFeature (vnp->data.ptrvalue, top);
27843
}
27844
else if (vnp->choice == OBJ_SEQDESC)
27845
{
27846
HandleTaxnameOptionsDescriptorCallback (vnp->data.ptrvalue, top);
27847
}
27848
}
27849
}
27850
27851
static void CollectBioSourceFeatureFieldCallback (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
27852
{
27853
if (sfp == NULL || userdata == NULL)
27854
{
27855
return;
27856
}
27857
ValNodeAddPointer ((ValNodePtr PNTR) userdata, OBJ_SEQFEAT, sfp);
27858
}
27859
27860
static void CollectBioSourceDescriptorFieldCallback (SeqDescrPtr sdp, Pointer userdata, FilterSetPtr fsp)
27861
{
27862
if (sdp == NULL || userdata == NULL)
27863
{
27864
return;
27865
}
27866
27867
ValNodeAddPointer ((ValNodePtr PNTR) userdata, OBJ_SEQDESC, sdp);
27868
}
27869
27870
27871
static void RemoveSourceQualEditNonMatches (ValNodePtr PNTR biosrc_list, ApplyValuePtr avp)
27872
{
27873
ValNodePtr vnp_prev = NULL, vnp_next, vnp_this;
27874
CharPtr val1, val2;
27875
Boolean do_remove;
27876
27877
if (biosrc_list == NULL || avp == NULL || StringHasNoText (avp->text_to_replace))
27878
{
27879
return;
27880
}
27881
27882
vnp_this = *biosrc_list;
27883
while (vnp_this != NULL)
27884
{
27885
vnp_next = vnp_this->next;
27886
do_remove = FALSE;
27887
if (vnp_this->choice == OBJ_SEQFEAT)
27888
{
27889
val1 = GetSourceQualFeatureString (vnp_this->data.ptrvalue, avp->field_list, NULL);
27890
}
27891
else if (vnp_this->choice == OBJ_SEQDESC)
27892
{
27893
val1 = GetSourceQualDescrString (vnp_this->data.ptrvalue, avp->field_list, NULL);
27894
}
27895
else
27896
{
27897
val1 = NULL;
27898
}
27899
if (val1 == NULL)
27900
{
27901
do_remove = TRUE;
27902
}
27903
else
27904
{
27905
val2 = HandleApplyValue (StringSave (val1), avp);
27906
if (StringCmp (val1, val2) == 0)
27907
{
27908
do_remove = TRUE;
27909
}
27910
val1 = MemFree (val1);
27911
val2 = MemFree (val2);
27912
}
27913
if (do_remove)
27914
{
27915
if (vnp_prev == NULL)
27916
{
27917
*biosrc_list = vnp_this->next;
27918
}
27919
else
27920
{
27921
vnp_prev->next = vnp_this->next;
27922
}
27923
vnp_this->next = NULL;
27924
vnp_this = ValNodeFree (vnp_this);
27925
}
27926
else
27927
{
27928
vnp_prev = vnp_this;
27929
}
27930
vnp_this = vnp_next;
27931
}
22844
27932
}
22845
27933
22846
27934
22857
27945
GetFeatureFieldString fieldstring_func,
22858
27946
GetDescriptorFieldString descrstring_func,
22859
27947
Boolean non_text,
22860
NameFromValNodeProc name_field_func)
27948
NameFromValNodeProc name_field_func,
27949
TaxnameOptionsPtr top)
22861
27950
22862
27951
{
22863
27952
SeqEntryPtr sep;
22867
27956
GetSamplePtr gsp;
22868
27957
Boolean rval = TRUE;
22869
27958
ValNodePtr vnp;
22870
MultiQualData mqd;
22871
27959
CharPtr field_name = NULL;
22872
27960
MsgAnswer ans;
27961
ValNodePtr biosrc_list = NULL;
27962
SourceQualDescPtr multi_sqdp = NULL;
22873
27963
22874
27964
sep = GetTopSeqEntryForEntityID (ap->input_entityID);
22875
27965
if (sp == NULL
22887
27977
WatchCursor ();
22888
27978
Update ();
22889
27979
27980
avd.where_to_replace = EditApplyFindLocation_anywhere;
27981
22890
27982
fsp = (FilterSetPtr) DialogToPointer (ap->constraints);
27983
27984
/* collect list of BioSources that will be acted upon */
27985
OperateOnSeqEntryConstrainedObjects (sep, fsp,
27986
CollectBioSourceFeatureFieldCallback,
27987
CollectBioSourceDescriptorFieldCallback,
27988
SEQFEAT_BIOSRC, 0, Seq_descr_source,
27989
&biosrc_list);
22891
27990
22892
27991
if (action_choice == AECR_CONVERT || action_choice == AECR_SWAP || action_choice == AECR_PARSE)
22893
27992
{
22894
27993
/* check for multiple sources */
22895
mqd.fsp = fsp;
22896
mqd.multi_found = FALSE;
22897
mqd.sqdp = sp->field_list->data.ptrvalue;
22898
VisitBioSourcesInSep (sep, &mqd, CheckForMultipleQuals);
22899
if (!mqd.multi_found && action_choice == AECR_SWAP) {
22900
mqd.sqdp = sp->field_list_to->data.ptrvalue;
22901
VisitBioSourcesInSep (sep, &mqd, CheckForMultipleQuals);
22902
}
22903
if (mqd.multi_found) {
27994
if ((sp->field_list->choice == 0
27995
&& (multi_sqdp = sp->field_list->data.ptrvalue) != NULL
27996
&& CheckBioSrcListForMultipleQuals(biosrc_list, multi_sqdp, fsp))
27997
|| (action_choice == AECR_SWAP && sp->field_list_to->choice == 0
27998
&& (multi_sqdp = sp->field_list_to->data.ptrvalue) != NULL
27999
&& CheckBioSrcListForMultipleQuals(biosrc_list, multi_sqdp, fsp))) {
22904
28000
if (name_field_func != NULL) {
22905
if (action_choice == AECR_SWAP && mqd.sqdp == sp->field_list_to->data.ptrvalue) {
28001
if (action_choice == AECR_SWAP && multi_sqdp == sp->field_list_to->data.ptrvalue) {
22906
28002
field_name = name_field_func(sp->field_list_to);
22907
28003
} else {
22908
28004
field_name = name_field_func(sp->field_list);
22932
28028
cfd.remove_d_str_func = descriptor_remove_action;
22933
28029
cfd.fsp = fsp;
22934
28030
cfd.strip_name_from_text = sp->strip_name_from_text;
28031
cfd.remove_parsed = sp->remove_parsed;
22935
28032
cfd.name_field_func = name_field_func;
22936
28033
cfd.text_portion = sp->text_portion;
22937
28034
if (action_choice == AECR_CONVERT)
22959
28056
gsp = CheckForConversionExistingTextInSeqEntry (sep, &cfd, fsp,
22960
28057
SEQFEAT_BIOSRC, 0,
22961
28058
Seq_descr_source);
22962
cfd.etp = GetExistingTextHandlerInfo (gsp, non_text);
28059
cfd.etp = GetExistingTextHandlerInfo (gsp == NULL ? 0 : gsp->num_found, non_text);
22963
28060
gsp = GetSampleFree (gsp);
22964
if (cfd.etp != NULL && cfd.etp->existing_text_choice == EXISTING_TEXT_CHOICE_CANCEL)
28061
if (cfd.etp != NULL && cfd.etp->existing_text_choice == eExistingTextChoiceCancel)
22965
28062
{
22966
28063
rval = FALSE;
22967
28064
}
23007
28104
ValNodeSimpleDataFree,
23008
28105
copy_vn_proc,
23009
28106
fsp, SEQFEAT_BIOSRC, 0, Seq_descr_source);
23010
avd.etp = GetExistingTextHandlerInfo (gsp, non_text);
28107
avd.etp = GetExistingTextHandlerInfo (gsp == NULL ? 0 : gsp->num_found, non_text);
23011
28108
gsp = GetSampleFree (gsp);
23012
28109
23013
28110
if (avd.etp != NULL
23014
&& avd.etp->existing_text_choice == EXISTING_TEXT_CHOICE_CANCEL)
28111
&& avd.etp->existing_text_choice == eExistingTextChoiceCancel)
23015
28112
{
23016
28113
rval = FALSE;
23017
28114
}
23024
28121
if (rval)
23025
28122
{
23026
28123
AddEditApplyDataToApplyValue (action_choice, sp->edit_apply, &avd);
28124
28125
if (action_choice == AECR_EDIT)
28126
{
28127
/* remove items that don't contain text that will be replaced */
28128
RemoveSourceQualEditNonMatches (&biosrc_list, &avd);
28129
}
28130
23027
28131
23028
28132
if (action_choice == AECR_EDIT || action_choice == AECR_APPLY)
23029
28133
{
23049
28153
}
23050
28154
avd.etp = MemFree (avd.etp);
23051
28155
}
28156
23052
28157
FilterSetFree (fsp);
23053
28158
23054
28159
if (rval)
23055
28160
{
28161
/* Handle taxname options */
28162
HandleTaxnameOptionsForBioSourceList (biosrc_list, top);
28163
23056
28164
ObjMgrSetDirtyFlag (ap->input_entityID, TRUE);
23057
28165
ObjMgrSendMsg (OM_MSG_UPDATE, ap->input_entityID, 0, 0);
23058
28166
}
28167
biosrc_list = ValNodeFree (biosrc_list);
23059
28168
ArrowCursor ();
23060
28169
Update ();
23061
28170
23102
28211
GetSourceQualFeatureString,
23103
28212
GetSourceQualDescrString,
23104
28213
FALSE,
23105
SourceQualValNodeName);
28214
SourceQualValNodeName,
28215
NULL);
23106
28216
break;
23107
28217
case QUALKIND_STRINGS :
23108
28218
rval = SourceQualQualApplyEditConvertRemoveAction (ap, sp->strings,
23115
28225
GetStringFromSourceFeature,
23116
28226
GetStringFromSourceDescriptor,
23117
28227
FALSE,
23118
NULL);
28228
NULL,
28229
sp->taxname_options);
23119
28230
break;
23120
28231
case QUALKIND_LOCATION :
23121
28232
rval = SourceQualQualApplyEditConvertRemoveAction (ap, sp->location,
23128
28239
GetLocationFromSourceFeature,
23129
28240
GetLocationFromSourceDescriptor,
23130
28241
TRUE,
23131
ValNodeStringName);
28242
ValNodeStringName,
28243
NULL);
23132
28244
break;
23133
28245
case QUALKIND_ORIGIN :
23134
28246
rval = SourceQualQualApplyEditConvertRemoveAction (ap, sp->origin,
23141
28253
GetOriginFromSourceFeature,
23142
28254
GetOriginFromSourceDescriptor,
23143
28255
TRUE,
23144
ValNodeStringName);
28256
ValNodeStringName,
28257
NULL);
23145
28258
break;
23146
28259
}
23147
28260
sp = SourceQualAECRFree (sp);
23177
28290
ssd.fieldstring_func = GetSourceQualFeatureString;
23178
28291
ssd.descrstring_func = GetSourceQualDescrString;
23179
28292
ssd.entityID = entityID;
23180
ssd.field_list = GetSourceQualDescList (TRUE, TRUE, TRUE);
28293
ssd.field_list = GetSourceQualDescList (TRUE, TRUE, TRUE, FALSE);
23181
28294
ValNodeAddPointer (&(ssd.field_list), 1, StringSave ("Scientific Name"));
23182
28295
ValNodeAddPointer (&(ssd.field_list), 1, StringSave ("Location"));
23183
28296
23200
28313
"Source Qual",
23201
28314
SourceQualAECRDialog,
23202
28315
FALSE, GetSourceQualSample,
23203
FALSE, TRUE, FALSE, FALSE, NULL,
28316
FALSE, TRUE, FALSE, FALSE, FALSE, NULL,
23204
28317
SourceQualApplyEditConvertRemoveAction, NULL,
23205
28318
ChangeSourceQualAction, NULL);
23206
28319
}
23240
28353
SourceQualApplyEditConvertRemove (i, AECR_REMOVE, FALSE);
23241
28354
}
23242
28355
23243
static CharPtr rna_sample_field_list [] = { "Name",
23244
"Comment",
23245
"Product GBQual" };
28356
static CharPtr rna_sample_field_list [] = { "Product",
28357
"Comment" };
23246
28358
static Int2 num_rna_sample_fields = sizeof (rna_sample_field_list) / sizeof (CharPtr);
23247
28359
23248
28360
23249
23250
28361
static CharPtr GetRNASampleFieldString (SeqFeatPtr sfp, ValNodePtr vnp, FilterSetPtr fsp)
23251
28362
{
23252
28363
RnaRefPtr rrp;
23253
28364
CharPtr str = NULL;
23254
GBQualPtr gbqual;
23255
28365
Int2 rna_subtype, rna_field_type;
23256
28366
GeneRefPtr grp;
23257
28367
SeqFeatPtr gene;
23269
28379
{
23270
28380
rna_subtype = (vnp->data.intvalue - 1) / (num_rna_sample_fields + num_gene_fields);
23271
28381
rna_field_type = (vnp->data.intvalue - 1) % (num_rna_sample_fields + num_gene_fields);
23272
if (rna_subtype == 0)
23273
{
23274
rna_subtype = 255;
23275
}
23276
if (rna_subtype != rrp->type)
23277
{
23278
vnp = vnp->next;
23279
continue;
23280
}
28382
switch (rna_subtype)
28383
{
28384
case 0:
28385
if (rrp->type != 255
28386
|| (rrp->ext.choice == 1
28387
&& (StringCmp (rrp->ext.value.ptrvalue, "ncRNA") == 0
28388
|| StringCmp (rrp->ext.value.ptrvalue, "tmRNA") == 0)))
28389
{
28390
vnp = vnp->next;
28391
continue;
28392
}
28393
break;
28394
case 1:
28395
case 2:
28396
case 3:
28397
case 4:
28398
if (rna_subtype != rrp->type)
28399
{
28400
vnp = vnp->next;
28401
continue;
28402
}
28403
break;
28404
case 5:
28405
if (rrp->type != 255
28406
|| rrp->ext.choice != 1
28407
|| StringCmp (rrp->ext.value.ptrvalue, "ncRNA") != 0)
28408
{
28409
vnp = vnp->next;
28410
continue;
28411
}
28412
break;
28413
case 6:
28414
if (rrp->type != 255
28415
|| rrp->ext.choice != 1
28416
|| StringCmp (rrp->ext.value.ptrvalue, "tmRNA") != 0)
28417
{
28418
vnp = vnp->next;
28419
continue;
28420
}
28421
break;
28422
}
28423
23281
28424
switch (rna_field_type)
23282
28425
{
23283
28426
case 0 :
23284
str = GetRNANameString (sfp);
28427
str = GetRNAProductString (sfp);
23285
28428
break;
23286
28429
case 1 :
23287
28430
if (!StringHasNoText (sfp->comment))
23289
28432
str = StringSave (sfp->comment);
23290
28433
}
23291
28434
break;
23292
case 2 :
23293
gbqual = sfp->qual;
23294
while (gbqual != NULL && str == NULL) {
23295
if (StringICmp (gbqual->qual, "product") == 0
23296
&& !StringHasNoText (gbqual->val))
23297
{
23298
str = StringSave (gbqual->val);
23299
}
23300
gbqual = gbqual->next;
23301
}
23302
break;
23303
28435
default :
23304
28436
vn.next = NULL;
23305
28437
vn.choice = 0;
23400
28532
return d;
23401
28533
}
23402
28534
23403
typedef struct applyrnaqual
28535
typedef struct aecrrnaqual
23404
28536
{
23405
28537
ValNodePtr field_list;
23406
ValNodePtr subtype_list;
28538
ValNodePtr field_list_to;
28539
RnaTypePtr rna_type;
23407
28540
EditApplyPtr edit_apply;
23408
28541
ValNodePtr codons;
23409
28542
SeqLocPtr anticodon;
23410
} ApplyRNAQualData, PNTR ApplyRNAQualPtr;
28543
TextPortionXPtr text_portion;
28544
Boolean leave_on_original;
28545
Boolean remove_parsed;
28546
} AECRRNAQualData, PNTR AECRRNAQualPtr;
23411
28547
23412
static ApplyRNAQualPtr ApplyRNAQualFree (ApplyRNAQualPtr ap)
28548
static AECRRNAQualPtr AECRRNAQualFree (AECRRNAQualPtr ap)
23413
28549
{
23414
28550
if (ap != NULL)
23415
28551
{
23416
28552
ap->field_list = ValNodeFree (ap->field_list);
23417
ap->subtype_list = ValNodeFree (ap->subtype_list);
28553
ap->field_list_to = ValNodeFree (ap->field_list_to);
28554
ap->rna_type = RnaTypeFree (ap->rna_type);
23418
28555
ap->edit_apply = EditApplyFree (ap->edit_apply);
23419
28556
ap->codons = ValNodeFreeData (ap->codons);
23420
28557
ap = MemFree (ap);
23422
28559
return ap;
23423
28560
}
23424
28561
23425
typedef struct applyrnaqualdlg
28562
typedef struct aecrrnaqualdlg
23426
28563
{
23427
28564
DIALOG_MESSAGE_BLOCK
23428
28565
DialoG field_list;
23429
DialoG subtype_list;
28566
DialoG field_list_to;
28567
DialoG rna_type;
23430
28568
DialoG edit_apply;
23431
28569
DialoG codons;
28570
DialoG ncrna_class;
28571
DialoG text_portion;
28572
ButtoN leave_on_original;
28573
ButtoN remove_parsed;
28574
23432
28575
Nlm_ChangeNotifyProc change_notify;
23433
28576
Pointer change_userdata;
23434
28577
Uint2 entityID;
23436
28579
/* The following is used to create the anticodon location dialog */
23437
28580
FeatureForm ff;
23438
28581
DialoG anticodon;
23439
} ApplyRNAQualDlgData, PNTR ApplyRNAQualDlgPtr;
28582
} AECRRNAQualDlgData, PNTR AECRRNAQualDlgPtr;
23440
28583
23441
static void ClearTextApplyRNAQualDlg (ApplyRNAQualDlgPtr dlg)
28584
static void ClearTextAECRRNAQualDlg (AECRRNAQualDlgPtr dlg)
23442
28585
{
23443
28586
if (dlg != NULL)
23444
28587
{
23445
28588
PointerToDialog (dlg->edit_apply, NULL);
23446
28589
PointerToDialog (dlg->codons, NULL);
28590
PointerToDialog (dlg->ncrna_class, NULL);
23447
28591
}
23448
28592
}
23449
28593
23450
static void ResetApplyRNAQualDlg (ApplyRNAQualDlgPtr dlg)
28594
static void ResetAECRRNAQualDlg (AECRRNAQualDlgPtr dlg)
23451
28595
{
23452
28596
if (dlg != NULL)
23453
28597
{
23454
28598
PointerToDialog (dlg->field_list, NULL);
28599
PointerToDialog (dlg->field_list_to, NULL);
23455
28600
SendMessageToDialog (dlg->field_list, NUM_VIB_MSG + 1);
23456
PointerToDialog (dlg->subtype_list, NULL);
23457
ClearTextApplyRNAQualDlg (dlg);
28601
PointerToDialog (dlg->rna_type, NULL);
28602
PointerToDialog (dlg->text_portion, NULL);
28603
SafeSetStatus (dlg->leave_on_original, FALSE);
28604
SafeSetStatus (dlg->remove_parsed, FALSE);
28605
ClearTextAECRRNAQualDlg (dlg);
23458
28606
}
23459
28607
}
23460
28608
23461
static void ApplyRNAQualToDialog (DialoG d, Pointer userdata)
28609
static void AECRRNAQualToDialog (DialoG d, Pointer userdata)
23462
28610
{
23463
ApplyRNAQualDlgPtr dlg;
23464
ApplyRNAQualPtr data;
28611
AECRRNAQualDlgPtr dlg;
28612
AECRRNAQualPtr data;
23465
28613
23466
dlg = (ApplyRNAQualDlgPtr) GetObjectExtra (d);
28614
dlg = (AECRRNAQualDlgPtr) GetObjectExtra (d);
23467
28615
if (dlg == NULL)
23468
28616
{
23469
28617
return;
23470
28618
}
23471
28619
23472
ResetApplyRNAQualDlg (dlg);
23473
data = (ApplyRNAQualPtr) userdata;
28620
ResetAECRRNAQualDlg (dlg);
28621
data = (AECRRNAQualPtr) userdata;
23474
28622
if (data != NULL)
23475
28623
{
23476
28624
PointerToDialog (dlg->field_list, data->field_list);
23477
PointerToDialog (dlg->subtype_list, data->subtype_list);
28625
PointerToDialog (dlg->field_list_to, data->field_list_to);
28626
PointerToDialog (dlg->rna_type, data->rna_type);
23478
28627
PointerToDialog (dlg->edit_apply, data->edit_apply);
23479
28628
PointerToDialog (dlg->codons, data->codons);
28629
if (data->field_list != NULL && data->field_list->data.intvalue == RNAFIELD_NCRNA_CLASS) {
28630
if (data->edit_apply == NULL) {
28631
PointerToDialog (dlg->ncrna_class, NULL);
28632
} else {
28633
PointerToDialog (dlg->ncrna_class, data->edit_apply->apply_txt);
28634
}
28635
}
23480
28636
PointerToDialog (dlg->anticodon, data->anticodon);
28637
PointerToDialog (dlg->text_portion, data->text_portion);
28638
SafeSetStatus (dlg->leave_on_original, data->leave_on_original);
28639
SafeSetStatus (dlg->remove_parsed, data->remove_parsed);
23481
28640
}
23482
28641
}
23483
28642
23484
static Pointer DialogToApplyRNAQual (DialoG d)
28643
static Pointer DialogToAECRRNAQual (DialoG d)
23485
28644
{
23486
ApplyRNAQualDlgPtr dlg;
23487
ApplyRNAQualPtr data;
28645
AECRRNAQualDlgPtr dlg;
28646
AECRRNAQualPtr data;
23488
28647
23489
dlg = (ApplyRNAQualDlgPtr) GetObjectExtra (d);
28648
dlg = (AECRRNAQualDlgPtr) GetObjectExtra (d);
23490
28649
if (dlg == NULL)
23491
28650
{
23492
28651
return NULL;
23493
28652
}
23494
28653
23495
data = (ApplyRNAQualPtr) MemNew (sizeof (ApplyRNAQualData));
28654
data = (AECRRNAQualPtr) MemNew (sizeof (AECRRNAQualData));
23496
28655
if (data != NULL)
23497
28656
{
23498
28657
data->field_list = DialogToPointer (dlg->field_list);
23499
data->subtype_list = DialogToPointer (dlg->subtype_list);
23500
data->edit_apply = DialogToPointer (dlg->edit_apply);
28658
data->field_list_to = DialogToPointer (dlg->field_list_to);
28659
data->rna_type = DialogToPointer (dlg->rna_type);
28660
if (data->field_list != NULL && data->field_list->data.intvalue == RNAFIELD_NCRNA_CLASS
28661
&& dlg->ncrna_class != NULL) {
28662
data->edit_apply = EditApplyNew ();
28663
data->edit_apply->apply_txt = DialogToPointer (dlg->ncrna_class);
28664
} else {
28665
data->edit_apply = DialogToPointer (dlg->edit_apply);
28666
}
23501
28667
data->codons = DialogToPointer (dlg->codons);
23502
28668
data->anticodon = DialogToPointer (dlg->anticodon);
28669
data->text_portion = DialogToPointer (dlg->text_portion);
28670
data->leave_on_original = (dlg->leave_on_original == NULL) ? FALSE : GetStatus (dlg->leave_on_original);
28671
data->remove_parsed = (dlg->remove_parsed == NULL) ? FALSE : GetStatus (dlg->remove_parsed);
23503
28672
}
23504
28673
return data;
23505
28674
}
23506
28675
28676
static ValNodePtr GetRNAFeatureList (SeqEntryPtr sep, FilterSetPtr fsp, RnaTypePtr rtp);
28677
static GetSamplePtr GetRnaExistingTextForList (ValNodePtr rna_list, ValNodePtr requested_field);
28678
23507
28679
static CharPtr
23508
28680
RNAQualAutopopulate
23509
(ValNodePtr subtype_list,
28681
(RnaTypePtr rna_type,
23510
28682
ValNodePtr field_list,
23511
28683
Uint2 entityID)
23512
28684
{
28685
SeqEntryPtr sep;
23513
28686
GetSamplePtr gsp;
28687
ValNodePtr rna_list;
23514
28688
CharPtr rval = NULL;
23515
ValNodePtr vnp;
23516
28689
23517
for (vnp = subtype_list; vnp != NULL && rval == NULL; vnp = vnp->next)
28690
sep = GetTopSeqEntryForEntityID (entityID);
28691
rna_list = GetRNAFeatureList (sep, NULL, rna_type);
28692
gsp = GetRnaExistingTextForList (rna_list, field_list);
28693
if (gsp != NULL && !StringHasNoText (gsp->sample_text))
23518
28694
{
23519
gsp = CheckForExistingText (entityID,
23520
field_list,
23521
GetRNAFieldString,
23522
NULL, NULL, IntValNodeCopy,
23523
NULL, SEQFEAT_RNA, vnp->data.intvalue, 0);
23524
if (gsp != NULL && !StringHasNoText (gsp->sample_text))
23525
{
23526
rval = gsp->sample_text;
23527
gsp->sample_text = NULL;
23528
}
23529
GetSampleFree (gsp);
28695
rval = gsp->sample_text;
28696
gsp->sample_text = NULL;
23530
28697
}
28698
GetSampleFree (gsp);
28699
rna_list = ValNodeFree (rna_list);
23531
28700
return rval;
23532
28701
}
23533
28702
23534
28703
static void RNAQualChangeNotify (Pointer userdata)
23535
28704
{
23536
ApplyRNAQualDlgPtr dlg;
23537
ValNodePtr field_list = NULL, subtype_list = NULL;
28705
AECRRNAQualDlgPtr dlg;
28706
ValNodePtr field_list = NULL;
28707
RnaTypePtr rna_type;
23538
28708
EditApplyPtr eap;
28709
CharPtr ncrna_class;
23539
28710
23540
dlg = (ApplyRNAQualDlgPtr) userdata;
28711
dlg = (AECRRNAQualDlgPtr) userdata;
23541
28712
if (dlg == NULL)
23542
28713
{
23543
28714
return;
23549
28720
Hide (dlg->edit_apply);
23550
28721
Hide (dlg->anticodon);
23551
28722
Hide (dlg->codons);
28723
Hide (dlg->ncrna_class);
23552
28724
}
23553
28725
else if (field_list->data.intvalue == RNAFIELD_CODONS_RECOGNIZED)
23554
28726
{
23555
28727
Show (dlg->codons);
23556
28728
Hide (dlg->edit_apply);
23557
28729
Hide (dlg->anticodon);
28730
Hide (dlg->ncrna_class);
23558
28731
}
23559
28732
else if (field_list->data.intvalue == RNAFIELD_ANTICODON)
23560
28733
{
23561
28734
Show (dlg->anticodon);
23562
28735
Hide (dlg->edit_apply);
23563
28736
Hide (dlg->codons);
28737
Hide (dlg->ncrna_class);
28738
}
28739
else if (field_list->data.intvalue == RNAFIELD_NCRNA_CLASS && dlg->ncrna_class != NULL)
28740
{
28741
Show (dlg->ncrna_class);
28742
Hide (dlg->codons);
28743
Hide (dlg->edit_apply);
28744
Hide (dlg->anticodon);
28745
/* autopopulate */
28746
rna_type = DialogToPointer (dlg->rna_type);
28747
ncrna_class = RNAQualAutopopulate (rna_type, field_list, dlg->entityID);
28748
PointerToDialog (dlg->ncrna_class, ncrna_class);
28749
ncrna_class = MemFree (ncrna_class);
23564
28750
}
23565
28751
else
23566
28752
{
23567
28753
Show (dlg->edit_apply);
23568
28754
Hide (dlg->codons);
23569
28755
Hide (dlg->anticodon);
28756
Hide (dlg->ncrna_class);
23570
28757
23571
28758
/* autopopulate text fields */
23572
subtype_list = DialogToPointer (dlg->subtype_list);
23573
eap = DialogToPointer (dlg->edit_apply);
23574
eap->apply_txt = MemFree (eap->apply_txt);
23575
eap->apply_txt = RNAQualAutopopulate (subtype_list, field_list, dlg->entityID);
23576
PointerToDialog (dlg->edit_apply, eap);
23577
EditApplyFree (eap);
23578
subtype_list = ValNodeFree (subtype_list);
28759
if (dlg->edit_apply != NULL)
28760
{
28761
rna_type = DialogToPointer (dlg->rna_type);
28762
eap = DialogToPointer (dlg->edit_apply);
28763
eap->apply_txt = MemFree (eap->apply_txt);
28764
eap->apply_txt = RNAQualAutopopulate (rna_type, field_list, dlg->entityID);
28765
PointerToDialog (dlg->edit_apply, eap);
28766
EditApplyFree (eap);
28767
rna_type = RnaTypeFree (rna_type);
28768
}
23579
28769
}
23580
28770
23581
28771
field_list = ValNodeFree (field_list);
23586
28776
}
23587
28777
}
23588
28778
23589
static void ApplyRNAQualMessage (DialoG d, Int2 mssg)
28779
static void AECRRNAQualMessage (DialoG d, Int2 mssg)
23590
28780
23591
28781
{
23592
ApplyRNAQualDlgPtr dlg;
28782
AECRRNAQualDlgPtr dlg;
23593
28783
23594
dlg = (ApplyRNAQualDlgPtr) GetObjectExtra (d);
28784
dlg = (AECRRNAQualDlgPtr) GetObjectExtra (d);
23595
28785
if (dlg != NULL) {
23596
28786
switch (mssg)
23597
28787
{
23598
28788
case VIB_MSG_INIT :
23599
28789
/* reset list */
23600
ResetApplyRNAQualDlg (dlg);
28790
ResetAECRRNAQualDlg (dlg);
23601
28791
break;
23602
28792
case VIB_MSG_ENTER :
23603
if (dlg->subtype_list != NULL)
23604
{
23605
Select (dlg->subtype_list);
23606
}
23607
else
23608
{
23609
Select (dlg->field_list);
23610
}
28793
Select (dlg->rna_type);
23611
28794
break;
23612
28795
case AECR_VIB_MSG_SET_DEFAULT :
23613
28796
SendMessageToDialog (dlg->field_list, AECR_VIB_MSG_SET_DEFAULT);
23614
SendMessageToDialog (dlg->subtype_list, AECR_VIB_MSG_SET_DEFAULT);
23615
ClearTextApplyRNAQualDlg (dlg);
28797
SendMessageToDialog (dlg->rna_type, AECR_VIB_MSG_SET_DEFAULT);
28798
ClearTextAECRRNAQualDlg (dlg);
23616
28799
break;
23617
28800
case AECR_VIB_MSG_CLEAR_TEXT :
23618
ClearTextApplyRNAQualDlg (dlg);
28801
ClearTextAECRRNAQualDlg (dlg);
23619
28802
break;
23620
28803
case AECR_VIB_MSG_AUTOPOPULATE:
23621
28804
RNAQualChangeNotify (dlg);
23626
28809
}
23627
28810
}
23628
28811
23629
static ValNodePtr TestApplyRNAQual (DialoG d)
28812
static ValNodePtr TestAECRRNAQual (DialoG d)
23630
28813
{
23631
ApplyRNAQualDlgPtr dlg;
23632
ValNodePtr err_list = NULL;
28814
AECRRNAQualDlgPtr dlg;
23633
28815
ValNodePtr total_err_list = NULL;
23634
28816
ValNodePtr field_list;
23635
28817
23636
dlg = (ApplyRNAQualDlgPtr) GetObjectExtra (d);
28818
dlg = (AECRRNAQualDlgPtr) GetObjectExtra (d);
23637
28819
if (dlg == NULL)
23638
28820
{
23639
28821
return NULL;
23640
28822
}
23641
28823
23642
total_err_list = TestDialog (dlg->subtype_list);
28824
total_err_list = TestDialog (dlg->rna_type);
23643
28825
23644
err_list = TestDialog (dlg->field_list);
23645
total_err_list = ValNodeAppend (total_err_list, err_list);
28826
ValNodeLink (&total_err_list, TestDialog (dlg->field_list));
23646
28827
23647
28828
field_list = DialogToPointer (dlg->field_list);
23648
if (field_list != NULL && field_list->data.intvalue != RNAFIELD_CODONS_RECOGNIZED)
23649
{
23650
err_list = TestDialog (dlg->edit_apply);
23651
total_err_list = ValNodeAppend (total_err_list, err_list);
28829
if (field_list != NULL) {
28830
if (field_list->data.intvalue == RNAFIELD_NCRNA_CLASS && dlg->ncrna_class != NULL) {
28831
ValNodeLink (&total_err_list, TestDialog (dlg->ncrna_class));
28832
} else if (field_list->data.intvalue != RNAFIELD_CODONS_RECOGNIZED) {
28833
ValNodeLink (&total_err_list, TestDialog (dlg->edit_apply));
28834
}
23652
28835
}
23653
28836
23654
28837
return total_err_list;
23655
28838
}
23656
28839
23657
static DialoG ApplyRNAQualDialog
28840
28841
static void AECRRNAQualButtonChange (ButtoN b)
28842
{
28843
AECRRNAQualDlgPtr dlg;
28844
28845
dlg = (AECRRNAQualDlgPtr) GetObjectExtra (b);
28846
if (dlg == NULL) return;
28847
28848
if (dlg->change_notify != NULL)
28849
{
28850
(dlg->change_notify) (dlg->change_userdata);
28851
}
28852
}
28853
28854
28855
static DialoG RNAQualListDialog
23658
28856
(GrouP h,
28857
Int4 action_choice,
23659
28858
Nlm_ChangeNotifyProc change_notify,
23660
28859
Pointer change_userdata,
23661
28860
Uint2 entityID)
23662
28861
{
23663
ApplyRNAQualDlgPtr dlg;
23664
GrouP p, g1, g2;
28862
AECRRNAQualDlgPtr dlg;
28863
GrouP p, g1, g2 = NULL;
23665
28864
SeqEntryPtr sep;
23666
28865
23667
dlg = (ApplyRNAQualDlgPtr) MemNew (sizeof (ApplyRNAQualDlgData));
28866
dlg = (AECRRNAQualDlgPtr) MemNew (sizeof (AECRRNAQualDlgData));
23668
28867
if (dlg == NULL)
23669
28868
{
23670
28869
return NULL;
23675
28874
SetGroupSpacing (p, 10, 10);
23676
28875
23677
28876
dlg->dialog = (DialoG) p;
23678
dlg->todialog = ApplyRNAQualToDialog;
23679
dlg->fromdialog = DialogToApplyRNAQual;
23680
dlg->dialogmessage = ApplyRNAQualMessage;
23681
dlg->testdialog = TestApplyRNAQual;
28877
dlg->todialog = AECRRNAQualToDialog;
28878
dlg->fromdialog = DialogToAECRRNAQual;
28879
dlg->dialogmessage = AECRRNAQualMessage;
28880
dlg->testdialog = TestAECRRNAQual;
23682
28881
dlg->change_notify = change_notify;
23683
28882
dlg->change_userdata = change_userdata;
23684
28883
dlg->entityID = entityID;
23685
23686
g1 = HiddenGroup (p, 2, 0, NULL);
23687
StaticPrompt (g1, "RNA Type", 0, dialogTextHeight, systemFont, 'l');
23688
StaticPrompt (g1, "RNA Field", 0, dialogTextHeight, systemFont, 'l');
23689
dlg->subtype_list = RNASubtypeSelectionDialog (g1, TRUE, NULL,
23690
RNAQualChangeNotify,
23691
dlg);
23692
dlg->field_list = RNAAddFieldSelectionDialog (g1, FALSE,
23693
RNAQualChangeNotify,
23694
dlg);
23695
23696
g2 = HiddenGroup (p, 0, 0, NULL);
23697
dlg->edit_apply = EditApplyDialog (g2, AECR_APPLY, "New Text",
23698
change_notify, change_userdata);
23699
23700
dlg->codons = CreateVisibleStringDialog (g2, 3, -1, 4);
23701
23702
sep = GetTopSeqEntryForEntityID (entityID);
23703
23704
dlg->anticodon = NULL;
23705
/*
23706
dlg->anticodon = CreateIntervalEditorDialogEx (g2, NULL, 2, 2, sep, TRUE, FALSE,
23707
TRUE, TRUE, FALSE,
23708
&(dlg->ff),
23709
NULL); */
23710
23711
AlignObjects (ALIGN_CENTER, (HANDLE) dlg->edit_apply,
23712
(HANDLE) dlg->codons,
23713
(HANDLE) dlg->anticodon,
23714
NULL);
28884
28885
28886
if (action_choice == AECR_CONVERT || action_choice == AECR_SWAP || action_choice == AECR_PARSE)
28887
{
28888
g1 = HiddenGroup (p, 3, 0, NULL);
28889
StaticPrompt (g1, "", 0, dialogTextHeight, systemFont, 'l');
28890
StaticPrompt (g1, "From", 0, dialogTextHeight, systemFont, 'l');
28891
StaticPrompt (g1, "To", 0, dialogTextHeight, systemFont, 'l');
28892
dlg->rna_type = RnaTypeDialog (g1, TRUE, RNAQualChangeNotify, dlg);
28893
28894
dlg->field_list = RNAFieldSelectionDialog (g1, FALSE,
28895
change_notify,
28896
change_userdata);
28897
dlg->field_list_to = RNAFieldSelectionDialog (g1, FALSE,
28898
change_notify,
28899
change_userdata);
28900
if (action_choice == AECR_CONVERT)
28901
{
28902
dlg->leave_on_original = CheckBox (p, "Leave on original", AECRRNAQualButtonChange);
28903
SetObjectExtra (dlg->leave_on_original, dlg, NULL);
28904
}
28905
}
28906
else
28907
{
28908
g1 = HiddenGroup (p, 2, 0, NULL);
28909
StaticPrompt (g1, "", 0, dialogTextHeight, systemFont, 'l');
28910
StaticPrompt (g1, "RNA Field", 0, dialogTextHeight, systemFont, 'l');
28911
dlg->rna_type = RnaTypeDialog (g1, TRUE, RNAQualChangeNotify, dlg);
28912
if (action_choice == AECR_REMOVE)
28913
{
28914
dlg->field_list = RNARemoveFieldSelectionDialog (g1, TRUE,
28915
RNAQualChangeNotify, dlg);
28916
}
28917
else
28918
{
28919
dlg->field_list = RNAFieldSelectionDialog (g1, FALSE,
28920
RNAQualChangeNotify,
28921
dlg);
28922
}
28923
}
28924
28925
if (action_choice == AECR_APPLY)
28926
{
28927
g2 = HiddenGroup (p, 0, 0, NULL);
28928
dlg->edit_apply = EditApplyDialog (g2, eEditApplyChoice_Apply, "New Text", NULL,
28929
change_notify, change_userdata);
28930
28931
dlg->codons = CreateVisibleStringDialog (g2, 3, -1, 4);
28932
28933
dlg->ncrna_class = CreatencRNAClassDialog (g2, FALSE, change_notify, change_userdata);
28934
28935
sep = GetTopSeqEntryForEntityID (entityID);
28936
28937
dlg->anticodon = NULL;
28938
/*
28939
dlg->anticodon = CreateIntervalEditorDialogEx (g2, NULL, 2, 2, sep, TRUE, FALSE,
28940
TRUE, TRUE, FALSE,
28941
&(dlg->ff),
28942
NULL); */
28943
28944
AlignObjects (ALIGN_CENTER, (HANDLE) dlg->edit_apply,
28945
(HANDLE) dlg->codons,
28946
(HANDLE) dlg->ncrna_class,
28947
(HANDLE) dlg->anticodon,
28948
NULL);
28949
}
28950
else if (action_choice == AECR_EDIT)
28951
{
28952
g2 = HiddenGroup (p, 1, 0, NULL);
28953
dlg->edit_apply = EditApplyDialog (g2, eEditApplyChoice_Edit,
28954
"New Text", NULL,
28955
change_notify, change_userdata);
28956
dlg->text_portion = NULL;
28957
dlg->remove_parsed = NULL;
28958
}
28959
else if (action_choice == AECR_PARSE)
28960
{
28961
g2 = HiddenGroup (p, -1, 0, NULL);
28962
dlg->edit_apply = NULL;
28963
dlg->text_portion = TextPortionXDialog(p);
28964
dlg->remove_parsed = CheckBox (p, "Remove from parsed field", SimpleAECRButtonChange);
28965
SetObjectExtra (dlg->remove_parsed, dlg, NULL);
28966
AlignObjects (ALIGN_CENTER, (HANDLE) dlg->edit_apply, (HANDLE) dlg->remove_parsed, NULL);
28967
}
28968
else
28969
{
28970
dlg->edit_apply = NULL;
28971
dlg->text_portion = NULL;
28972
dlg->remove_parsed = NULL;
28973
}
28974
23715
28975
23716
28976
AlignObjects (ALIGN_CENTER, (HANDLE) g1, (HANDLE) g2, NULL);
23717
28977
23720
28980
return (DialoG) p;
23721
28981
}
23722
28982
23723
static DialoG RNAQualListDialog
23724
(GrouP h,
23725
Int4 action_choice,
23726
Nlm_ChangeNotifyProc change_notify,
23727
Pointer change_userdata,
23728
Uint2 entityID)
23729
{
23730
DialoG d = NULL;
23731
23732
switch (action_choice)
23733
{
23734
case AECR_REMOVE:
23735
d = SimpleAECRDialog (h, action_choice, change_notify, change_userdata,
23736
NULL, NULL,
23737
RNARemoveFieldSelectionDialog,
23738
RNASubtypeSelectionDialog,
23739
NULL,
23740
"RNA Field", "RNA type", FALSE, entityID);
23741
break;
23742
case AECR_CONVERT:
23743
case AECR_SWAP:
23744
case AECR_PARSE:
23745
d = SimpleAECRDialog (h, action_choice, change_notify, change_userdata,
23746
NULL, NULL,
23747
RNAFieldSelectionDialog,
23748
RNASubtypeSelectionDialog,
23749
NULL,
23750
"RNA Field", "RNA type", TRUE, entityID);
23751
break;
23752
break;
23753
case AECR_EDIT:
23754
d = SimpleAECRDialog (h, action_choice, change_notify, change_userdata,
23755
NULL, NULL,
23756
RNAFieldSelectionDialog,
23757
RNASubtypeSelectionDialog,
23758
RNAQualAutopopulate,
23759
"RNA Field", "RNA type", TRUE, entityID);
23760
break;
23761
case AECR_APPLY:
23762
d = ApplyRNAQualDialog (h, change_notify, change_userdata, entityID);
23763
break;
23764
}
23765
return d;
23766
}
23767
28983
23768
28984
static void ApplyRNACodonsCallback (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
23769
28985
{
23818
29034
}
23819
29035
}
23820
29036
23821
static Boolean AcceptRNAApply (ApplyEditConvertRemovePtr ap)
23822
{
23823
ApplyRNAQualPtr rp;
23824
FilterSetPtr fsp;
29037
29038
static void CollectRNAFeaturesCallback (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
29039
{
29040
if (sfp != NULL && sfp->data.choice == SEQFEAT_RNA && userdata != NULL)
29041
{
29042
ValNodeAddPointer ((ValNodePtr PNTR) userdata, OBJ_SEQFEAT, sfp);
29043
}
29044
29045
}
29046
29047
29048
static ValNodePtr GetRNAFeatureList (SeqEntryPtr sep, FilterSetPtr fsp, RnaTypePtr rtp)
29049
{
29050
ValNodePtr rna_list = NULL, vnp_rna;
29051
ValNodePtr not_match;
29052
SeqFeatPtr sfp;
29053
Boolean matches;
29054
29055
if (sep == NULL) return NULL;
29056
29057
OperateOnSeqEntryConstrainedObjects (sep, fsp, CollectRNAFeaturesCallback,
29058
NULL, SEQFEAT_RNA, 0, 0, &rna_list);
29059
29060
if (rtp != NULL)
29061
{
29062
for (vnp_rna = rna_list; vnp_rna != NULL; vnp_rna = vnp_rna->next)
29063
{
29064
matches = FALSE;
29065
sfp = vnp_rna->data.ptrvalue;
29066
if (!MatchesRnaType (sfp, rtp))
29067
{
29068
vnp_rna->choice = 0;
29069
}
29070
}
29071
29072
not_match = ValNodeExtractList (&rna_list, 0);
29073
not_match = ValNodeFree (not_match);
29074
}
29075
return rna_list;
29076
}
29077
29078
29079
static GetSamplePtr GetRnaExistingTextForList (ValNodePtr rna_list, ValNodePtr requested_field)
29080
{
29081
GetSamplePtr gsp;
29082
ValNodePtr vnp;
29083
SeqFeatPtr sfp;
29084
29085
if (rna_list == NULL || requested_field == NULL) return NULL;
29086
29087
gsp = GetSampleNew ();
29088
gsp->sample_text = NULL;
29089
gsp->fieldstring_func = GetRNAFieldString;
29090
gsp->descrstring_func = NULL;
29091
gsp->free_vn_proc = NULL;
29092
gsp->copy_vn_proc = IntValNodeCopy;
29093
gsp->requested_field = (gsp->copy_vn_proc) (requested_field);
29094
gsp->num_found = 0;
29095
gsp->all_same = TRUE;
29096
29097
for (vnp = rna_list; vnp != NULL; vnp = vnp->next)
29098
{
29099
sfp = vnp->data.ptrvalue;
29100
GetSampleFeatureCallback (sfp, gsp, NULL);
29101
}
29102
return gsp;
29103
}
29104
29105
29106
static Boolean ApplyToRNAList (ValNodePtr rna_list, AECRRNAQualPtr rp, FilterSetPtr fsp)
29107
{
29108
ValNodePtr vnp_rna;
29109
SeqFeatPtr sfp;
23825
29110
ApplyValueData avd;
23826
29111
Boolean rval = TRUE;
23827
SeqEntryPtr sep;
23828
ValNodePtr vnp;
23829
GetSamplePtr gsp, gsp_new, gsp_sum;
23830
23831
if (ap == NULL)
23832
{
23833
return FALSE;
23834
}
23835
23836
rp = DialogToPointer (ap->aecr_pages[AECR_APPLY - 1]);
23837
23838
sep = GetTopSeqEntryForEntityID (ap->input_entityID);
23839
if (rp->subtype_list == NULL || rp->field_list == NULL)
23840
{
23841
rp = ApplyRNAQualFree (rp);
23842
return FALSE;
23843
}
23844
23845
fsp = (FilterSetPtr) DialogToPointer (ap->constraints);
23846
29112
GetSamplePtr gsp;
29113
29114
if (rna_list == NULL || rp == NULL || rp->field_list == NULL)
29115
{
29116
return FALSE;
29117
}
29118
23847
29119
if (rp->field_list->data.intvalue == RNAFIELD_CODONS_RECOGNIZED)
23848
29120
{
23849
for (vnp = rp->subtype_list; vnp != NULL; vnp = vnp->next)
29121
for (vnp_rna = rna_list; vnp_rna != NULL; vnp_rna = vnp_rna->next)
23850
29122
{
23851
OperateOnSeqEntryConstrainedObjects (sep, fsp, ApplyRNACodonsCallback,
23852
NULL, SEQFEAT_RNA, FEATDEF_tRNA, 0, rp->codons);
29123
sfp = vnp_rna->data.ptrvalue;
29124
if (sfp->idx.subtype == FEATDEF_tRNA)
29125
{
29126
ApplyRNACodonsCallback (sfp, rp->codons, fsp);
29127
}
23853
29128
}
23854
29129
}
23855
29130
else if (rp->field_list->data.intvalue == RNAFIELD_ANTICODON)
23856
29131
{
23857
for (vnp = rp->subtype_list; vnp != NULL; vnp = vnp->next)
29132
for (vnp_rna = rna_list; vnp_rna != NULL; vnp_rna = vnp_rna->next)
23858
29133
{
23859
OperateOnSeqEntryConstrainedObjects (sep, fsp, ApplyRNAAnticodonCallback,
23860
NULL, SEQFEAT_RNA, FEATDEF_tRNA, 0, rp->anticodon);
29134
sfp = vnp_rna->data.ptrvalue;
29135
if (sfp->idx.subtype == FEATDEF_tRNA)
29136
{
29137
ApplyRNAAnticodonCallback (sfp, rp->anticodon, fsp);
29138
}
23861
29139
}
23862
29140
}
23863
29141
else
23864
29142
{
23865
29143
avd.field_list = rp->field_list;
29144
avd.where_to_replace = EditApplyFindLocation_anywhere;
23866
29145
23867
29146
/* get handling for existing text */
23868
gsp_sum = NULL;
23869
for (vnp = rp->subtype_list; vnp != NULL; vnp = vnp->next)
23870
{
23871
gsp = CheckForExistingText (ap->input_entityID,
23872
avd.field_list,
23873
GetRNAFieldString,
23874
NULL, NULL, IntValNodeCopy,
23875
fsp, SEQFEAT_RNA, vnp->data.intvalue, 0);
23876
gsp_new = GetSampleAdd (gsp_sum, gsp);
23877
gsp = GetSampleFree (gsp);
23878
gsp_sum = GetSampleFree (gsp_sum);
23879
gsp_sum = gsp_new;
23880
}
23881
avd.etp = GetExistingTextHandlerInfo (gsp_sum, FALSE);
23882
gsp_sum = GetSampleFree (gsp_sum);
29147
gsp = GetRnaExistingTextForList (rna_list, rp->field_list);
29148
avd.etp = GetExistingTextHandlerInfo (gsp == NULL ? 0 : gsp->num_found, FALSE);
29149
gsp = GetSampleFree (gsp);
23883
29150
23884
29151
if (avd.etp != NULL
23885
&& avd.etp->existing_text_choice == EXISTING_TEXT_CHOICE_CANCEL)
29152
&& avd.etp->existing_text_choice == eExistingTextChoiceCancel)
23886
29153
{
23887
29154
rval = FALSE;
23888
29155
}
23891
29158
{
23892
29159
AddEditApplyDataToApplyValue (AECR_APPLY, rp->edit_apply, &avd);
23893
29160
23894
for (vnp = rp->subtype_list; vnp != NULL; vnp = vnp->next)
29161
for (vnp_rna = rna_list; vnp_rna != NULL; vnp_rna = vnp_rna->next)
23895
29162
{
23896
OperateOnSeqEntryConstrainedObjects (sep, fsp, SetRNAFieldString,
23897
NULL, SEQFEAT_RNA, vnp->data.intvalue, 0, &avd);
29163
sfp = vnp_rna->data.ptrvalue;
29164
SetRNAFieldString (sfp, &avd, fsp);
23898
29165
}
23899
29166
avd.text_to_replace = MemFree (avd.text_to_replace);
23900
29167
avd.new_text = MemFree (avd.new_text);
23901
29168
}
23902
29169
avd.etp = MemFree (avd.etp);
23903
29170
}
23904
23905
FilterSetFree (fsp);
23906
23907
29171
return rval;
23908
29172
}
23909
29173
29174
23910
29175
static Boolean
23911
AcceptRNAQualEditRemoveConvert
23912
(ApplyEditConvertRemovePtr ap,
23913
Int4 action_choice,
23914
SimpleAECRPtr rp)
29176
RNAQualConvertSwapParseList
29177
(ValNodePtr rna_list,
29178
AECRRNAQualPtr rp,
29179
Int4 action_choice,
29180
FilterSetPtr fsp)
23915
29181
{
23916
SeqEntryPtr sep;
23917
FilterSetPtr fsp;
23918
ConvertFieldData cfd;
23919
GetSamplePtr gsp, gsp_new, gsp_sum;
23920
ValNodePtr vnp;
23921
ApplyValueData avd;
23922
Boolean rval = TRUE;
29182
ConvertFieldData cfd;
29183
ConversionConflictData ccd;
29184
ValNodePtr vnp_rna;
29185
ApplyValueData avd;
29186
Boolean rval = TRUE;
29187
SeqFeatPtr sfp;
23923
29188
23924
if (ap == NULL
29189
if (rna_list == NULL
29190
|| rp == NULL
23925
29191
|| action_choice < AECR_EDIT
23926
29192
|| action_choice > NUM_AECR
23927
|| rp == NULL
23928
|| rp->subtype_list == NULL || rp->field_list == NULL
23929
|| ((action_choice == AECR_CONVERT || action_choice == AECR_SWAP || action_choice == AECR_PARSE)
23930
&& rp->field_list_to == NULL))
29193
|| rp->field_list == NULL
29194
|| rp->field_list_to == NULL)
23931
29195
{
23932
29196
return FALSE;
23933
29197
}
23934
29198
23935
sep = GetTopSeqEntryForEntityID (ap->input_entityID);
23936
23937
fsp = (FilterSetPtr) DialogToPointer (ap->constraints);
29199
avd.where_to_replace = EditApplyFindLocation_anywhere;
23938
29200
23939
if (action_choice == AECR_CONVERT || action_choice == AECR_SWAP || action_choice == AECR_PARSE)
29201
cfd.src_field_list = rp->field_list;
29202
cfd.dst_field_list = rp->field_list_to;
29203
cfd.etp = NULL;
29204
cfd.get_str_func = GetRNAFieldString;
29205
cfd.set_str_func = SetRNAFieldString;
29206
cfd.remove_str_func = RemoveRNAField;
29207
cfd.get_d_str_func = NULL;
29208
cfd.set_d_str_func = NULL;
29209
cfd.remove_d_str_func = NULL;
29210
cfd.fsp = fsp;
29211
cfd.strip_name_from_text = FALSE;
29212
cfd.name_field_func = NULL;
29213
cfd.text_portion = rp->text_portion;
29214
cfd.remove_parsed = rp->remove_parsed;
29215
29216
if (action_choice == AECR_CONVERT)
23940
29217
{
23941
cfd.src_field_list = rp->field_list;
23942
cfd.dst_field_list = rp->field_list_to;
23943
cfd.etp = NULL;
23944
cfd.get_str_func = GetRNAFieldString;
23945
cfd.set_str_func = SetRNAFieldString;
23946
cfd.remove_str_func = RemoveRNAField;
23947
cfd.get_d_str_func = NULL;
23948
cfd.set_d_str_func = NULL;
23949
cfd.remove_d_str_func = NULL;
23950
cfd.fsp = fsp;
23951
cfd.strip_name_from_text = rp->strip_name_from_text;
23952
cfd.name_field_func = NULL;
23953
cfd.text_portion = rp->text_portion;
23954
23955
if (action_choice == AECR_CONVERT)
23956
{
23957
if (rp->leave_on_original)
23958
{
23959
cfd.convert_type = CONVERT_TYPE_COPY;
23960
}
23961
else
23962
{
23963
cfd.convert_type = CONVERT_TYPE_MOVE;
23964
}
23965
}
23966
else if (action_choice == AECR_SWAP)
23967
{
23968
cfd.convert_type = CONVERT_TYPE_SWAP;
23969
}
23970
else if (action_choice == AECR_PARSE)
23971
{
23972
cfd.convert_type = CONVERT_TYPE_PARSE;
23973
}
23974
23975
if (cfd.convert_type == CONVERT_TYPE_MOVE || cfd.convert_type == CONVERT_TYPE_COPY || cfd.convert_type == CONVERT_TYPE_PARSE)
23976
{
23977
/* get existing text sample */
23978
gsp_sum = NULL;
23979
for (vnp = rp->subtype_list; vnp != NULL; vnp = vnp->next)
23980
{
23981
gsp = CheckForConversionExistingTextInSeqEntry (sep, &cfd, fsp,
23982
SEQFEAT_RNA,
23983
vnp->data.intvalue,
23984
0);
23985
gsp_new = GetSampleAdd (gsp_sum, gsp);
23986
gsp = GetSampleFree (gsp);
23987
gsp_sum = GetSampleFree (gsp_sum);
23988
gsp_sum = gsp_new;
23989
}
23990
cfd.etp = GetExistingTextHandlerInfo (gsp_sum, FALSE);
23991
gsp_sum = GetSampleFree (gsp_sum);
23992
if (cfd.etp != NULL && cfd.etp->existing_text_choice == EXISTING_TEXT_CHOICE_CANCEL)
23993
{
23994
rval = FALSE;
23995
}
29218
if (rp->leave_on_original)
29219
{
29220
cfd.convert_type = CONVERT_TYPE_COPY;
23996
29221
}
23997
29222
else
23998
29223
{
23999
cfd.etp = NULL;
24000
}
29224
cfd.convert_type = CONVERT_TYPE_MOVE;
29225
}
29226
}
29227
else if (action_choice == AECR_SWAP)
29228
{
29229
cfd.convert_type = CONVERT_TYPE_SWAP;
29230
}
29231
else if (action_choice == AECR_PARSE)
29232
{
29233
cfd.convert_type = CONVERT_TYPE_PARSE;
29234
}
29235
29236
if (cfd.convert_type == CONVERT_TYPE_MOVE || cfd.convert_type == CONVERT_TYPE_COPY || cfd.convert_type == CONVERT_TYPE_PARSE)
29237
{
29238
/* get existing text sample */
29239
ccd.cfp = &cfd;
29240
ccd.gsp = GetSampleNew();
24001
29241
24002
if (rval)
24003
{
24004
for (vnp = rp->subtype_list; vnp != NULL; vnp = vnp->next)
24005
{
24006
OperateOnSeqEntryConstrainedObjects (sep, fsp,
24007
ConvertFeatureFieldCallback, NULL,
24008
SEQFEAT_RNA, vnp->data.intvalue,
24009
0, &cfd);
24010
}
29242
for (vnp_rna = rna_list; vnp_rna != NULL; vnp_rna = vnp_rna->next)
29243
{
29244
sfp = vnp_rna->data.ptrvalue;
29245
GetConversionConflictsFeatureCallback (sfp, &ccd, fsp);
29246
}
29247
cfd.etp = GetExistingTextHandlerInfo (ccd.gsp == NULL ? 0 : ccd.gsp->num_found, FALSE);
29248
ccd.gsp = GetSampleFree (ccd.gsp);
29249
if (cfd.etp != NULL && cfd.etp->existing_text_choice == eExistingTextChoiceCancel)
29250
{
29251
rval = FALSE;
24011
29252
}
24012
29253
}
24013
29254
else
24014
29255
{
24015
avd.field_list = rp->field_list;
24016
avd.etp = NULL;
24017
AddEditApplyDataToApplyValue (action_choice, rp->edit_apply, &avd);
24018
24019
for (vnp = rp->subtype_list; vnp != NULL; vnp = vnp->next)
29256
cfd.etp = NULL;
29257
}
29258
29259
if (rval)
29260
{
29261
for (vnp_rna = rna_list; vnp_rna != NULL; vnp_rna = vnp_rna->next)
24020
29262
{
24021
if (action_choice == AECR_EDIT)
24022
{
24023
OperateOnSeqEntryConstrainedObjects (sep, fsp, SetRNAFieldString,
24024
NULL, SEQFEAT_RNA, vnp->data.intvalue, 0, &avd);
24025
}
24026
else if (action_choice == AECR_REMOVE)
24027
{
24028
OperateOnSeqEntryConstrainedObjects (sep, fsp, RemoveRNAField,
24029
NULL, SEQFEAT_RNA, vnp->data.intvalue, 0, &avd);
24030
}
29263
sfp = vnp_rna->data.ptrvalue;
29264
ConvertFeatureFieldCallback (sfp, &cfd, fsp);
24031
29265
}
24032
avd.text_to_replace = MemFree (avd.text_to_replace);
24033
avd.new_text = MemFree (avd.new_text);
24034
29266
}
24035
29267
24036
FilterSetFree (fsp);
24037
29268
return rval;
24038
24039
}
29269
}
29270
29271
29272
static Boolean RNAQualEditRemoveList
29273
(ValNodePtr rna_list,
29274
AECRRNAQualPtr rp,
29275
Int4 action_choice,
29276
FilterSetPtr fsp)
29277
{
29278
SeqFeatPtr sfp;
29279
ValNodePtr vnp_rna;
29280
ApplyValueData avd;
29281
Boolean rval = TRUE;
29282
29283
if (rna_list == NULL
29284
|| rp == NULL
29285
|| (action_choice != AECR_EDIT && action_choice != AECR_REMOVE)
29286
|| rp->field_list == NULL)
29287
{
29288
return FALSE;
29289
}
29290
29291
avd.where_to_replace = EditApplyFindLocation_anywhere;
29292
avd.field_list = rp->field_list;
29293
avd.etp = NULL;
29294
AddEditApplyDataToApplyValue (action_choice, rp->edit_apply, &avd);
29295
29296
for (vnp_rna = rna_list; vnp_rna != NULL; vnp_rna = vnp_rna->next)
29297
{
29298
sfp = vnp_rna->data.ptrvalue;
29299
if (action_choice == AECR_EDIT)
29300
{
29301
SetRNAFieldString (sfp, &avd, fsp);
29302
}
29303
else if (action_choice == AECR_REMOVE)
29304
{
29305
RemoveRNAField (sfp, &avd, fsp);
29306
}
29307
}
29308
29309
avd.text_to_replace = MemFree (avd.text_to_replace);
29310
avd.new_text = MemFree (avd.new_text);
29311
return TRUE;
29312
}
29313
29314
29315
24040
29316
24041
29317
static Boolean AcceptRNAQualApplyEditRemoveConvert (Pointer userdata)
24042
29318
{
24043
29319
ApplyEditConvertRemovePtr ap;
24044
SimpleAECRPtr rp = NULL;
29320
AECRRNAQualPtr rp;
24045
29321
Int4 action_choice;
24046
29322
Boolean rval = TRUE;
29323
FilterSetPtr fsp;
29324
ValNodePtr rna_list;
29325
SeqEntryPtr sep;
24047
29326
24048
29327
ap = (ApplyEditConvertRemovePtr) userdata;
24049
29328
if (ap == NULL)
24062
29341
{
24063
29342
action_choice = GetValue (ap->action_popup);
24064
29343
}
29344
29345
rp = (AECRRNAQualPtr) DialogToPointer (ap->aecr_pages[action_choice - 1]);
29346
if (rp == NULL) return FALSE;
29347
29348
fsp = (FilterSetPtr) DialogToPointer (ap->constraints);
29349
sep = GetTopSeqEntryForEntityID (ap->input_entityID);
29350
rna_list = GetRNAFeatureList (sep, fsp, rp->rna_type);
24065
29351
24066
29352
if (action_choice == AECR_APPLY)
24067
29353
{
24068
rval = AcceptRNAApply (ap);
29354
rval = ApplyToRNAList (rna_list, rp, fsp);
29355
}
29356
else if (action_choice == AECR_CONVERT || action_choice == AECR_SWAP
29357
|| action_choice == AECR_PARSE)
29358
{
29359
rval = RNAQualConvertSwapParseList (rna_list, rp, action_choice, fsp);
24069
29360
}
24070
29361
else if (action_choice > AECR_APPLY && action_choice <= NUM_AECR)
24071
29362
{
24072
rp = (SimpleAECRPtr) DialogToPointer (ap->aecr_pages[action_choice - 1]);
24073
rval = AcceptRNAQualEditRemoveConvert (ap, action_choice, rp);
24074
rp = SimpleAECRFree (rp);
29363
rval = RNAQualEditRemoveList (rna_list, rp, action_choice, fsp);
24075
29364
}
24076
29365
24077
29366
if (rval)
24094
29383
ApplyEditConvertRemoveCombo (i, first_action_choice, crippled,
24095
29384
"RNA Qualifiers",
24096
29385
RNAQualListDialog, TRUE, GetRNAQualSample,
24097
TRUE, FALSE, TRUE, FALSE, "Where feature text",
29386
TRUE, FALSE, TRUE, FALSE, FALSE, "Where feature text",
24098
29387
AcceptRNAQualApplyEditRemoveConvert, NULL, NULL,
24099
29388
CheckFeaturesForPresample);
24100
29389
}
24158
29447
{
24159
29448
ValNodePtr field_list;
24160
29449
ValNodePtr subtype_list;
24161
StringConstraintPtr scp;
29450
StringConstraintXPtr scp;
24162
29451
Boolean use_field_list;
24163
29452
} RemoveGBQualData, PNTR RemoveGBQualPtr;
24164
29453
24168
29457
{
24169
29458
ap->field_list = ValNodeFree (ap->field_list);
24170
29459
ap->subtype_list = ValNodeFree (ap->subtype_list);
24171
ap->scp = StringConstraintFree (ap->scp);
29460
ap->scp = StringConstraintXFree (ap->scp);
24172
29461
ap = MemFree (ap);
24173
29462
}
24174
29463
return ap;
24336
29625
static void GBQualChangeNotify (GrouP b)
24337
29626
{
24338
29627
RemoveGBQualDlgPtr dlg;
24339
ValNodePtr field_list = NULL, subtype_list = NULL;
24340
29628
24341
29629
dlg = (RemoveGBQualDlgPtr) GetObjectExtra (b);
24342
29630
if (dlg == NULL)
24405
29693
dlg->field_list = GBQualSelectionDialog (dlg->list_or_txt_grp, FALSE,
24406
29694
change_notify,
24407
29695
change_userdata);
24408
dlg->qual_name_constraint = StringConstraintDialog (dlg->list_or_txt_grp, "Where qualifier name contains", FALSE);
29696
dlg->qual_name_constraint = StringConstraintDialogX (dlg->list_or_txt_grp, "Where qualifier name contains", FALSE);
24409
29697
SetValue (dlg->list_or_txt_grp, 1);
24410
29698
Disable (dlg->qual_name_constraint);
24411
29699
24488
29776
Boolean rval = TRUE;
24489
29777
24490
29778
ValNodePtr field_list = NULL;
24491
ValNodePtr field_list_to = NULL;
24492
29779
ValNodePtr subtype_list = NULL;
24493
Boolean leave_on_original = FALSE;
24494
EditApplyPtr edit_apply = NULL;
24495
FreeValNodeProc free_field_vn_proc = NULL;
24496
FreeValNodeProc free_subtype_vn_proc = NULL;
24497
29780
EditApplyPtr eap = NULL;
24498
29781
24499
29782
24515
29798
{
24516
29799
return FALSE;
24517
29800
}
29801
29802
avd.where_to_replace = EditApplyFindLocation_anywhere;
24518
29803
24519
29804
if (action_choice == AECR_REMOVE)
24520
29805
{
24569
29854
cfd.remove_d_str_func = NULL;
24570
29855
cfd.fsp = fsp;
24571
29856
cfd.strip_name_from_text = gp->strip_name_from_text;
29857
cfd.remove_parsed = gp->remove_parsed;
24572
29858
cfd.name_field_func = NULL;
24573
29859
cfd.text_portion = gp->text_portion;
24574
29860
24607
29893
gsp_sum = GetSampleFree (gsp_sum);
24608
29894
gsp_sum = gsp_new;
24609
29895
}
24610
cfd.etp = GetExistingTextHandlerInfo (gsp_sum, FALSE);
29896
cfd.etp = GetExistingTextHandlerInfo (gsp_sum == NULL ? 0 : gsp_sum->num_found, FALSE);
24611
29897
gsp_sum = GetSampleFree (gsp_sum);
24612
if (cfd.etp != NULL && cfd.etp->existing_text_choice == EXISTING_TEXT_CHOICE_CANCEL)
29898
if (cfd.etp != NULL && cfd.etp->existing_text_choice == eExistingTextChoiceCancel)
24613
29899
{
24614
29900
rval = FALSE;
24615
29901
}
24647
29933
gsp = GetGBQualExistingText (sep, subtype_list,
24648
29934
avd.field_list,
24649
29935
fsp);
24650
avd.etp = GetExistingTextHandlerInfo (gsp, FALSE);
29936
avd.etp = GetExistingTextHandlerInfo (gsp == NULL ? 0 : gsp->num_found, FALSE);
24651
29937
gsp = GetSampleFree (gsp);
24652
29938
24653
29939
if (avd.etp != NULL
24654
&& avd.etp->existing_text_choice == EXISTING_TEXT_CHOICE_CANCEL)
29940
&& avd.etp->existing_text_choice == eExistingTextChoiceCancel)
24655
29941
{
24656
29942
rval = FALSE;
24657
29943
}
24831
30117
ApplyEditConvertRemoveCombo (i, first_action_choice, crippled,
24832
30118
"Import Qualifiers",
24833
30119
GBQualListDialog, FALSE, GetGBQualSample,
24834
TRUE, FALSE, TRUE, FALSE, "Where feature text",
30120
TRUE, FALSE, TRUE, FALSE, FALSE, "Where feature text",
24835
30121
AcceptGBQualApplyEditRemoveConvert, NULL, NULL,
24836
30122
CheckFeaturesForPresample);
24837
30123
}
24872
30158
}
24873
30159
24874
30160
30161
static CharPtr alltargetsTabs [] = {
30162
"BioSource", "GenBank Qualifiers", "RNA Qualifiers", "CDS-Gene-Prot-mRNA", NULL
30163
};
30164
30165
typedef enum
30166
{
30167
eAllTargetsAllActions_BioSource = 0,
30168
eAllTargetsAllActions_GBQual,
30169
eAllTargetsAllActions_RNAQual,
30170
eAllTargetsAllActions_CDSGeneProtmRNA,
30171
eNumAllTargetsAllActions
30172
} EAllTargetsAllActions;
30173
30174
typedef struct allactionsalltargetsdlg
30175
{
30176
DIALOG_MESSAGE_BLOCK
30177
DialoG tbs; /* folder tab for switching between target types */
30178
Int2 currentPage;
30179
GrouP target_pages [eNumAllTargetsAllActions];
30180
DialoG aecr_pages [NUM_AECR * eNumAllTargetsAllActions];
30181
PopuP action_popup;
30182
30183
DialoG accept_cancel;
30184
DialoG constraints;
30185
ButtoN clear_constraints_on_action_change;
30186
Nlm_ChangeAECRActionProc change_action;
30187
Int4 prev_page;
30188
Boolean crippled;
30189
Int4 crippled_action;
30190
Uint2 entityID;
30191
Nlm_ChangeNotifyProc change_notify;
30192
Pointer change_userdata;
30193
} AllActionsAllTargetsDlgData, PNTR AllActionsAllTargetsDlgPtr;
30194
30195
30196
static void ChangeAllActionsAllTargetsTarget (VoidPtr data, Int2 newval, Int2 oldval)
30197
{
30198
AllActionsAllTargetsDlgPtr dlg;
30199
30200
dlg = (AllActionsAllTargetsDlgPtr) data;
30201
if (dlg != NULL) {
30202
dlg->currentPage = newval;
30203
SafeHide (dlg->target_pages [oldval]);
30204
SafeShow (dlg->target_pages [newval]);
30205
Update ();
30206
if (dlg->change_notify != NULL) {
30207
(dlg->change_notify) (dlg->change_userdata);
30208
}
30209
}
30210
}
30211
30212
static void ChangeAllActionsAllTargetsAction (PopuP p)
30213
{
30214
AllActionsAllTargetsDlgPtr dlg;
30215
Int4 i;
30216
30217
dlg = (AllActionsAllTargetsDlgPtr) GetObjectExtra (p);
30218
if (dlg == NULL) return;
30219
30220
for (i = 0; i < NUM_AECR; i++)
30221
{
30222
Hide (dlg->aecr_pages[(dlg->currentPage * NUM_AECR) + i]);
30223
}
30224
i = GetValue (dlg->action_popup);
30225
if (i > 0 && i <= NUM_AECR)
30226
{
30227
Show (dlg->aecr_pages[(dlg->currentPage * NUM_AECR) + i - 1]);
30228
SendMessageToDialog (dlg->aecr_pages[(dlg->currentPage * NUM_AECR) + i - 1], VIB_MSG_ENTER);
30229
}
30230
30231
}
30232
30233
static DialoG AllActionsAllTargetsDialog (GrouP h, Uint2 entityID, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata)
30234
{
30235
AllActionsAllTargetsDlgPtr dlg;
30236
GrouP p, g;
30237
Int4 i;
30238
30239
dlg = (AllActionsAllTargetsDlgPtr) MemNew (sizeof (AllActionsAllTargetsDlgData));
30240
30241
p = HiddenGroup (h, -1, 0, NULL);
30242
SetObjectExtra (p, dlg, StdCleanupExtraProc);
30243
SetGroupSpacing (p, 10, 10);
30244
30245
dlg->dialog = (DialoG) p;
30246
dlg->todialog = NULL;
30247
dlg->fromdialog = NULL;
30248
dlg->dialogmessage = NULL;
30249
dlg->testdialog = NULL;
30250
dlg->change_notify = change_notify;
30251
dlg->change_userdata = change_userdata;
30252
dlg->entityID = entityID;
30253
30254
dlg->action_popup = PopupList (p, TRUE, ChangeAllActionsAllTargetsAction);
30255
SetObjectExtra (dlg->action_popup, dlg, NULL);
30256
PopupItem (dlg->action_popup, "Apply");
30257
PopupItem (dlg->action_popup, "Edit");
30258
PopupItem (dlg->action_popup, "Convert");
30259
PopupItem (dlg->action_popup, "Swap");
30260
PopupItem (dlg->action_popup, "Parse");
30261
PopupItem (dlg->action_popup, "Remove");
30262
SetValue (dlg->action_popup, 1);
30263
30264
30265
dlg->tbs = CreateFolderTabs (p, alltargetsTabs, eAllTargetsAllActions_BioSource,
30266
0, 0, SYSTEM_FOLDER_TAB,
30267
ChangeAllActionsAllTargetsTarget, (Pointer) dlg);
30268
30269
g = HiddenGroup (p, 0, 0, NULL);
30270
dlg->target_pages[eAllTargetsAllActions_BioSource] = HiddenGroup (g, 0, 0, NULL);
30271
for (i = 0; i < NUM_AECR; i++)
30272
{
30273
dlg->aecr_pages[(eAllTargetsAllActions_BioSource * NUM_AECR) + i]
30274
= SourceQualAECRDialog (dlg->target_pages[eAllTargetsAllActions_BioSource],
30275
i + 1, change_notify, change_userdata, entityID);
30276
Hide (dlg->aecr_pages[(eAllTargetsAllActions_BioSource * NUM_AECR) + i]);
30277
}
30278
30279
dlg->target_pages[eAllTargetsAllActions_GBQual] = HiddenGroup (g, 0, 0, NULL);
30280
for (i = 0; i < NUM_AECR; i++)
30281
{
30282
dlg->aecr_pages[(eAllTargetsAllActions_GBQual * NUM_AECR) + i]
30283
= GBQualListDialog (dlg->target_pages[eAllTargetsAllActions_GBQual],
30284
i + 1, change_notify, change_userdata, entityID);
30285
Hide (dlg->aecr_pages[(eAllTargetsAllActions_GBQual * NUM_AECR) + i]);
30286
}
30287
30288
dlg->target_pages[eAllTargetsAllActions_RNAQual] = HiddenGroup (g, 0, 0, NULL);
30289
for (i = 0; i < NUM_AECR; i++)
30290
{
30291
dlg->aecr_pages[(eAllTargetsAllActions_RNAQual * NUM_AECR) + i]
30292
= RNAQualListDialog (dlg->target_pages[eAllTargetsAllActions_RNAQual],
30293
i + 1, change_notify, change_userdata, entityID);
30294
Hide (dlg->aecr_pages[(eAllTargetsAllActions_RNAQual * NUM_AECR) + i]);
30295
}
30296
30297
dlg->target_pages[eAllTargetsAllActions_CDSGeneProtmRNA] = HiddenGroup (g, 0, 0, NULL);
30298
for (i = 0; i < NUM_AECR; i++)
30299
{
30300
dlg->aecr_pages[(eAllTargetsAllActions_CDSGeneProtmRNA * NUM_AECR) + i]
30301
= CDSGeneProtAECRDialog (dlg->target_pages[eAllTargetsAllActions_CDSGeneProtmRNA],
30302
i + 1, change_notify, change_userdata, entityID);
30303
Hide (dlg->aecr_pages[(eAllTargetsAllActions_CDSGeneProtmRNA * NUM_AECR) + i]);
30304
}
30305
30306
AlignObjects (ALIGN_CENTER, (HANDLE) dlg->tbs, (HANDLE) g, NULL);
30307
30308
return (DialoG) p;
30309
}
30310
30311
30312
extern void AllActionsAllTargets (IteM i)
30313
{
30314
30315
}
30316
24875
30317
typedef struct locustagtooldlocustag
24876
30318
{
24877
30319
FORM_MESSAGE_BLOCK
25003
30445
h = HiddenGroup (w, -1, 0, NULL);
25004
30446
SetGroupSpacing (h, 10, 10);
25005
30447
25006
mp->constraints = FilterGroup (h, TRUE, FALSE, TRUE, FALSE, "Where feature text");
30448
mp->constraints = FilterGroup (h, TRUE, FALSE, TRUE, FALSE, FALSE, "Where feature text");
25007
30449
mp->accept_cancel = AcceptCancelDialog (h, LocusTagToOldLocusTagAction, NULL,
25008
30450
LocusTagToOldLocusTagActionClear,
25009
30451
LocusTagToOldLocusTagActionClearText,
25212
30654
25213
30655
Int2 action_choice;
25214
30656
Boolean cover_sequence;
25215
StringConstraintPtr string_constraint;
30657
StringConstraintXPtr string_constraint;
25216
30658
LogInfoPtr lip;
25217
30659
25218
30660
/* for string constraint */
25256
30698
&& !DoesObjectMatchStringConstraint (ccp->omtp, ccp->aip, sfp, &(ccp->ohsd)))
25257
30699
{
25258
30700
sfp = SeqMgrGetDesiredFeature (ccp->input_entityID, NULL, 0, 0, sfp, &fcontext);
25259
if (sfp == NULL || !DoesStringMatchConstraint (fcontext.label, ccp->ohsd.scp))
30701
if (sfp == NULL || !DoesStringMatchConstraintX (fcontext.label, ccp->ohsd.scp))
25260
30702
{
25261
30703
return;
25262
30704
}
25499
30941
25500
30942
CloseLog (ccp->lip);
25501
30943
FreeLog (ccp->lip);
25502
ccp->string_constraint = StringConstraintFree (ccp->string_constraint);
30944
ccp->string_constraint = StringConstraintXFree (ccp->string_constraint);
25503
30945
Remove (ccp->form);
25504
30946
DeleteMarkedObjects (ccp->input_entityID, 0, NULL);
25505
30947
ObjMgrSetDirtyFlag (ccp->input_entityID, TRUE);
25587
31029
SetValue (ccp->prod_name_choice_grp, 1);
25588
31030
Disable (ccp->prod_name_txt);
25589
31031
25590
ccp->string_constraint_dlg = StringConstraintDialog (ccp->new_cds_grp, "Where CDS field", TRUE);
31032
ccp->string_constraint_dlg = StringConstraintDialogX (ccp->new_cds_grp, "Where CDS field", TRUE);
25591
31033
Disable (ccp->new_cds_grp);
25592
31034
25593
31035
AlignObjects (ALIGN_CENTER, (HANDLE) ccp->cover_sequence_btn,
25780
31222
p = StaticPrompt (g, "Move features to protein of type", 0, dialogTextHeight, systemFont, 'l');
25781
31223
25782
31224
mtpp->feature_selection = FeatureSelectionDialogEx (g, TRUE, sep, NULL, NULL);
25783
mtpp->constraints = FilterGroup (g, TRUE, FALSE, FALSE, FALSE, "Where feature text");
31225
mtpp->constraints = FilterGroup (g, TRUE, FALSE, FALSE, FALSE, FALSE, "Where feature text");
25784
31226
AlignObjects (ALIGN_CENTER, (HANDLE) p, (HANDLE) mtpp->feature_selection, (HANDLE) mtpp->constraints, NULL);
25785
31227
25786
31228
c = HiddenGroup (w, 2, 0, NULL);
25793
31235
Select (w);
25794
31236
Update ();
25795
31237
}
31238
31239
31240
typedef struct uniquevaluecollection {
31241
ValNodePtr requested_field;
31242
GetFeatureFieldString fieldstring_func;
31243
GetDescriptorFieldString descrstring_func;
31244
FreeValNodeProc free_vn_proc;
31245
CopyValNodeDataProc copy_vn_proc;
31246
ValNodePtr value_lists;
31247
} UniqueValueCollectionData, PNTR UniqueValueCollectionPtr;
31248
31249
31250
static ClickableItemPtr FindExistingCategory (CharPtr description, ValNodePtr category_list)
31251
{
31252
ClickableItemPtr cip;
31253
31254
while (category_list != NULL) {
31255
cip = (ClickableItemPtr) category_list->data.ptrvalue;
31256
if (cip != NULL &&
31257
(StringCmp (description, cip->description) == 0
31258
|| (StringHasNoText (description) && StringHasNoText (cip->description)))) {
31259
return cip;
31260
}
31261
category_list = category_list->next;
31262
}
31263
return NULL;
31264
}
31265
31266
31267
static ValNodePtr DataInValNodeList (ValNodePtr list, Uint1 choice, Pointer ptrvalue)
31268
{
31269
while (list != NULL) {
31270
if (choice == list->choice && ptrvalue == list->data.ptrvalue) {
31271
return list;
31272
}
31273
list = list->next;
31274
}
31275
return NULL;
31276
}
31277
31278
31279
static void CombineClickableItemLists (ValNodePtr PNTR list1, ValNodePtr list2)
31280
{
31281
ValNodePtr add_vnp, prev_vnp = NULL, next_vnp;
31282
31283
if (*list1 == NULL) {
31284
*list1 = list2;
31285
return;
31286
} else if (list2 == NULL) {
31287
return;
31288
}
31289
31290
add_vnp = list2;
31291
while (add_vnp != NULL) {
31292
next_vnp = add_vnp->next;
31293
if (DataInValNodeList (*list1, add_vnp->choice, add_vnp->data.ptrvalue)) {
31294
if (prev_vnp == NULL) {
31295
list2 = next_vnp;
31296
} else {
31297
prev_vnp->next = next_vnp;
31298
}
31299
add_vnp->next = NULL;
31300
ValNodeFree (add_vnp);
31301
} else {
31302
prev_vnp = add_vnp;
31303
}
31304
add_vnp = next_vnp;
31305
}
31306
ValNodeLink (list1, list2);
31307
}
31308
31309
31310
static void CombineClickableLists (ValNodePtr PNTR list1, ValNodePtr list2)
31311
{
31312
ClickableItemPtr cip1, cip2;
31313
ValNodePtr vnp;
31314
for (vnp = list2; vnp != NULL; vnp = vnp->next) {
31315
cip2 = vnp->data.ptrvalue;
31316
if (cip2 != NULL) {
31317
cip1 = FindExistingCategory (cip2->description, *list1);
31318
if (cip1 == NULL) {
31319
ValNodeAddPointer (list1, 0, cip2);
31320
vnp->data.ptrvalue = NULL;
31321
} else {
31322
CombineClickableItemLists (&(cip1->item_list), cip2->item_list);
31323
cip2->item_list = NULL;
31324
}
31325
}
31326
}
31327
list2 = FreeClickableList (list2);
31328
}
31329
31330
31331
static void GetUniqueValuesFeatureCallback (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
31332
{
31333
UniqueValueCollectionPtr uvcp;
31334
CharPtr str;
31335
ValNodePtr check_vnp;
31336
ClickableItemPtr cip;
31337
31338
if (sfp == NULL || userdata == NULL)
31339
{
31340
return;
31341
}
31342
31343
uvcp = (UniqueValueCollectionPtr) userdata;
31344
if (uvcp->fieldstring_func == NULL)
31345
{
31346
return;
31347
}
31348
31349
str = uvcp->fieldstring_func (sfp, uvcp->requested_field, NULL);
31350
cip = FindExistingCategory (str, uvcp->value_lists);
31351
if (cip == NULL) {
31352
cip = (ClickableItemPtr) MemNew (sizeof (ClickableItemData));
31353
MemSet (cip, 0, sizeof (ClickableItemData));
31354
cip->description = str;
31355
ValNodeAddPointer (&cip->item_list, OBJ_SEQFEAT, sfp);
31356
ValNodeAddPointer (&(uvcp->value_lists), 0, cip);
31357
} else {
31358
str = MemFree (str);
31359
/* make sure feature isn't already in the list */
31360
for (check_vnp = cip->item_list; check_vnp != NULL; check_vnp = check_vnp->next) {
31361
if (check_vnp->choice == OBJ_SEQFEAT && sfp == check_vnp->data.ptrvalue) break;
31362
}
31363
if (check_vnp == NULL) {
31364
ValNodeAddPointer (&cip->item_list, OBJ_SEQFEAT, sfp);
31365
}
31366
}
31367
}
31368
31369
static void GetUniqueValuesDescriptorCallback (SeqDescrPtr sdp, Pointer userdata, FilterSetPtr fsp)
31370
{
31371
UniqueValueCollectionPtr uvcp;
31372
ClickableItemPtr cip;
31373
CharPtr str;
31374
ValNodePtr check_vnp;
31375
31376
if (sdp == NULL || userdata == NULL)
31377
{
31378
return;
31379
}
31380
31381
uvcp = (UniqueValueCollectionPtr) userdata;
31382
if (uvcp->descrstring_func == NULL)
31383
{
31384
return;
31385
}
31386
31387
str = uvcp->descrstring_func (sdp, uvcp->requested_field, NULL);
31388
31389
cip = FindExistingCategory (str, uvcp->value_lists);
31390
31391
if (cip == NULL) {
31392
cip = (ClickableItemPtr) MemNew (sizeof (ClickableItemData));
31393
MemSet (cip, 0, sizeof (ClickableItemData));
31394
cip->description = str;
31395
ValNodeAddPointer (&cip->item_list, OBJ_SEQDESC, sdp);
31396
ValNodeAddPointer (&(uvcp->value_lists), 0, cip);
31397
} else {
31398
str = MemFree (str);
31399
/* make sure feature isn't already in the list */
31400
for (check_vnp = cip->item_list; check_vnp != NULL; check_vnp = check_vnp->next) {
31401
if (check_vnp->choice == OBJ_SEQDESC && sdp == check_vnp->data.ptrvalue) break;
31402
}
31403
if (check_vnp == NULL) {
31404
ValNodeAddPointer (&cip->item_list, OBJ_SEQDESC, sdp);
31405
}
31406
}
31407
}
31408
31409
31410
static ValNodePtr CheckForUniqueValuesInSeqEntry
31411
(SeqEntryPtr sep,
31412
ValNodePtr requested_field,
31413
GetFeatureFieldString fieldstring_func,
31414
GetDescriptorFieldString descrstring_func,
31415
FreeValNodeProc free_vn_proc,
31416
CopyValNodeDataProc copy_vn_proc,
31417
FilterSetPtr fsp,
31418
Uint1 seqfeat_choice,
31419
Uint1 featdef_choice,
31420
Uint1 descr_choice)
31421
{
31422
UniqueValueCollectionData uvcd;
31423
31424
uvcd.fieldstring_func = fieldstring_func;
31425
uvcd.descrstring_func = descrstring_func;
31426
uvcd.free_vn_proc = free_vn_proc;
31427
uvcd.copy_vn_proc = copy_vn_proc;
31428
uvcd.requested_field = (copy_vn_proc) (requested_field);
31429
uvcd.value_lists = NULL;
31430
OperateOnSeqEntryConstrainedObjects (sep, fsp, GetUniqueValuesFeatureCallback,
31431
GetUniqueValuesDescriptorCallback,
31432
seqfeat_choice, featdef_choice,
31433
descr_choice, &uvcd);
31434
return uvcd.value_lists;
31435
}
31436
31437
31438
static ValNodePtr
31439
GetUniqueValueListForSeqEntry
31440
(SeqEntryPtr sep,
31441
Uint2 entityID,
31442
ParseFieldPtr dst_field_data,
31443
FilterSetPtr fsp)
31444
{
31445
ValNodePtr unique_values = NULL;
31446
ValNodePtr requested_field = NULL, vnp;
31447
SeqEntryPtr orig_sep;
31448
31449
if (sep == NULL || dst_field_data == NULL)
31450
{
31451
return NULL;
31452
}
31453
31454
switch (dst_field_data->parse_field_type)
31455
{
31456
case PARSE_FIELD_SOURCE_QUAL :
31457
unique_values = CheckForUniqueValuesInSeqEntry (sep,
31458
dst_field_data->feature_field,
31459
GetSourceQualFeatureString,
31460
GetSourceQualDescrString,
31461
ValNodeSimpleDataFree,
31462
SourceQualValNodeDataCopy,
31463
fsp,
31464
SEQFEAT_BIOSRC, 0,
31465
Seq_descr_source);
31466
break;
31467
case PARSE_FIELD_DEFLINE:
31468
requested_field = ValNodeNew (NULL);
31469
requested_field->data.intvalue = Seq_descr_title;
31470
unique_values = CheckForUniqueValuesInSeqEntry (sep, requested_field,
31471
NULL,
31472
GetStringFromStringDescriptor,
31473
NULL, IntValNodeCopy,
31474
fsp, 0, 0, Seq_descr_title);
31475
requested_field = ValNodeFree (requested_field);
31476
break;
31477
case PARSE_FIELD_BIOSRC_STRING:
31478
unique_values = CheckForUniqueValuesInSeqEntry (sep,
31479
dst_field_data->feature_field,
31480
GetSourceFeatureString,
31481
GetSourceDescriptorString,
31482
NULL, IntValNodeCopy,
31483
fsp,
31484
SEQFEAT_BIOSRC, 0,
31485
Seq_descr_source);
31486
break;
31487
case PARSE_FIELD_DBXREF:
31488
unique_values = CheckForUniqueValuesInSeqEntry (sep, dst_field_data->feature_field,
31489
GetBioSourceFeatureDbxrefString,
31490
GetBioSourceDescriptorDbxrefString,
31491
ValNodeSimpleDataFree,
31492
ValNodeStringCopy,
31493
fsp,
31494
SEQFEAT_BIOSRC, 0, Seq_descr_source);
31495
break;
31496
case PARSE_FIELD_GENE_FIELD:
31497
unique_values = CheckForUniqueValuesInSeqEntry (sep,
31498
dst_field_data->feature_field,
31499
GetGeneFieldString,
31500
NULL,
31501
NULL, IntValNodeCopy,
31502
fsp,
31503
SEQFEAT_GENE, 0, 0);
31504
break;
31505
case PARSE_FIELD_RNA_FIELD:
31506
unique_values = CheckForUniqueValuesInSeqEntry (sep,
31507
dst_field_data->feature_field,
31508
GetRNAFieldString,
31509
NULL,
31510
NULL, IntValNodeCopy,
31511
fsp,
31512
SEQFEAT_RNA,
31513
dst_field_data->feature_subtype == NULL ? 0 : dst_field_data->feature_subtype->data.intvalue,
31514
0);
31515
break;
31516
case PARSE_FIELD_CDS_COMMENT:
31517
unique_values = CheckForUniqueValuesInSeqEntry (sep,
31518
NULL,
31519
GetCDSComment,
31520
NULL,
31521
NULL, IntValNodeCopy,
31522
fsp,
31523
SEQFEAT_CDREGION, FEATDEF_CDS, 0);
31524
break;
31525
case PARSE_FIELD_COMMENT_DESC:
31526
requested_field = ValNodeNew (NULL);
31527
requested_field->data.intvalue = Seq_descr_comment;
31528
31529
unique_values = CheckForUniqueValuesInSeqEntry (sep, requested_field,
31530
NULL,
31531
GetStringFromStringDescriptor,
31532
NULL, IntValNodeCopy,
31533
fsp, 0, 0, Seq_descr_comment);
31534
requested_field = ValNodeFree (requested_field);
31535
break;
31536
case PARSE_FIELD_PROTEIN_FIELD:
31537
unique_values = CheckForUniqueValuesInSeqEntry (sep,
31538
dst_field_data->feature_field,
31539
GetProteinFieldString,
31540
NULL,
31541
NULL, IntValNodeCopy,
31542
fsp,
31543
SEQFEAT_PROT, 0, 0);
31544
break;
31545
case PARSE_FIELD_IMPORT_QUAL:
31546
orig_sep = sep;
31547
for (vnp = dst_field_data->feature_subtype; vnp != NULL; vnp = vnp->next)
31548
{
31549
CombineClickableLists (&unique_values,
31550
CheckForUniqueValuesInSeqEntry (sep,
31551
dst_field_data->feature_field,
31552
GetGBQualString,
31553
NULL,
31554
NULL, IntValNodeCopy,
31555
fsp, 0, vnp->choice, 0));
31556
/* if we are also looking at features other than mat_peptides, use
31557
* original SeqEntry */
31558
sep = orig_sep;
31559
}
31560
break;
31561
case PARSE_FIELD_FEATURE_NOTE:
31562
orig_sep = sep;
31563
for (vnp = dst_field_data->feature_field; vnp != NULL; vnp = vnp->next)
31564
{
31565
CombineClickableLists (&unique_values,
31566
CheckForUniqueValuesInSeqEntry (sep, vnp,
31567
GetFeatureNote,
31568
NULL,
31569
ValNodeSimpleDataFree,
31570
ValNodeStringCopy,
31571
fsp, 0, vnp->choice, 0));
31572
/* if we are also looking at features other than mat_peptides, use
31573
* original SeqEntry */
31574
sep = orig_sep;
31575
}
31576
break;
31577
}
31578
return unique_values;
31579
}
31580
31581
31582
static SeqEntryPtr GetBestSeqEntryForItem (ValNodePtr vnp)
31583
{
31584
SeqFeatPtr sfp;
31585
SeqDescrPtr sdp;
31586
ObjValNodePtr ovp;
31587
SeqEntryPtr sep = NULL;
31588
BioseqPtr bsp;
31589
31590
if (vnp == NULL || vnp->data.ptrvalue == NULL) return NULL;
31591
31592
if (vnp->choice == OBJ_SEQFEAT) {
31593
sfp = vnp->data.ptrvalue;
31594
sep = GetBestTopParentForData (sfp->idx.entityID, BioseqFindFromSeqLoc (sfp->location));
31595
} else if (vnp->choice == OBJ_SEQDESC) {
31596
sdp = vnp->data.ptrvalue;
31597
if (sdp->extended != 0) {
31598
ovp = (ObjValNodePtr) sdp;
31599
if (ovp->idx.parenttype == OBJ_BIOSEQSET) {
31600
sep = SeqMgrGetSeqEntryForData (ovp->idx.parentptr);
31601
} else if (ovp->idx.parenttype == OBJ_BIOSEQ) {
31602
sep = GetBestTopParentForData (ovp->idx.entityID, ovp->idx.parentptr);
31603
}
31604
}
31605
} else if (vnp->choice == OBJ_BIOSEQ) {
31606
bsp = (BioseqPtr) vnp->data.ptrvalue;
31607
sep = GetBestTopParentForData (bsp->idx.entityID, bsp);
31608
} else if (vnp->choice == OBJ_SEQENTRY) {
31609
sep = vnp->data.ptrvalue;
31610
}
31611
return sep;
31612
}
31613
31614
static ValNodePtr GetSeqEntryListForItem (ValNodePtr vnp)
31615
{
31616
SeqFeatPtr sfp;
31617
SeqDescrPtr sdp;
31618
ObjValNodePtr ovp;
31619
SeqEntryPtr sep = NULL;
31620
BioseqPtr bsp;
31621
BioseqSetPtr bssp;
31622
ValNodePtr sep_list = NULL;
31623
31624
if (vnp == NULL || vnp->data.ptrvalue == NULL) return NULL;
31625
31626
if (vnp->choice == OBJ_SEQFEAT) {
31627
sfp = vnp->data.ptrvalue;
31628
sep = GetBestTopParentForData (sfp->idx.entityID, BioseqFindFromSeqLoc (sfp->location));
31629
ValNodeAddPointer (&sep_list, OBJ_SEQENTRY, sep);
31630
} else if (vnp->choice == OBJ_SEQDESC) {
31631
sdp = vnp->data.ptrvalue;
31632
if (sdp->extended != 0) {
31633
ovp = (ObjValNodePtr) sdp;
31634
if (ovp->idx.parenttype == OBJ_BIOSEQSET) {
31635
bssp = (BioseqSetPtr) ovp->idx.parentptr;
31636
if (bssp != NULL) {
31637
/* nuc_prot sets, segsets, and members of parts should travel together */
31638
if (bssp->_class == BioseqseqSet_class_nuc_prot) {
31639
sep = SeqMgrGetSeqEntryForData (bssp);
31640
if (sep != NULL) {
31641
ValNodeAddPointer (&sep_list, OBJ_SEQENTRY, sep);
31642
}
31643
} else if (bssp->_class == BioseqseqSet_class_segset
31644
|| bssp->_class == BioseqseqSet_class_parts) {
31645
sep = bssp->seq_set;
31646
if (sep != NULL && IS_Bioseq (sep)) {
31647
bsp = sep->data.ptrvalue;
31648
sep = GetBestTopParentForData (bsp->idx.entityID, bsp);
31649
if (sep != NULL) {
31650
ValNodeAddPointer (&sep_list, OBJ_SEQENTRY, sep);
31651
}
31652
}
31653
} else {
31654
sep = bssp->seq_set;
31655
while (sep != NULL) {
31656
ValNodeAddPointer (&sep_list, OBJ_SEQENTRY, sep);
31657
sep = sep->next;
31658
}
31659
}
31660
}
31661
} else if (ovp->idx.parenttype == OBJ_BIOSEQ) {
31662
sep = GetBestTopParentForData (ovp->idx.entityID, ovp->idx.parentptr);
31663
if (sep != NULL) {
31664
ValNodeAddPointer (&sep_list, OBJ_SEQENTRY, sep);
31665
}
31666
}
31667
}
31668
} else if (vnp->choice == OBJ_BIOSEQ) {
31669
bsp = (BioseqPtr) vnp->data.ptrvalue;
31670
sep = GetBestTopParentForData (bsp->idx.entityID, bsp);
31671
} else if (vnp->choice == OBJ_SEQENTRY) {
31672
sep = vnp->data.ptrvalue;
31673
}
31674
return sep_list;
31675
}
31676
31677
31678
static Boolean RemoveItemAndCategory (ClickableItemPtr cip, Uint1 choice, Pointer ptrvalue)
31679
{
31680
ValNodePtr vnp, prev = NULL;
31681
Boolean found = FALSE;
31682
CharPtr description = NULL;
31683
ClickableItemPtr subcat;
31684
31685
vnp = cip->item_list;
31686
while (vnp != NULL) {
31687
if (vnp->choice == choice && vnp->data.ptrvalue == ptrvalue) {
31688
found = TRUE;
31689
if (prev == NULL) {
31690
cip->item_list = vnp->next;
31691
} else {
31692
prev->next = vnp->next;
31693
}
31694
vnp->next = NULL;
31695
description = GetDiscrepancyItemText (vnp);
31696
vnp = ValNodeFree (vnp);
31697
} else {
31698
prev = vnp;
31699
vnp = vnp->next;
31700
}
31701
}
31702
if (found) {
31703
/* also remove subcategory */
31704
prev = NULL;
31705
vnp = cip->subcategories;
31706
while (vnp != NULL) {
31707
subcat = (ClickableItemPtr) vnp->data.ptrvalue;
31708
if (subcat != NULL && StringCmp (subcat->description, description) == 0) {
31709
if (prev == NULL) {
31710
cip->subcategories = vnp->next;
31711
} else {
31712
prev->next = vnp->next;
31713
}
31714
vnp->next = NULL;
31715
vnp = FreeClickableList (vnp);
31716
} else {
31717
prev = vnp;
31718
vnp = vnp->next;
31719
}
31720
}
31721
}
31722
return found;
31723
}
31724
31725
static ValNodePtr RearrangeForSeqEntriesInMultipleCategories (ValNodePtr value_lists)
31726
{
31727
ClickableItemPtr cip1, cip2, existing_cat;
31728
ValNodePtr vnp, check_vnp, last_vnp, vnp_item1, prev, vnp_next;
31729
Boolean found;
31730
CharPtr new_description;
31731
31732
/* now check for SeqEntries that appear in multiple lists */
31733
for (vnp = value_lists; vnp != NULL && vnp->next != NULL; vnp = vnp->next) {
31734
if (vnp->data.ptrvalue == NULL) continue;
31735
last_vnp = vnp->next;
31736
while (last_vnp->next != NULL) {
31737
last_vnp = last_vnp->next;
31738
}
31739
cip1 = (ClickableItemPtr) vnp->data.ptrvalue;
31740
for (vnp_item1 = cip1->item_list;
31741
vnp_item1 != NULL;
31742
vnp_item1 = vnp_next) {
31743
vnp_next = vnp_item1->next;
31744
found = FALSE;
31745
if (vnp_item1->data.ptrvalue != NULL && vnp_item1->choice == OBJ_SEQENTRY) {
31746
check_vnp = vnp->next;
31747
while (check_vnp != NULL && !found) {
31748
if (check_vnp->data.ptrvalue != NULL) {
31749
cip2 = check_vnp->data.ptrvalue;
31750
found = RemoveItemAndCategory (cip2, vnp_item1->choice, vnp_item1->data.ptrvalue);
31751
}
31752
if (!found) {
31753
if (check_vnp == last_vnp) {
31754
check_vnp = NULL;
31755
} else {
31756
check_vnp = check_vnp->next;
31757
}
31758
}
31759
}
31760
}
31761
if (found) {
31762
/* need to take this SeqEntry out of both lists, put in new category */
31763
new_description = (CharPtr) MemNew (sizeof (Char) * (StringLen (cip1->description)
31764
+ StringLen (cip2->description) + 6));
31765
if (StringCmp (cip1->description, cip2->description) < 0) {
31766
sprintf (new_description, "%s AND %s", cip1->description, cip2->description);
31767
} else {
31768
sprintf (new_description, "%s AND %s", cip2->description, cip1->description);
31769
}
31770
existing_cat = FindExistingCategory (new_description, check_vnp->next);
31771
if (existing_cat == NULL) {
31772
/* make new category, add to end of list */
31773
existing_cat = (ClickableItemPtr) MemNew (sizeof (ClickableItemData));
31774
MemSet (existing_cat, 0, sizeof (ClickableItemData));
31775
existing_cat->description = new_description;
31776
ValNodeAddPointer (&value_lists, 0, existing_cat);
31777
} else {
31778
new_description = MemFree (new_description);
31779
}
31780
/* don't add item twice */
31781
if (!DataInValNodeList (existing_cat->item_list, vnp_item1->choice, vnp_item1->data.ptrvalue)) {
31782
ValNodeAddPointer (&(existing_cat->item_list), vnp_item1->choice, vnp_item1->data.ptrvalue);
31783
}
31784
/* remove from cip1 */
31785
RemoveItemAndCategory (cip1, vnp_item1->choice, vnp_item1->data.ptrvalue);
31786
}
31787
}
31788
}
31789
31790
/* remove empty categories */
31791
for (vnp = value_lists, prev = NULL; vnp != NULL; vnp = vnp_next) {
31792
vnp_next = vnp->next;
31793
cip1 = (ClickableItemPtr) vnp->data.ptrvalue;
31794
if (cip1 == NULL || cip1->item_list == NULL) {
31795
if (prev == NULL) {
31796
value_lists = vnp->next;
31797
} else {
31798
prev->next = vnp->next;
31799
}
31800
vnp->next = NULL;
31801
vnp = FreeClickableList (vnp);
31802
} else {
31803
prev = vnp;
31804
}
31805
}
31806
return value_lists;
31807
}
31808
31809
31810
static ValNodePtr ChangeUniqueValueListsToSeqEntryLists (ValNodePtr value_lists)
31811
{
31812
ValNodePtr vnp, vnp_item, new_item_list, new_vnp, sep_list, sep_vnp;
31813
ClickableItemPtr cip, subcat;
31814
SeqEntryPtr sep;
31815
CharPtr description;
31816
31817
/* First, add SeqEntry for each feature or descriptor to the item list */
31818
for (vnp = value_lists; vnp != NULL; vnp = vnp->next) {
31819
cip = (ClickableItemPtr) vnp->data.ptrvalue;
31820
new_item_list = NULL;
31821
if (cip != NULL) {
31822
for (vnp_item = cip->item_list; vnp_item != NULL; vnp_item = vnp_item->next) {
31823
if (vnp_item->data.ptrvalue == NULL) continue;
31824
sep_list = GetSeqEntryListForItem (vnp_item);
31825
for (sep_vnp = sep_list; sep_vnp != NULL; sep_vnp = sep_vnp->next) {
31826
sep = sep_vnp->data.ptrvalue;
31827
new_vnp = DataInValNodeList (new_item_list, OBJ_SEQENTRY, sep);
31828
/* add to list for this category */
31829
if (new_vnp == NULL) {
31830
new_vnp = ValNodeAddPointer (&new_item_list, OBJ_SEQENTRY, sep);
31831
}
31832
description = GetDiscrepancyItemText(new_vnp);
31833
subcat = FindExistingCategory (description, cip->subcategories);
31834
if (subcat == NULL) {
31835
subcat = (ClickableItemPtr) MemNew (sizeof (ClickableItemData));
31836
MemSet (subcat, 0, sizeof (ClickableItemData));
31837
subcat->description = description;
31838
ValNodeAddPointer (&(cip->subcategories), 0, subcat);
31839
} else {
31840
description = MemFree (description);
31841
}
31842
/* don't add item twice */
31843
if (!DataInValNodeList (subcat->item_list, vnp_item->choice, vnp_item->data.ptrvalue)) {
31844
ValNodeAddPointer (&(subcat->item_list), vnp_item->choice, vnp_item->data.ptrvalue);
31845
}
31846
}
31847
sep_list = ValNodeFree (sep_list);
31848
}
31849
31850
cip->item_list = ValNodeFree (cip->item_list);
31851
cip->item_list = new_item_list;
31852
}
31853
}
31854
value_lists = RearrangeForSeqEntriesInMultipleCategories (value_lists);
31855
return value_lists;
31856
}
31857
31858
31859
static void GetMolTypes (SeqDescrPtr sdp, Pointer userdata)
31860
{
31861
ValNodePtr PNTR type_list;
31862
ClickableItemPtr cip;
31863
CharPtr str;
31864
MolInfoPtr mip;
31865
31866
if (sdp == NULL || sdp->choice != Seq_descr_molinfo || sdp->data.ptrvalue == NULL || userdata == NULL)
31867
{
31868
return;
31869
}
31870
31871
type_list = (ValNodePtr PNTR) userdata;
31872
31873
mip = (MolInfoPtr) sdp->data.ptrvalue;
31874
/* don't look for peptides */
31875
if (mip->biomol == 8) return;
31876
31877
str = GetMoleculeTypeName (mip->biomol);
31878
31879
cip = FindExistingCategory (str, *type_list);
31880
31881
if (cip == NULL) {
31882
cip = (ClickableItemPtr) MemNew (sizeof (ClickableItemData));
31883
MemSet (cip, 0, sizeof (ClickableItemData));
31884
cip->description = StringSave (str);
31885
ValNodeAddPointer (&cip->item_list, OBJ_SEQDESC, sdp);
31886
ValNodeAddPointer (type_list, 0, cip);
31887
} else {
31888
/* make sure feature isn't already in the list */
31889
if (DataInValNodeList (cip->item_list, OBJ_SEQDESC, sdp) == NULL) {
31890
ValNodeAddPointer (&cip->item_list, OBJ_SEQDESC, sdp);
31891
}
31892
}
31893
}
31894
31895
static void GetMolClasses (BioseqPtr bsp, Pointer userdata)
31896
{
31897
ValNodePtr PNTR type_list;
31898
ClickableItemPtr cip;
31899
CharPtr str;
31900
31901
if (bsp == NULL || ISA_aa(bsp->mol) || userdata == NULL)
31902
{
31903
return;
31904
}
31905
31906
type_list = (ValNodePtr PNTR) userdata;
31907
31908
str = GetMoleculeClassName (bsp->mol);
31909
31910
cip = FindExistingCategory (str, *type_list);
31911
31912
if (cip == NULL) {
31913
cip = (ClickableItemPtr) MemNew (sizeof (ClickableItemData));
31914
MemSet (cip, 0, sizeof (ClickableItemData));
31915
cip->description = StringSave (str);
31916
ValNodeAddPointer (&cip->item_list, OBJ_BIOSEQ, bsp);
31917
ValNodeAddPointer (type_list, 0, cip);
31918
} else {
31919
/* make sure feature isn't already in the list */
31920
if (DataInValNodeList (cip->item_list, OBJ_BIOSEQ, bsp) == NULL) {
31921
ValNodeAddPointer (&cip->item_list, OBJ_BIOSEQ, bsp);
31922
}
31923
}
31924
}
31925
31926
31927
typedef struct segfeatures {
31928
Uint2 featdef;
31929
ValNodePtr feature_list;
31930
} SegFeaturesData, PNTR SegFeaturesPtr;
31931
31932
static void FindFeaturesForSeg (SeqFeatPtr sfp, Pointer userdata)
31933
{
31934
SegFeaturesPtr fp;
31935
31936
if (sfp == NULL || userdata == NULL) return;
31937
31938
fp = (SegFeaturesPtr) userdata;
31939
31940
if (sfp->idx.subtype == fp->featdef) {
31941
ValNodeAddPointer (&(fp->feature_list), OBJ_SEQFEAT, sfp);
31942
}
31943
}
31944
31945
typedef struct segdescriptors {
31946
Uint2 desc_type;
31947
ValNodePtr descriptor_list;
31948
} SegDescriptorsData, PNTR SegDescriptorsPtr;
31949
31950
static void FindDescriptorsForSeg (SeqDescrPtr sdp, Pointer userdata)
31951
{
31952
SegDescriptorsPtr fp;
31953
31954
if (sdp == NULL || userdata == NULL) return;
31955
31956
fp = (SegDescriptorsPtr) userdata;
31957
31958
if (sdp->choice == fp->desc_type) {
31959
ValNodeAddPointer (&(fp->descriptor_list), OBJ_SEQDESC, sdp);
31960
}
31961
}
31962
31963
31964
extern ValNodePtr
31965
CreateSeqEntryListsForUniqueValues
31966
(SeqEntryPtr sep,
31967
Uint2 entityID,
31968
ParseFieldPtr dst_field_data,
31969
FilterSetPtr fsp)
31970
{
31971
ValNodePtr value_lists;
31972
31973
value_lists = GetUniqueValueListForSeqEntry (sep, entityID, dst_field_data, fsp);
31974
31975
value_lists = ChangeUniqueValueListsToSeqEntryLists (value_lists);
31976
return value_lists;
31977
}
31978
31979
static void AddPubFeatureWithText (SeqFeatPtr sfp, Pointer userdata)
31980
{
31981
ValNodePtr PNTR pub_list;
31982
31983
if (sfp == NULL || userdata == NULL) return;
31984
pub_list = (ValNodePtr PNTR) userdata;
31985
31986
ValNodeAddPointer (pub_list, OBJ_SEQFEAT, sfp);
31987
}
31988
31989
static void AddPubDescriptorWithText (SeqDescrPtr sdp, Pointer userdata)
31990
{
31991
ValNodePtr PNTR pub_list;
31992
31993
if (sdp == NULL || userdata == NULL || sdp->choice != Seq_descr_pub) return;
31994
pub_list = (ValNodePtr PNTR) userdata;
31995
31996
ValNodeAddPointer (pub_list, OBJ_SEQDESC, sdp);
31997
}
31998
31999
static ValNodePtr GetTextPubListsForSeqEntry (SeqEntryPtr sep, CharPtr search_text)
32000
{
32001
FeaturesWithTextData ftd;
32002
DescriptorsWithTextData dtd;
32003
ValNodePtr obj_list = NULL;
32004
32005
ftd.seqFeatChoice = SEQFEAT_PUB;
32006
ftd.featDefChoice = FEATDEF_PUB;
32007
ftd.search_text = search_text;
32008
ftd.act_when_string_not_present = FALSE;
32009
ftd.case_insensitive = TRUE;
32010
ftd.whole_word = FALSE;
32011
ftd.no_text = FALSE;
32012
ftd.callback = AddPubFeatureWithText;
32013
ftd.userdata = &obj_list;
32014
32015
dtd.search_text = search_text;
32016
dtd.act_when_string_not_present = FALSE;
32017
dtd.case_insensitive = TRUE;
32018
dtd.whole_word = FALSE;
32019
dtd.no_text = FALSE;
32020
dtd.callback = AddPubDescriptorWithText;
32021
dtd.userdata = &obj_list;
32022
32023
OperateOnSeqEntryFeaturesWithText (sep, &ftd);
32024
OperateOnSeqEntryDescriptorsWithText (sep, &dtd);
32025
32026
return obj_list;
32027
}
32028
32029
static ValNodePtr GetTextSeqEntryListForSeqEntry (SeqEntryPtr sep, Uint2 entityID, CharPtr search_text, ParseFieldPtr dst_field_data)
32030
{
32031
ValNodePtr value_lists = NULL;
32032
ValNodePtr obj_list = NULL, tmp_list, vnp;
32033
ClickableItemPtr cip;
32034
CharPtr desc_fmt = "%d sequences contain %s";
32035
StringConstraintData scd;
32036
ChoiceConstraintData ccd;
32037
FilterSetData fsd;
32038
32039
if (dst_field_data == NULL) {
32040
/* do nothing */
32041
} else if (dst_field_data->parse_field_type == SEARCH_FIELD_PUBLICATION) {
32042
obj_list = GetTextPubListsForSeqEntry(sep, search_text);
32043
} else {
32044
scd.match_text = search_text;
32045
scd.match_location = 1;
32046
scd.insensitive = TRUE;
32047
scd.whole_word = FALSE;
32048
scd.not_present = FALSE;
32049
32050
ccd.constraint_type = CHOICE_CONSTRAINT_STRING;
32051
ccd.qual_choice =
32052
ccd.qual_choice_match = NULL;
32053
ccd.string_constraint = &scd;
32054
ccd.pseudo_constraint = NULL;
32055
ccd.free_vn_proc = NULL;
32056
ccd.copy_vn_proc = NULL;
32057
32058
MemSet (&fsd, 0, sizeof (FilterSetData));
32059
fsd.ccp = &ccd;
32060
32061
tmp_list = GetUniqueValueListForSeqEntry (sep, entityID, dst_field_data, NULL);
32062
32063
for (vnp = tmp_list; vnp != NULL; vnp = vnp->next) {
32064
cip = (ClickableItemPtr) vnp->data.ptrvalue;
32065
if (cip != NULL && StringISearch (cip->description, search_text) != NULL) {
32066
ValNodeLink (&obj_list, cip->item_list);
32067
cip->item_list = NULL;
32068
}
32069
}
32070
tmp_list = FreeClickableList (tmp_list);
32071
}
32072
if (obj_list != NULL) {
32073
cip = (ClickableItemPtr) MemNew (sizeof (ClickableItemData));
32074
MemSet (cip, 0, sizeof (ClickableItemData));
32075
cip->description = StringSave (search_text);
32076
cip->item_list = obj_list;
32077
cip->chosen = TRUE;
32078
ValNodeAddPointer (&value_lists, 0, cip);
32079
value_lists = ChangeUniqueValueListsToSeqEntryLists (value_lists);
32080
/* rename description */
32081
if (value_lists != NULL) {
32082
cip = value_lists->data.ptrvalue;
32083
if (cip != NULL) {
32084
cip->description = MemFree (cip->description);
32085
cip->description = (CharPtr) MemNew (sizeof(Char) * (StringLen (desc_fmt) + StringLen (search_text) + 15));
32086
sprintf (cip->description, desc_fmt, ValNodeLen (cip->item_list), search_text);
32087
}
32088
}
32089
}
32090
32091
return value_lists;
32092
}
32093
32094
static void AddNewUniqueDescriptors (SeqDescrPtr PNTR new_set, SeqDescrPtr parent_set)
32095
{
32096
SeqDescrPtr sdp, sdp_next, sdp_tmp, sdp_tmp_next;
32097
Boolean found_match;
32098
32099
if (new_set == NULL || parent_set == NULL) return;
32100
32101
if (*new_set == NULL) {
32102
ValNodeLink (new_set,
32103
AsnIoMemCopy ((Pointer) parent_set,
32104
(AsnReadFunc) SeqDescrAsnRead,
32105
(AsnWriteFunc) SeqDescrAsnWrite));
32106
} else {
32107
sdp = parent_set;
32108
while (sdp != NULL) {
32109
sdp_next = sdp->next;
32110
sdp->next = NULL;
32111
for (sdp_tmp = *new_set, found_match = FALSE;
32112
sdp_tmp != NULL && !found_match;
32113
sdp_tmp = sdp_tmp->next) {
32114
sdp_tmp_next = sdp_tmp->next;
32115
sdp_tmp->next = NULL;
32116
if (AsnIoMemComp (sdp, sdp_tmp, (AsnWriteFunc) SeqDescrAsnWrite)) {
32117
found_match = TRUE;
32118
}
32119
sdp_tmp->next = sdp_tmp_next;
32120
}
32121
if (!found_match) {
32122
ValNodeLink (new_set,
32123
AsnIoMemCopy ((Pointer) sdp,
32124
(AsnReadFunc) SeqDescrAsnRead,
32125
(AsnWriteFunc) SeqDescrAsnWrite));
32126
}
32127
sdp->next = sdp_next;
32128
sdp = sdp->next;
32129
}
32130
}
32131
}
32132
32133
static void AddNewUniqueDescriptorsToSeqEntry (SeqEntryPtr sep, SeqDescrPtr parent_set)
32134
{
32135
BioseqPtr bsp;
32136
BioseqSetPtr bssp;
32137
32138
if (IS_Bioseq(sep)) {
32139
bsp = (BioseqPtr) sep->data.ptrvalue;
32140
if (bsp != NULL) {
32141
AddNewUniqueDescriptors (&(bsp->descr), parent_set);
32142
}
32143
} else if (IS_Bioseq_set (sep)) {
32144
bssp = (BioseqSetPtr) sep->data.ptrvalue;
32145
if (bssp != NULL) {
32146
AddNewUniqueDescriptors (&(bssp->descr), parent_set);
32147
}
32148
}
32149
}
32150
32151
static void AddNewUniqueAnnotations (SeqAnnotPtr PNTR new_set, SeqAnnotPtr parent_set)
32152
{
32153
SeqAnnotPtr sap, sap_next, sap_tmp, sap_tmp_next, sap_copy, last_sap;
32154
Boolean found_match;
32155
32156
if (new_set == NULL || parent_set == NULL) return;
32157
32158
sap = parent_set;
32159
while (sap != NULL) {
32160
sap_next = sap->next;
32161
sap->next = NULL;
32162
last_sap = NULL;
32163
for (sap_tmp = *new_set, found_match = FALSE;
32164
sap_tmp != NULL && !found_match;
32165
sap_tmp = sap_tmp->next) {
32166
sap_tmp_next = sap_tmp->next;
32167
sap_tmp->next = NULL;
32168
if (AsnIoMemComp (sap, sap_tmp, (AsnWriteFunc) SeqAnnotAsnWrite)) {
32169
found_match = TRUE;
32170
}
32171
sap_tmp->next = sap_tmp->next;
32172
last_sap = sap_tmp;
32173
}
32174
if (!found_match) {
32175
sap_copy = (SeqAnnotPtr) AsnIoMemCopy ((Pointer) sap, (AsnReadFunc) SeqAnnotAsnRead, (AsnWriteFunc) SeqAnnotAsnWrite);
32176
if (last_sap == NULL) {
32177
*new_set = sap_copy;
32178
} else {
32179
last_sap->next = sap_copy;
32180
}
32181
}
32182
sap->next = sap_next;
32183
sap = sap->next;
32184
}
32185
}
32186
32187
32188
static void AddNewUniqueAnnotationsToSeqEntry (SeqEntryPtr sep, SeqAnnotPtr parent_set)
32189
{
32190
BioseqPtr bsp;
32191
BioseqSetPtr bssp;
32192
32193
if (IS_Bioseq(sep)) {
32194
bsp = (BioseqPtr) sep->data.ptrvalue;
32195
if (bsp != NULL) {
32196
AddNewUniqueAnnotations (&(bsp->annot), parent_set);
32197
}
32198
} else if (IS_Bioseq_set (sep)) {
32199
bssp = (BioseqSetPtr) sep->data.ptrvalue;
32200
if (bssp != NULL) {
32201
AddNewUniqueAnnotations (&(bssp->annot), parent_set);
32202
}
32203
}
32204
}
32205
32206
32207
static void AddCategorySeqEntriesToSet (BioseqSetPtr newset, ClickableItemPtr category)
32208
{
32209
ValNodePtr vnp_item;
32210
SeqEntryPtr sep, last_sep, prev_sep, remove_sep;
32211
BioseqSetPtr bssp, orig_parent;
32212
BioseqPtr bsp;
32213
32214
if (newset == NULL || category == NULL || category->item_list == NULL) return;
32215
32216
if (category->chosen) {
32217
last_sep = newset->seq_set;
32218
while (last_sep != NULL && last_sep->next != NULL) {
32219
last_sep = last_sep->next;
32220
}
32221
32222
for (vnp_item = category->item_list; vnp_item != NULL; vnp_item = vnp_item->next) {
32223
sep = GetBestSeqEntryForItem (vnp_item);
32224
if (sep == NULL || sep->data.ptrvalue == NULL) continue;
32225
orig_parent = NULL;
32226
if (IS_Bioseq (sep)) {
32227
bsp = sep->data.ptrvalue;
32228
if (bsp->idx.parenttype == OBJ_BIOSEQSET) {
32229
orig_parent = bsp->idx.parentptr;
32230
bsp->idx.parentptr = NULL;
32231
}
32232
} else if (IS_Bioseq_set (sep)) {
32233
bssp = sep->data.ptrvalue;
32234
if (bssp->idx.parenttype == OBJ_BIOSEQSET) {
32235
orig_parent = bssp->idx.parentptr;
32236
bssp->idx.parentptr = NULL;
32237
}
32238
} else {
32239
continue;
32240
}
32241
32242
if (orig_parent != NULL) {
32243
/* remove this seq-entry from the original parent */
32244
prev_sep = NULL;
32245
for (remove_sep = orig_parent->seq_set;
32246
remove_sep != NULL && remove_sep != sep;
32247
remove_sep = remove_sep->next) {
32248
prev_sep = remove_sep;
32249
}
32250
if (remove_sep == sep) {
32251
if (prev_sep == NULL) {
32252
orig_parent->seq_set = orig_parent->seq_set->next;
32253
if (orig_parent->seq_set == NULL) {
32254
orig_parent->idx.deleteme = TRUE;
32255
}
32256
} else {
32257
prev_sep->next = sep->next;
32258
}
32259
}
32260
/* set class type if not already set */
32261
if (newset->_class == BioseqseqSet_class_genbank) {
32262
newset->_class = orig_parent->_class;
32263
}
32264
}
32265
/* add descriptors from the orig_parent to the new parent */
32266
AddNewUniqueDescriptors (&(newset->descr), orig_parent->descr);
32267
32268
/* add annotations from the orig_parent to the new parent */
32269
AddNewUniqueAnnotations (&(newset->annot), orig_parent->annot);
32270
32271
/* add to new parent */
32272
sep->next = NULL;
32273
if (last_sep == NULL) {
32274
newset->seq_set = sep;
32275
} else {
32276
last_sep->next = sep;
32277
}
32278
last_sep = sep;
32279
SeqMgrLinkSeqEntry (sep, OBJ_BIOSEQSET, newset);
32280
}
32281
} else {
32282
for (vnp_item = category->subcategories; vnp_item != NULL; vnp_item = vnp_item->next) {
32283
AddCategorySeqEntriesToSet (newset, vnp_item->data.ptrvalue);
32284
}
32285
}
32286
}
32287
32288
static Boolean AnyDiscrepanciesChosen (ValNodePtr cip_list)
32289
{
32290
ClickableItemPtr cip;
32291
Boolean any_chosen = FALSE;
32292
32293
while (cip_list != NULL && !any_chosen) {
32294
cip = (ClickableItemPtr) cip_list->data.ptrvalue;
32295
if (cip != NULL
32296
&& (cip->chosen
32297
|| (cip->expanded && AnyDiscrepanciesChosen (cip->subcategories)))) {
32298
any_chosen = TRUE;
32299
}
32300
cip_list = cip_list->next;
32301
}
32302
return any_chosen;
32303
}
32304
32305
static Boolean NeedsNewSet (SeqEntryPtr sep)
32306
{
32307
BioseqSetPtr bssp;
32308
while (sep != NULL) {
32309
if (IS_Bioseq (sep)) {
32310
return TRUE;
32311
} else if (IS_Bioseq_set (sep)) {
32312
bssp = (BioseqSetPtr) sep->data.ptrvalue;
32313
if (bssp != NULL
32314
&& (bssp->_class == BioseqseqSet_class_nuc_prot
32315
|| bssp->_class == BioseqseqSet_class_segset)) {
32316
return TRUE;
32317
}
32318
}
32319
sep = sep->next;
32320
}
32321
return FALSE;
32322
}
32323
32324
static BioseqSetPtr MakeGroupsForUniqueValues
32325
(BioseqSetPtr bssp,
32326
ValNodePtr value_lists)
32327
{
32328
ObjMgrDataPtr omdptop;
32329
ObjMgrData omdata;
32330
Uint2 parenttype;
32331
Pointer parentptr;
32332
BioseqSetPtr parent_set;
32333
SeqEntryPtr sep, first_new_sep = NULL;
32334
SeqEntryPtr tmp;
32335
BioseqSetPtr newset;
32336
ValNodePtr vnp;
32337
ClickableItemPtr cip;
32338
Uint1 child_class;
32339
Uint2 entityID;
32340
Boolean child_became_parent = FALSE;
32341
32342
if (bssp == NULL) return NULL;
32343
entityID = bssp->idx.entityID;
32344
32345
sep = SeqMgrGetSeqEntryForData (bssp);
32346
32347
WatchCursor ();
32348
Update ();
32349
SaveSeqEntryObjMgrData (sep, &omdptop, &omdata);
32350
GetSeqEntryParent (sep, &parentptr, &parenttype);
32351
32352
parent_set = (BioseqSetPtr)(bssp->idx.parentptr);
32353
32354
if (parent_set == NULL || parent_set->seq_set == NULL) {
32355
/* this set has no parent, so make it the parent set, class GenBank,
32356
* and create two new sets using the original set class as members of this set
32357
*/
32358
parent_set = bssp;
32359
child_class = parent_set->_class;
32360
child_became_parent = TRUE;
32361
} else {
32362
/* we already have a parent set. */
32363
child_class = bssp->_class;
32364
}
32365
32366
for (vnp = value_lists; vnp != NULL; vnp = vnp->next) {
32367
cip = (ClickableItemPtr) vnp->data.ptrvalue;
32368
if (cip == NULL || (!cip->chosen && ! AnyDiscrepanciesChosen (cip->subcategories))) {
32369
continue;
32370
}
32371
32372
newset = BioseqSetNew ();
32373
newset->_class = child_class;
32374
/* add SeqEntries for this category here */
32375
AddCategorySeqEntriesToSet (newset, cip);
32376
32377
/* check - is any member of the newset also a set? */
32378
tmp = newset->seq_set;
32379
while (tmp != NULL && IS_Bioseq (tmp)) {
32380
tmp = tmp->next;
32381
}
32382
32383
/* add to members for parent_set */
32384
tmp = SeqEntryNew ();
32385
tmp->choice = 2;
32386
tmp->data.ptrvalue = (Pointer) newset;
32387
32388
tmp->next = parent_set->seq_set;
32389
parent_set->seq_set = tmp;
32390
32391
if (parent_set->idx.deleteme) {
32392
parent_set->idx.deleteme = FALSE;
32393
}
32394
if (first_new_sep == NULL) {
32395
first_new_sep = tmp;
32396
}
32397
32398
SeqMgrLinkSeqEntry (tmp, OBJ_BIOSEQSET, parent_set);
32399
}
32400
32401
RestoreSeqEntryObjMgrData (sep, omdptop, &omdata);
32402
DeleteMarkedObjects (entityID, 0, NULL);
32403
32404
if (child_became_parent) {
32405
if (NeedsNewSet (first_new_sep->next)) {
32406
/* make new set to hold what wasn't moved */
32407
newset = BioseqSetNew ();
32408
/* contents of set are unmoved sequences */
32409
newset->seq_set = first_new_sep->next;
32410
/* set class type */
32411
newset->_class = parent_set->_class;
32412
/* add descriptors from the parent */
32413
ValNodeLink (&(newset->descr),
32414
AsnIoMemCopy ((Pointer) parent_set->descr,
32415
(AsnReadFunc) SeqDescrAsnRead,
32416
(AsnWriteFunc) SeqDescrAsnWrite));
32417
32418
32419
tmp = SeqEntryNew();
32420
tmp->choice = 2;
32421
tmp->data.ptrvalue = (Pointer) newset;
32422
tmp->next = NULL;
32423
first_new_sep->next = tmp;
32424
SeqMgrLinkSeqEntry (tmp, OBJ_BIOSEQSET, parent_set);
32425
} else {
32426
sep = first_new_sep->next;
32427
while (sep != NULL) {
32428
AddNewUniqueDescriptorsToSeqEntry (sep, parent_set->descr);
32429
sep = sep->next;
32430
}
32431
}
32432
/* set parent class to GenBank set */
32433
parent_set->_class = BioseqseqSet_class_genbank;
32434
/* remove descriptors on parent, they will all have been copied down */
32435
parent_set->descr = SeqDescrFree (parent_set->descr);
32436
}
32437
32438
ObjMgrSetDirtyFlag (entityID, TRUE);
32439
ObjMgrSendMsg (OM_MSG_UPDATE, entityID, 0, 0);
32440
32441
ArrowCursor ();
32442
Update ();
32443
return parent_set;
32444
}
32445
32446
typedef enum {
32447
eSegPageId = 1,
32448
eSegPageText,
32449
eSegPageField,
32450
eSegPageMolInfo,
32451
eSegPageFeatureType,
32452
eSegPageDescriptorType,
32453
eNumSegPages
32454
} ESegPage;
32455
32456
typedef struct segbyfield {
32457
FORM_MESSAGE_BLOCK
32458
GrouP seg_choice_grp;
32459
32460
GrouP pages[eNumSegPages];
32461
/* for segregating by field */
32462
DialoG field_dlg;
32463
DialoG group_list_dlg;
32464
32465
/* for segregating by molinfo */
32466
ButtoN mol_type_btn;
32467
ButtoN mol_class_btn;
32468
32469
/* for segregating by feature */
32470
DialoG feature_select;
32471
32472
/* for segregating by descriptor */
32473
DialoG descriptor_select;
32474
32475
/* for segregating by text */
32476
DialoG search_field;
32477
TexT search_text;
32478
32479
/* for segregating by ID */
32480
DialoG id_constraint;
32481
32482
ButtoN accept;
32483
ButtoN leave_dlg_up;
32484
BioseqSetPtr target_set;
32485
ValNodePtr value_lists;
32486
} SegByFieldData, PNTR SegByFieldPtr;
32487
32488
static void ChooseAllDiscrepancies (ValNodePtr cip_list)
32489
{
32490
ClickableItemPtr cip;
32491
32492
while (cip_list != NULL) {
32493
cip = cip_list->data.ptrvalue;
32494
if (cip != NULL) {
32495
cip->chosen = TRUE;
32496
}
32497
cip_list = cip_list->next;
32498
}
32499
}
32500
32501
static void ChangeSegChoice (GrouP g);
32502
32503
32504
static void PullChosenIntoOneGroup (ValNodePtr PNTR value_list, ClickableItemPtr chosen)
32505
{
32506
ValNodePtr vnp_prev = NULL, vnp_next, vnp_this;
32507
ClickableItemPtr cip;
32508
32509
if (value_list == NULL || chosen == NULL) return;
32510
32511
vnp_this = *value_list;
32512
while (vnp_this != NULL)
32513
{
32514
vnp_next = vnp_this->next;
32515
cip = (ClickableItemPtr) vnp_this->data.ptrvalue;
32516
if (cip == NULL)
32517
{
32518
vnp_this->next = NULL;
32519
if (vnp_prev == NULL)
32520
{
32521
*value_list = vnp_next;
32522
}
32523
else
32524
{
32525
vnp_prev->next = vnp_next;
32526
}
32527
vnp_this = ValNodeFree (vnp_this);
32528
}
32529
else if (cip->chosen)
32530
{
32531
vnp_this->next = NULL;
32532
if (vnp_prev == NULL)
32533
{
32534
*value_list = vnp_next;
32535
}
32536
else
32537
{
32538
vnp_prev->next = vnp_next;
32539
}
32540
ValNodeLink (&(chosen->item_list), cip->item_list);
32541
cip->item_list = NULL;
32542
vnp_this = FreeClickableList (vnp_this);
32543
}
32544
else
32545
{
32546
PullChosenIntoOneGroup (&(cip->subcategories), chosen);
32547
vnp_prev = vnp_this;
32548
}
32549
vnp_this = vnp_next;
32550
}
32551
}
32552
32553
32554
static void SegregateByField_Callback (ButtoN b)
32555
{
32556
SegByFieldPtr sfp;
32557
Int4 num_chosen = 0;
32558
ClickableItemPtr cip;
32559
32560
sfp = (SegByFieldPtr) GetObjectExtra (b);
32561
if (sfp == NULL) return;
32562
32563
num_chosen = CountChosenDiscrepancies (sfp->value_lists, FALSE);
32564
if (num_chosen < 1) {
32565
if (ANS_OK == Message (MSG_OKC, "You have not chosen any groups. Create all?")) {
32566
ChooseAllDiscrepancies (sfp->value_lists);
32567
} else {
32568
return;
32569
}
32570
}
32571
32572
if (GetValue (sfp->seg_choice_grp) == eSegPageId) {
32573
/* put all selected sequences into one group */
32574
cip = (ClickableItemPtr) MemNew (sizeof (ClickableItemData));
32575
cip->chosen = TRUE;
32576
PullChosenIntoOneGroup (&(sfp->value_lists), cip);
32577
ValNodeAddPointer (&(sfp->value_lists), 0, cip);
32578
}
32579
32580
sfp->target_set = MakeGroupsForUniqueValues (sfp->target_set, sfp->value_lists);
32581
32582
if (GetStatus (sfp->leave_dlg_up)) {
32583
ChangeSegChoice (sfp->seg_choice_grp);
32584
} else {
32585
Remove (sfp->form);
32586
}
32587
}
32588
32589
static void ChangeSegField (Pointer userdata)
32590
{
32591
SegByFieldPtr sfp = (SegByFieldPtr) userdata;
32592
SeqEntryPtr sep;
32593
ParseFieldPtr dst_field_data;
32594
32595
if (sfp == NULL || sfp->target_set == NULL) return;
32596
32597
WatchCursor();
32598
Update();
32599
sep = SeqMgrGetSeqEntryForData (sfp->target_set);
32600
32601
PointerToDialog (sfp->group_list_dlg, NULL);
32602
sfp->value_lists = FreeClickableList (sfp->value_lists);
32603
32604
dst_field_data = DialogToPointer (sfp->field_dlg);
32605
if (dst_field_data == NULL) {
32606
Disable (sfp->accept);
32607
return;
32608
}
32609
32610
sfp->value_lists = CreateSeqEntryListsForUniqueValues (sep, sfp->target_set->idx.entityID, dst_field_data, NULL);
32611
dst_field_data = ParseFieldFree (dst_field_data);
32612
PointerToDialog (sfp->group_list_dlg, sfp->value_lists);
32613
if (ValNodeLen (sfp->value_lists) < 2) {
32614
Disable(sfp->accept);
32615
} else {
32616
Enable (sfp->accept);
32617
}
32618
ArrowCursor();
32619
Update();
32620
}
32621
32622
static void SegTextChangeNotify (Pointer userdata)
32623
{
32624
SegByFieldPtr sfp = (SegByFieldPtr) userdata;
32625
SeqEntryPtr sep;
32626
ParseFieldPtr dst_field_data;
32627
CharPtr search_text;
32628
32629
if (sfp == NULL || sfp->target_set == NULL) return;
32630
32631
WatchCursor();
32632
Update();
32633
sep = SeqMgrGetSeqEntryForData (sfp->target_set);
32634
32635
PointerToDialog (sfp->group_list_dlg, NULL);
32636
sfp->value_lists = FreeClickableList (sfp->value_lists);
32637
32638
if (TextHasNoText (sfp->search_text)) {
32639
Disable (sfp->accept);
32640
ArrowCursor();
32641
Update();
32642
return;
32643
}
32644
dst_field_data = DialogToPointer (sfp->search_field);
32645
if (dst_field_data == NULL) {
32646
Disable (sfp->accept);
32647
ArrowCursor();
32648
Update();
32649
return;
32650
}
32651
search_text = SaveStringFromText (sfp->search_text);
32652
32653
sfp->value_lists = GetTextSeqEntryListForSeqEntry (sep, sfp->target_set->idx.entityID, search_text, dst_field_data);
32654
32655
search_text = MemFree (search_text);
32656
32657
dst_field_data = ParseFieldFree (dst_field_data);
32658
PointerToDialog (sfp->group_list_dlg, sfp->value_lists);
32659
if (sfp->value_lists == NULL) {
32660
Disable(sfp->accept);
32661
} else {
32662
Enable (sfp->accept);
32663
}
32664
ArrowCursor();
32665
Update();
32666
}
32667
32668
static void SegTextChange (TexT t)
32669
{
32670
SegByFieldPtr sfp;
32671
32672
sfp = (SegByFieldPtr) GetObjectExtra (t);
32673
32674
SegTextChangeNotify (sfp);
32675
32676
}
32677
32678
32679
extern void ListAllSequences (BioseqPtr bsp, Pointer userdata)
32680
{
32681
ClickableItemPtr cip;
32682
Char id_str[100];
32683
32684
if (bsp != NULL && userdata != NULL && ! ISA_aa (bsp->mol))
32685
{
32686
cip = (ClickableItemPtr) MemNew (sizeof (ClickableItemData));
32687
SeqIdWrite (SeqIdFindBest (bsp->id, SEQID_GENBANK), id_str, PRINTID_REPORT, sizeof (id_str) - 1);
32688
cip->description = StringSave (id_str);
32689
32690
ValNodeAddPointer (&(cip->item_list), OBJ_BIOSEQ, bsp);
32691
ValNodeAddPointer ((ValNodePtr PNTR) userdata, 0, cip);
32692
}
32693
}
32694
32695
32696
static void ChooseSegId (Pointer userdata)
32697
{
32698
SegByFieldPtr sfp = (SegByFieldPtr) userdata;
32699
SeqEntryPtr sep;
32700
32701
if (sfp == NULL || sfp->target_set == NULL) return;
32702
32703
WatchCursor();
32704
Update();
32705
sep = SeqMgrGetSeqEntryForData (sfp->target_set);
32706
32707
PointerToDialog (sfp->group_list_dlg, NULL);
32708
sfp->value_lists = FreeClickableList (sfp->value_lists);
32709
32710
VisitBioseqsInSep (sep, &sfp->value_lists, ListAllSequences);
32711
32712
PointerToDialog (sfp->group_list_dlg, sfp->value_lists);
32713
if (sfp->value_lists == NULL) {
32714
Disable(sfp->accept);
32715
} else {
32716
Enable (sfp->accept);
32717
}
32718
ArrowCursor();
32719
Update();
32720
}
32721
32722
32723
static void ChangeMol (ButtoN b)
32724
{
32725
SegByFieldPtr sfp;
32726
SeqEntryPtr sep;
32727
32728
sfp = (SegByFieldPtr) GetObjectExtra (b);
32729
32730
if (sfp == NULL) return;
32731
32732
WatchCursor ();
32733
Update();
32734
sep = SeqMgrGetSeqEntryForData (sfp->target_set);
32735
32736
PointerToDialog (sfp->group_list_dlg, NULL);
32737
sfp->value_lists = FreeClickableList (sfp->value_lists);
32738
32739
if (GetStatus (sfp->mol_class_btn)) {
32740
VisitBioseqsInSep (sep, &(sfp->value_lists), GetMolClasses);
32741
}
32742
if (GetStatus (sfp->mol_type_btn)) {
32743
VisitDescriptorsInSep (sep, &(sfp->value_lists), GetMolTypes);
32744
}
32745
32746
sfp->value_lists = ChangeUniqueValueListsToSeqEntryLists (sfp->value_lists);
32747
32748
PointerToDialog (sfp->group_list_dlg, sfp->value_lists);
32749
if (ValNodeLen (sfp->value_lists) < 2) {
32750
Disable(sfp->accept);
32751
} else {
32752
Enable (sfp->accept);
32753
}
32754
ArrowCursor();
32755
Update();
32756
}
32757
32758
32759
static void SegFeatureChangeNotify (Pointer userdata)
32760
{
32761
SegByFieldPtr sfp = (SegByFieldPtr) userdata;
32762
SeqEntryPtr sep;
32763
SegFeaturesData sfd;
32764
ClickableItemPtr cip;
32765
ValNodePtr vnp;
32766
CharPtr desc_fmt = "%d %ss";
32767
32768
if (sfp == NULL) return;
32769
32770
vnp = DialogToPointer (sfp->feature_select);
32771
if (vnp == NULL) {
32772
PointerToDialog (sfp->group_list_dlg, NULL);
32773
sfp->value_lists = FreeClickableList (sfp->value_lists);
32774
Disable (sfp->accept);
32775
return;
32776
}
32777
32778
WatchCursor ();
32779
Update();
32780
sep = SeqMgrGetSeqEntryForData (sfp->target_set);
32781
32782
PointerToDialog (sfp->group_list_dlg, NULL);
32783
sfp->value_lists = FreeClickableList (sfp->value_lists);
32784
32785
sfd.featdef = vnp->choice;
32786
sfd.feature_list = NULL;
32787
VisitFeaturesInSep (sep, &sfd, FindFeaturesForSeg);
32788
32789
if (sfd.feature_list != NULL) {
32790
cip = (ClickableItemPtr) MemNew (sizeof (ClickableItemData));
32791
MemSet (cip, 0, sizeof (ClickableItemData));
32792
cip->description = (CharPtr) MemNew (sizeof(Char) * (StringLen (desc_fmt) + StringLen (vnp->data.ptrvalue) + 15));
32793
sprintf (cip->description, desc_fmt, ValNodeLen (sfd.feature_list), vnp->data.ptrvalue);
32794
cip->item_list = sfd.feature_list;
32795
cip->chosen = TRUE;
32796
ValNodeAddPointer (&(sfp->value_lists), 0, cip);
32797
sfp->value_lists = ChangeUniqueValueListsToSeqEntryLists (sfp->value_lists);
32798
}
32799
vnp = ValNodeFree (vnp);
32800
32801
PointerToDialog (sfp->group_list_dlg, sfp->value_lists);
32802
32803
if (sfp->value_lists == NULL) {
32804
Disable (sfp->accept);
32805
} else {
32806
Enable (sfp->accept);
32807
}
32808
ArrowCursor();
32809
Update();
32810
}
32811
32812
static void SegDescriptorChangeNotify (Pointer data)
32813
{
32814
SegByFieldPtr sfp;
32815
ValNodePtr vnp;
32816
SegDescriptorsData sdd;
32817
ClickableItemPtr cip;
32818
CharPtr desc_fmt = "%d %ss";
32819
SeqEntryPtr sep;
32820
32821
sfp = (SegByFieldPtr) data;
32822
if (sfp == NULL) return;
32823
32824
vnp = DialogToPointer (sfp->descriptor_select);
32825
if (vnp == NULL) {
32826
PointerToDialog (sfp->group_list_dlg, NULL);
32827
sfp->value_lists = FreeClickableList (sfp->value_lists);
32828
Disable (sfp->accept);
32829
return;
32830
}
32831
32832
WatchCursor ();
32833
Update();
32834
sep = SeqMgrGetSeqEntryForData (sfp->target_set);
32835
32836
PointerToDialog (sfp->group_list_dlg, NULL);
32837
sfp->value_lists = FreeClickableList (sfp->value_lists);
32838
32839
sdd.desc_type = vnp->choice;
32840
sdd.descriptor_list = NULL;
32841
VisitDescriptorsInSep (sep, &sdd, FindDescriptorsForSeg);
32842
32843
if (sdd.descriptor_list != NULL) {
32844
cip = (ClickableItemPtr) MemNew (sizeof (ClickableItemData));
32845
MemSet (cip, 0, sizeof (ClickableItemData));
32846
cip->description = (CharPtr) MemNew (sizeof(Char) * (StringLen (desc_fmt) + StringLen (vnp->data.ptrvalue) + 15));
32847
sprintf (cip->description, desc_fmt, ValNodeLen (sdd.descriptor_list), vnp->data.ptrvalue);
32848
cip->item_list = sdd.descriptor_list;
32849
cip->chosen = TRUE;
32850
ValNodeAddPointer (&(sfp->value_lists), 0, cip);
32851
sfp->value_lists = ChangeUniqueValueListsToSeqEntryLists (sfp->value_lists);
32852
}
32853
vnp = ValNodeFree (vnp);
32854
32855
PointerToDialog (sfp->group_list_dlg, sfp->value_lists);
32856
32857
if (sfp->value_lists == NULL) {
32858
Disable (sfp->accept);
32859
} else {
32860
Enable (sfp->accept);
32861
}
32862
ArrowCursor();
32863
Update();
32864
32865
}
32866
32867
static void ChangeSegChoice (GrouP g)
32868
{
32869
SegByFieldPtr sfp;
32870
Int4 seg_choice, i;
32871
32872
sfp = (SegByFieldPtr) GetObjectExtra (g);
32873
if (sfp == NULL) return;
32874
32875
seg_choice = GetValue (sfp->seg_choice_grp);
32876
32877
for (i = 0; i < eNumSegPages; i++) {
32878
if (i == seg_choice - 1) {
32879
Show (sfp->pages[i]);
32880
} else {
32881
Hide (sfp->pages[i]);
32882
}
32883
}
32884
switch (seg_choice) {
32885
case eSegPageField:
32886
ChangeSegField (sfp);
32887
break;
32888
case eSegPageMolInfo:
32889
ChangeMol(sfp->mol_class_btn);
32890
break;
32891
case eSegPageFeatureType:
32892
SegFeatureChangeNotify (sfp);
32893
break;
32894
case eSegPageDescriptorType:
32895
SegDescriptorChangeNotify (sfp);
32896
break;
32897
case eSegPageText:
32898
SegTextChangeNotify (sfp);
32899
break;
32900
case eSegPageId:
32901
ChooseSegId (sfp);
32902
break;
32903
}
32904
if (seg_choice == eSegPageId) {
32905
SetClickableListDialogTitles (sfp->group_list_dlg, "Sequences for New Set", "",
32906
"Use checkbox to mark sequences for new set",
32907
"Single click to navigate to sequence in record");
32908
} else {
32909
SetClickableListDialogTitles (sfp->group_list_dlg, "New Sets", "Sequences in Highlighted Set",
32910
"Use checkbox to mark sets to create",
32911
"");
32912
}
32913
}
32914
32915
32916
extern void ChooseCategories (ValNodePtr value_list, Boolean do_choose)
32917
{
32918
ClickableItemPtr cip;
32919
32920
while (value_list != NULL) {
32921
cip = (ClickableItemPtr) value_list->data.ptrvalue;
32922
if (cip != NULL) {
32923
cip->chosen = do_choose;
32924
ChooseCategories (cip->subcategories, FALSE);
32925
}
32926
value_list = value_list->next;
32927
}
32928
}
32929
32930
32931
extern void ChooseCategoriesByStringConstraint (ValNodePtr value_list, StringConstraintXPtr scp, Boolean do_choose)
32932
{
32933
ClickableItemPtr cip;
32934
32935
while (value_list != NULL) {
32936
cip = (ClickableItemPtr) value_list->data.ptrvalue;
32937
if (cip != NULL) {
32938
if (cip->item_list != NULL
32939
&& cip->item_list->choice == OBJ_BIOSEQ
32940
&& cip->item_list->data.ptrvalue != NULL
32941
&& DoesIDListMeetStringConstraint (((BioseqPtr) cip->item_list->data.ptrvalue)->id, scp)) {
32942
cip->chosen = do_choose;
32943
} else {
32944
ChooseCategoriesByStringConstraint (cip->subcategories, scp, do_choose);
32945
}
32946
}
32947
value_list = value_list->next;
32948
}
32949
}
32950
32951
32952
static void SelectSegCategories (ButtoN b)
32953
{
32954
SegByFieldPtr sfp;
32955
32956
sfp = (SegByFieldPtr) GetObjectExtra (b);
32957
if (sfp != NULL) {
32958
ChooseCategories (sfp->value_lists, TRUE);
32959
PointerToDialog (sfp->group_list_dlg, sfp->value_lists);
32960
}
32961
}
32962
32963
32964
static void UnselectSegCategories (ButtoN b)
32965
{
32966
SegByFieldPtr sfp;
32967
32968
sfp = (SegByFieldPtr) GetObjectExtra (b);
32969
if (sfp != NULL) {
32970
ChooseCategories (sfp->value_lists, FALSE);
32971
PointerToDialog (sfp->group_list_dlg, sfp->value_lists);
32972
}
32973
}
32974
32975
32976
static void SelectSequenceIDsForSegregate (ButtoN b)
32977
{
32978
SegByFieldPtr sfp;
32979
StringConstraintXPtr scp;
32980
32981
sfp = (SegByFieldPtr) GetObjectExtra (b);
32982
if (sfp == NULL) return;
32983
32984
scp = DialogToPointer (sfp->id_constraint);
32985
ChooseCategoriesByStringConstraint (sfp->value_lists, scp, TRUE);
32986
PointerToDialog (sfp->group_list_dlg, sfp->value_lists);
32987
scp = StringConstraintXFree (scp);
32988
}
32989
32990
32991
static void CleanupSegregateByFieldForm (GraphiC g, VoidPtr data)
32992
32993
{
32994
SegByFieldPtr sfp;
32995
32996
sfp = (SegByFieldPtr) data;
32997
if (sfp != NULL) {
32998
sfp->value_lists = FreeClickableList (sfp->value_lists);
32999
}
33000
StdCleanupFormProc (g, data);
33001
}
33002
33003
33004
33005
extern Int2 LIBCALLBACK SegregateSetsByField (Pointer data)
33006
{
33007
GrouP c;
33008
SegByFieldPtr cfp;
33009
GrouP h, k, page_grp, g1, g2, g3;
33010
OMProcControlPtr ompcp;
33011
PrompT p, p2;
33012
StdEditorProcsPtr sepp;
33013
WindoW w;
33014
ButtoN b;
33015
StringConstraintData scd;
33016
33017
/* Check parameters and get a pointer to the current data */
33018
33019
ompcp = (OMProcControlPtr) data;
33020
if (ompcp == NULL
33021
|| ompcp->input_itemtype != OBJ_BIOSEQSET
33022
|| ompcp->input_data == NULL) {
33023
Message (MSG_ERROR, "You must select a set to segregate!");
33024
return OM_MSG_RET_ERROR;
33025
}
33026
33027
/* Create a new window, and a struct */
33028
/* to pass around the data in. */
33029
33030
cfp = (SegByFieldPtr) MemNew (sizeof (SegByFieldData));
33031
if (cfp == NULL)
33032
return OM_MSG_RET_ERROR;
33033
cfp->target_set = (BioseqSetPtr)ompcp->input_data;
33034
33035
w = FixedWindow (-50, -33, -10, -10, "Segregate By Field",
33036
StdCloseWindowProc);
33037
SetObjectExtra (w, cfp, CleanupSegregateByFieldForm);
33038
cfp->form = (ForM) w;
33039
33040
sepp = (StdEditorProcsPtr) GetAppProperty ("StdEditorForm");
33041
if (sepp != NULL) {
33042
SetActivate (w, sepp->activateForm);
33043
cfp->appmessage = sepp->handleMessages;
33044
}
33045
33046
cfp->input_entityID = ompcp->input_entityID;
33047
cfp->input_itemID = ompcp->input_itemID;
33048
cfp->input_itemtype = ompcp->input_itemtype;
33049
33050
sepp = (StdEditorProcsPtr) GetAppProperty ("StdEditorForm");
33051
if (sepp != NULL) {
33052
SetActivate (w, sepp->activateForm);
33053
cfp->appmessage = sepp->handleMessages;
33054
}
33055
33056
h = HiddenGroup (w, -1, 0, NULL);
33057
SetGroupSpacing (h, 10, 10);
33058
33059
cfp->group_list_dlg = CreateClickableListDialogEx (h, "New Sets", "Sequences for New Set",
33060
"Use checkbox to mark sets to create",
33061
"",
33062
ScrollToDiscrepancyItem, EditDiscrepancyItem, NULL,
33063
GetDiscrepancyItemText,
33064
stdCharWidth * 30,
33065
stdCharWidth * 30 + 5,
33066
TRUE, FALSE);
33067
33068
g3 = NormalGroup (h, 2, 0, "", programFont, NULL);
33069
SetGroupSpacing (g3, 10, 10);
33070
StaticPrompt (g3, "Segregate Based on", 0, dialogTextHeight, programFont, 'c');
33071
cfp->seg_choice_grp = HiddenGroup (g3, eNumSegPages, 0, ChangeSegChoice);
33072
SetObjectExtra (cfp->seg_choice_grp, cfp, NULL);
33073
SetGroupSpacing (cfp->seg_choice_grp, 10, 10);
33074
33075
RadioButton (cfp->seg_choice_grp, "ID");
33076
RadioButton (cfp->seg_choice_grp, "Text");
33077
RadioButton (cfp->seg_choice_grp, "Field");
33078
RadioButton (cfp->seg_choice_grp, "MolInfo");
33079
RadioButton (cfp->seg_choice_grp, "Feature Type");
33080
RadioButton (cfp->seg_choice_grp, "Descriptor Type");
33081
33082
page_grp = HiddenGroup (h, 0, 0, NULL);
33083
/* identical fields */
33084
cfp->pages[eSegPageField - 1] = HiddenGroup (page_grp, 2, 0, NULL);
33085
SetGroupSpacing (cfp->pages[eSegPageField - 1], 10, 10);
33086
p = StaticPrompt (cfp->pages[eSegPageField - 1], "Segregate sequences with identical", 0, dialogTextHeight,
33087
programFont, 'c');
33088
cfp->field_dlg = ParseFieldDestDialog (cfp->pages[eSegPageField - 1], ChangeSegField, cfp);
33089
33090
/* molinfo */
33091
cfp->pages[eSegPageMolInfo - 1] = HiddenGroup (page_grp, 0, 2, NULL);
33092
SetGroupSpacing (cfp->pages[eSegPageMolInfo - 1], 10, 10);
33093
cfp->mol_class_btn = CheckBox (cfp->pages[eSegPageMolInfo - 1], "Molecule Class", ChangeMol);
33094
SetObjectExtra (cfp->mol_class_btn, cfp, NULL);
33095
SetStatus (cfp->mol_class_btn, TRUE);
33096
cfp->mol_type_btn = CheckBox (cfp->pages[eSegPageMolInfo - 1], "Molecule Type", ChangeMol);
33097
SetObjectExtra (cfp->mol_type_btn, cfp, NULL);
33098
SetStatus (cfp->mol_type_btn, TRUE);
33099
33100
/* features */
33101
cfp->pages[eSegPageFeatureType - 1] = HiddenGroup (page_grp, 2, 0, NULL);
33102
SetGroupSpacing (cfp->pages[eSegPageFeatureType - 1], 10, 10);
33103
StaticPrompt (cfp->pages[eSegPageFeatureType - 1], "Segregate by Feature", 0, dialogTextHeight,
33104
programFont, 'c');
33105
cfp->feature_select = FeatureSelectionDialogEx (cfp->pages[eSegPageFeatureType - 1], FALSE, NULL,
33106
SegFeatureChangeNotify,
33107
cfp);
33108
33109
/* descriptors */
33110
cfp->pages[eSegPageDescriptorType - 1] = HiddenGroup (page_grp, 2, 0, NULL);
33111
SetGroupSpacing (cfp->pages[eSegPageDescriptorType - 1], 10, 10);
33112
StaticPrompt (cfp->pages[eSegPageDescriptorType - 1], "Segregate by Descriptor", 0, dialogTextHeight,
33113
programFont, 'c');
33114
cfp->descriptor_select = DescriptorSelectionDialog (cfp->pages[eSegPageDescriptorType - 1], FALSE,
33115
SegDescriptorChangeNotify, cfp);
33116
33117
/* text */
33118
cfp->pages[eSegPageText - 1] = HiddenGroup (page_grp, 4, 0, NULL);
33119
SetGroupSpacing (cfp->pages[eSegPageText - 1], 10, 10);
33120
StaticPrompt (cfp->pages[eSegPageText - 1], "Create set with sequences where", 0, dialogTextHeight, programFont, 'l');
33121
cfp->search_text = DialogText (cfp->pages[eSegPageText - 1], "", 10, SegTextChange);
33122
SetObjectExtra (cfp->search_text, cfp, NULL);
33123
StaticPrompt (cfp->pages[eSegPageText - 1], "appears in", 0, dialogTextHeight, programFont, 'l');
33124
cfp->search_field = SearchFieldDialog (cfp->pages[eSegPageText - 1], SegTextChangeNotify, cfp);
33125
33126
/* id */
33127
cfp->pages[eSegPageId - 1] = HiddenGroup (page_grp, -1, 0, NULL);
33128
SetGroupSpacing (cfp->pages[eSegPageId - 1], 10, 10);
33129
p2 = StaticPrompt (cfp->pages[eSegPageId - 1], "Create set with marked sequences", 0, dialogTextHeight, programFont, 'l');
33130
g1 = HiddenGroup (cfp->pages[eSegPageId - 1], 3, 0, NULL);
33131
g2 = HiddenGroup (cfp->pages[eSegPageId - 1], 2, 0, NULL);
33132
cfp->id_constraint = StringConstraintDialogX (g2, "Mark sequences where sequence ID", TRUE);
33133
scd.insensitive = TRUE;
33134
scd.match_location = eStringConstraintInList;
33135
scd.match_text = NULL;
33136
scd.not_present = FALSE;
33137
scd.whole_word = FALSE;
33138
PointerToDialog (cfp->id_constraint, &scd);
33139
b = PushButton (g2, "Mark", SelectSequenceIDsForSegregate);
33140
SetObjectExtra (b, cfp, NULL);
33141
AlignObjects (ALIGN_CENTER, (HANDLE) p2, (HANDLE) g1, (HANDLE) g2, NULL);
33142
33143
AlignObjects (ALIGN_CENTER, (HANDLE) cfp->pages[0],
33144
(HANDLE) cfp->pages[1],
33145
(HANDLE) cfp->pages[2],
33146
(HANDLE) cfp->pages[3],
33147
(HANDLE) cfp->pages[4],
33148
(HANDLE) cfp->pages[5],
33149
NULL);
33150
33151
SetValue (cfp->seg_choice_grp, 1);
33152
33153
/* add select all/unselect all buttons */
33154
k = HiddenGroup (h, 2, 0, NULL);
33155
b = PushButton (k, "Mark All", SelectSegCategories);
33156
SetObjectExtra (b, cfp, NULL);
33157
b = PushButton (k, "Unmark All", UnselectSegCategories);
33158
SetObjectExtra (b, cfp, NULL);
33159
33160
33161
/* Add Accept and Cancel buttons */
33162
33163
c = HiddenGroup (h, 3, 0, NULL);
33164
cfp->accept = DefaultButton (c, "Accept", SegregateByField_Callback);
33165
SetObjectExtra (cfp->accept, cfp, NULL);
33166
Disable (cfp->accept);
33167
PushButton (c, "Cancel", StdCancelButtonProc);
33168
cfp->leave_dlg_up = CheckBox (c, "Leave Dialog Up", NULL);
33169
33170
/* Line things up nicely */
33171
33172
AlignObjects (ALIGN_CENTER, (HANDLE) g3,
33173
(HANDLE) cfp->group_list_dlg,
33174
(HANDLE) page_grp,
33175
(HANDLE) k,
33176
(HANDLE) c, NULL);
33177
33178
/* initialize the display */
33179
ChangeSegChoice (cfp->seg_choice_grp);
33180
33181
/* Display the window now */
33182
33183
RealizeWindow (w);
33184
Show (w);
33185
Select (w);
33186
Select (cfp->accept);
33187
Update ();
33188
return OM_MSG_RET_OK;
33189
}
33190
33191
typedef struct fixcase {
33192
FORM_MESSAGE_BLOCK
33193
DialoG field_dlg;
33194
DialoG case_dlg;
33195
ButtoN accept;
33196
ButtoN leave_dlg_up;
33197
33198
ValNodePtr requested_field;
33199
GetFeatureFieldString fieldstring_func;
33200
GetDescriptorFieldString descrstring_func;
33201
SetFeatureFieldString feature_apply_action;
33202
SetDescriptorFieldString descriptor_apply_action;
33203
FreeValNodeProc free_vn_proc;
33204
CopyValNodeDataProc copy_vn_proc;
33205
ChangeCasePtr ccp;
33206
ValNodePtr orgnames;
33207
} FixCaseData, PNTR FixCasePtr;
33208
33209
33210
static void FixCaseFeatureCallback (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
33211
{
33212
FixCasePtr fcp;
33213
CharPtr str;
33214
ApplyValueData avd;
33215
33216
if (sfp == NULL || userdata == NULL) return;
33217
fcp = (FixCasePtr) userdata;
33218
if (fcp->fieldstring_func == NULL || fcp->feature_apply_action == NULL
33219
|| fcp->ccp == NULL || fcp->ccp->change == eChangeCaseNone)
33220
{
33221
return;
33222
}
33223
33224
str = fcp->fieldstring_func (sfp, fcp->requested_field, fsp);
33225
if (StringHasNoText (str)) {
33226
str = MemFree (str);
33227
return;
33228
} else {
33229
avd.text_to_replace = NULL;
33230
avd.where_to_replace = EditApplyFindLocation_anywhere;
33231
avd.etp = NULL;
33232
avd.field_list = fcp->requested_field;
33233
ChangeCase (&str, fcp->ccp, fcp->orgnames);
33234
avd.new_text = str;
33235
(fcp->feature_apply_action) (sfp, &avd, fsp);
33236
}
33237
}
33238
33239
static void FixCaseDescriptorCallback (SeqDescrPtr sdp, Pointer userdata, FilterSetPtr fsp)
33240
{
33241
FixCasePtr fcp;
33242
CharPtr str;
33243
ApplyValueData avd;
33244
33245
if (sdp == NULL || userdata == NULL) return;
33246
fcp = (FixCasePtr) userdata;
33247
if (fcp->descrstring_func == NULL || fcp->descriptor_apply_action == NULL
33248
|| fcp->ccp == NULL || fcp->ccp->change == eChangeCaseNone)
33249
{
33250
return;
33251
}
33252
33253
str = fcp->descrstring_func (sdp, fcp->requested_field, fsp);
33254
if (StringHasNoText (str)) {
33255
str = MemFree (str);
33256
return;
33257
} else {
33258
avd.text_to_replace = NULL;
33259
avd.where_to_replace = EditApplyFindLocation_anywhere;
33260
avd.etp = NULL;
33261
avd.field_list = fcp->requested_field;
33262
ChangeCase (&str, fcp->ccp, fcp->orgnames);
33263
avd.new_text = str;
33264
(fcp->descriptor_apply_action) (sdp, &avd, fsp);
33265
}
33266
}
33267
33268
33269
static void FixCaseByFieldCallback (ButtoN b)
33270
{
33271
FixCasePtr fcp;
33272
SeqEntryPtr sep;
33273
ParseFieldPtr dst_field_data;
33274
FilterSetPtr fsp = NULL;
33275
ValNodePtr vnp;
33276
33277
fcp = (FixCasePtr) GetObjectExtra (b);
33278
if (fcp == NULL) return;
33279
33280
sep = GetTopSeqEntryForEntityID (fcp->input_entityID);
33281
33282
if (sep == NULL) return;
33283
33284
dst_field_data = DialogToPointer (fcp->field_dlg);
33285
if (dst_field_data == NULL) return;
33286
fcp->ccp = DialogToPointer (fcp->case_dlg);
33287
if (fcp->ccp == NULL || fcp->ccp->change == eChangeCaseNone) {
33288
dst_field_data = ParseFieldFree (dst_field_data);
33289
fcp->ccp = MemFree (fcp->ccp);
33290
return;
33291
}
33292
33293
WatchCursor();
33294
Update();
33295
33296
/* if we will be fixing capitalization, get org names to use in fixes */
33297
if (dst_field_data->parse_field_type != PARSE_FIELD_BIOSRC_STRING
33298
|| dst_field_data->feature_field == NULL
33299
|| dst_field_data->feature_field->data.intvalue != PARSE_FIELD_BIOSRC_TAXNAME) {
33300
VisitBioSourcesInSep (sep, &(fcp->orgnames), GetOrgNamesInRecordCallback);
33301
}
33302
33303
switch (dst_field_data->parse_field_type)
33304
{
33305
case PARSE_FIELD_SOURCE_QUAL :
33306
fcp->fieldstring_func = GetSourceQualFeatureString;
33307
fcp->descrstring_func = GetSourceQualDescrString;
33308
fcp->feature_apply_action = ApplySourceQualFeatureCallback;
33309
fcp->descriptor_apply_action = ApplySourceQualDescriptorCallback,
33310
fcp->free_vn_proc = ValNodeSimpleDataFree;
33311
fcp->copy_vn_proc = SourceQualValNodeDataCopy;
33312
fcp->requested_field = dst_field_data->feature_field;
33313
OperateOnSeqEntryConstrainedObjects (sep, fsp, FixCaseFeatureCallback,
33314
FixCaseDescriptorCallback,
33315
SEQFEAT_BIOSRC, 0,
33316
Seq_descr_source, fcp);
33317
33318
break;
33319
case PARSE_FIELD_DEFLINE:
33320
fcp->fieldstring_func = NULL;
33321
fcp->descrstring_func = GetStringFromStringDescriptor;
33322
fcp->feature_apply_action = NULL;
33323
fcp->descriptor_apply_action = ApplyTitleDescriptorCallback;
33324
fcp->free_vn_proc = NULL;
33325
fcp->copy_vn_proc = IntValNodeCopy;
33326
fcp->requested_field = ValNodeNew (NULL);
33327
fcp->requested_field->data.intvalue = Seq_descr_title;
33328
OperateOnSeqEntryConstrainedObjects (sep, fsp, NULL,
33329
FixCaseDescriptorCallback,
33330
0, 0,
33331
Seq_descr_title, fcp);
33332
fcp->requested_field = ValNodeFree (fcp->requested_field);
33333
33334
break;
33335
case PARSE_FIELD_BIOSRC_STRING:
33336
fcp->fieldstring_func = GetSourceFeatureString;
33337
fcp->descrstring_func = GetSourceDescriptorString;
33338
fcp->feature_apply_action = ApplySourceStringFeatureCallback;
33339
fcp->descriptor_apply_action = ApplySourceStringDescriptorCallback;
33340
fcp->free_vn_proc = NULL;
33341
fcp->copy_vn_proc = IntValNodeCopy;
33342
fcp->requested_field = dst_field_data->feature_field;
33343
OperateOnSeqEntryConstrainedObjects (sep, fsp, FixCaseFeatureCallback,
33344
FixCaseDescriptorCallback,
33345
SEQFEAT_BIOSRC, 0,
33346
Seq_descr_source, fcp);
33347
break;
33348
case PARSE_FIELD_DBXREF:
33349
fcp->fieldstring_func = GetBioSourceFeatureDbxrefString;
33350
fcp->descrstring_func = GetBioSourceDescriptorDbxrefString;
33351
fcp->feature_apply_action = ApplyBioSourceDbxrefFeatureCallback;
33352
fcp->descriptor_apply_action = ApplyBioSourceDbxrefDescriptorCallback;
33353
fcp->free_vn_proc = ValNodeSimpleDataFree;
33354
fcp->copy_vn_proc = ValNodeStringCopy;
33355
fcp->requested_field = dst_field_data->feature_field;
33356
OperateOnSeqEntryConstrainedObjects (sep, fsp, FixCaseFeatureCallback,
33357
FixCaseDescriptorCallback,
33358
SEQFEAT_BIOSRC, 0,
33359
Seq_descr_source, fcp);
33360
break;
33361
case PARSE_FIELD_GENE_FIELD:
33362
fcp->fieldstring_func = GetGeneFieldString;
33363
fcp->descrstring_func = NULL;
33364
fcp->feature_apply_action = SetGeneFieldString;
33365
fcp->descriptor_apply_action = NULL;
33366
fcp->free_vn_proc = NULL;
33367
fcp->copy_vn_proc = IntValNodeCopy;
33368
fcp->requested_field = dst_field_data->feature_field;
33369
OperateOnSeqEntryConstrainedObjects (sep, fsp, FixCaseFeatureCallback,
33370
NULL,
33371
SEQFEAT_GENE, 0,
33372
0, fcp);
33373
break;
33374
case PARSE_FIELD_RNA_FIELD:
33375
fcp->fieldstring_func = GetRNAFieldString;
33376
fcp->descrstring_func = NULL;
33377
fcp->feature_apply_action = SetRNAFieldString;
33378
fcp->descriptor_apply_action = NULL;
33379
fcp->free_vn_proc = NULL;
33380
fcp->copy_vn_proc = IntValNodeCopy;
33381
fcp->requested_field = dst_field_data->feature_field;
33382
OperateOnSeqEntryConstrainedObjects (sep, fsp, FixCaseFeatureCallback,
33383
NULL,
33384
SEQFEAT_RNA,
33385
dst_field_data->feature_subtype == NULL ? 0 : dst_field_data->feature_subtype->data.intvalue,
33386
0, fcp);
33387
break;
33388
case PARSE_FIELD_CDS_COMMENT:
33389
fcp->fieldstring_func = GetCDSComment;
33390
fcp->descrstring_func = NULL;
33391
fcp->feature_apply_action = SetCDSComment;
33392
fcp->descriptor_apply_action = NULL;
33393
fcp->free_vn_proc = NULL;
33394
fcp->copy_vn_proc = IntValNodeCopy;
33395
fcp->requested_field = dst_field_data->feature_field;
33396
OperateOnSeqEntryConstrainedObjects (sep, fsp, FixCaseFeatureCallback,
33397
NULL,
33398
SEQFEAT_CDREGION, FEATDEF_CDS,
33399
0, fcp);
33400
break;
33401
case PARSE_FIELD_COMMENT_DESC:
33402
fcp->requested_field = ValNodeNew (NULL);
33403
fcp->requested_field->data.intvalue = Seq_descr_comment;
33404
fcp->fieldstring_func = NULL;
33405
fcp->descrstring_func = GetStringFromStringDescriptor;
33406
fcp->feature_apply_action = NULL;
33407
fcp->descriptor_apply_action = ApplyTitleDescriptorCallback;
33408
fcp->free_vn_proc = NULL;
33409
fcp->copy_vn_proc = IntValNodeCopy;
33410
OperateOnSeqEntryConstrainedObjects (sep, fsp, NULL,
33411
FixCaseDescriptorCallback,
33412
0, 0,
33413
Seq_descr_comment, fcp);
33414
fcp->requested_field = ValNodeFree (fcp->requested_field);
33415
break;
33416
case PARSE_FIELD_PROTEIN_FIELD:
33417
fcp->fieldstring_func = GetProteinFieldString;
33418
fcp->descrstring_func = NULL;
33419
fcp->feature_apply_action = SetProteinFieldString;
33420
fcp->descriptor_apply_action = NULL;
33421
fcp->free_vn_proc = NULL;
33422
fcp->copy_vn_proc = IntValNodeCopy;
33423
fcp->requested_field = dst_field_data->feature_field;
33424
OperateOnSeqEntryConstrainedObjects (sep, fsp, FixCaseFeatureCallback,
33425
NULL,
33426
SEQFEAT_PROT, 0,
33427
0, fcp);
33428
break;
33429
case PARSE_FIELD_IMPORT_QUAL:
33430
fcp->requested_field = dst_field_data->feature_field;
33431
fcp->fieldstring_func = GetGBQualString;
33432
fcp->descrstring_func = NULL;
33433
fcp->feature_apply_action = SetGBQualString;
33434
fcp->descriptor_apply_action = NULL;
33435
fcp->free_vn_proc = NULL;
33436
fcp->copy_vn_proc = IntValNodeCopy;
33437
33438
for (vnp = dst_field_data->feature_subtype; vnp != NULL; vnp = vnp->next)
33439
{
33440
OperateOnSeqEntryConstrainedObjects (sep, fsp, FixCaseFeatureCallback,
33441
NULL,
33442
0, vnp->choice,
33443
0, fcp);
33444
}
33445
break;
33446
case PARSE_FIELD_FEATURE_NOTE:
33447
fcp->fieldstring_func = GetFeatureNote;
33448
fcp->descrstring_func = NULL;
33449
fcp->feature_apply_action = SetFeatureNote;
33450
fcp->descriptor_apply_action = NULL;
33451
fcp->free_vn_proc = ValNodeSimpleDataFree;
33452
fcp->copy_vn_proc = ValNodeStringCopy;
33453
33454
for (vnp = dst_field_data->feature_field; vnp != NULL; vnp = vnp->next)
33455
{
33456
fcp->requested_field = vnp;
33457
OperateOnSeqEntryConstrainedObjects (sep, fsp, FixCaseFeatureCallback,
33458
NULL,
33459
0, vnp->choice,
33460
0, fcp);
33461
}
33462
break;
33463
}
33464
fcp->orgnames = ValNodeFree (fcp->orgnames);
33465
dst_field_data = ParseFieldFree (dst_field_data);
33466
fcp->ccp = MemFree (fcp->ccp);
33467
33468
ObjMgrSetDirtyFlag (fcp->input_entityID, TRUE);
33469
ObjMgrSendMsg (OM_MSG_UPDATE, fcp->input_entityID, 0, 0);
33470
ArrowCursor ();
33471
Update ();
33472
33473
if (!GetStatus (fcp->leave_dlg_up)) {
33474
Remove (fcp->form);
33475
}
33476
}
33477
33478
extern void FixCaseByField (IteM i)
33479
{
33480
GrouP c;
33481
FixCasePtr cfp;
33482
ChangeCaseData ccd;
33483
GrouP h;
33484
WindoW w;
33485
BaseFormPtr bfp;
33486
33487
#ifdef WIN_MAC
33488
bfp = currentFormDataPtr;
33489
#else
33490
bfp = GetObjectExtra (i);
33491
#endif
33492
if (bfp == NULL) return;
33493
33494
/* Create a new window, and a struct */
33495
/* to pass around the data in. */
33496
33497
cfp = (FixCasePtr) MemNew (sizeof (FixCaseData));
33498
if (cfp == NULL)
33499
return;
33500
33501
w = FixedWindow (-50, -33, -10, -10, "Fix Case By Field",
33502
StdCloseWindowProc);
33503
SetObjectExtra (w, cfp, StdCleanupFormProc);
33504
cfp->form = (ForM) w;
33505
cfp->input_entityID = bfp->input_entityID;
33506
33507
h = HiddenGroup (w, -1, 0, NULL);
33508
SetGroupSpacing (h, 10, 10);
33509
33510
cfp->field_dlg = ParseFieldDestDialogEx (h, NULL, NULL, FALSE, TRUE);
33511
33512
cfp->case_dlg = ChangeCaseDialog (h);
33513
ccd.change = eChangeCaseAllLower;
33514
PointerToDialog (cfp->case_dlg, &ccd);
33515
33516
/* Add Accept and Cancel buttons */
33517
33518
c = HiddenGroup (h, 3, 0, NULL);
33519
cfp->accept = DefaultButton (c, "Accept", FixCaseByFieldCallback);
33520
SetObjectExtra (cfp->accept, cfp, NULL);
33521
PushButton (c, "Cancel", StdCancelButtonProc);
33522
cfp->leave_dlg_up = CheckBox (c, "Leave Dialog Up", NULL);
33523
33524
/* Line things up nicely */
33525
33526
AlignObjects (ALIGN_CENTER, (HANDLE) cfp->field_dlg,
33527
(HANDLE) cfp->case_dlg,
33528
(HANDLE) c, NULL);
33529
33530
33531
/* Display the window now */
33532
33533
RealizeWindow (w);
33534
Show (w);
33535
Select (w);
33536
Select (cfp->accept);
33537
Update ();
33538
}
33539
33540
static void FormatBoxColumn (ColPtr col)
33541
{
33542
if (col == NULL) return;
33543
col->pixWidth = stdCharWidth;
33544
col->pixInset = 0;
33545
col->charWidth = 0;
33546
col->charInset = 0;
33547
col->font = NULL;
33548
col->just = 'l';
33549
col->wrap = 1;
33550
col->bar = 0;
33551
col->underline = 0;
33552
col->left = 0;
33553
col->last = FALSE;
33554
}
33555
33556
static ColPtr AllocateDocColumnsForFieldList (BulkEdFieldPtr field_list, Int4Ptr p_len, Int4 last_sorted_col)
33557
{
33558
Int4 i, num_columns = 3, len = 0, col;
33559
ColPtr col_list;
33560
33561
if (field_list == NULL) {
33562
return NULL;
33563
}
33564
33565
/* set the font so that the pixwidth will be correct */
33566
SelectFont (programFont);
33567
33568
/* start with 3 columns, one for expand/collapse and one for checkbox for row selection and one for final blank */
33569
for (i = 0; field_list[i].name != NULL; i++) {
33570
num_columns ++;
33571
}
33572
col_list = (ColPtr) MemNew (num_columns * sizeof (ColData));
33573
col = 0;
33574
FormatBoxColumn (col_list + col);
33575
len += col_list[col].pixWidth;
33576
col++;
33577
33578
for (i = 0; field_list[i].name != NULL; i++) {
33579
if (i == last_sorted_col) {
33580
FormatBoxColumn (col_list + col);
33581
len += col_list[col].pixWidth;
33582
col++;
33583
}
33584
len += (field_list[i].format_col_func) (col_list + col, field_list[i].name);
33585
col_list[col].last = FALSE;
33586
col++;
33587
}
33588
33589
/* final blank column */
33590
col_list[col].pixWidth = 0;
33591
col_list[col].pixInset = 0;
33592
col_list[col].charWidth = 0;
33593
col_list[col].charInset = 0;
33594
col_list[col].font = NULL;
33595
col_list[col].just = 'l';
33596
col_list[col].wrap = 1;
33597
col_list[col].bar = 0;
33598
col_list[col].underline = 0;
33599
col_list[col].left = 0;
33600
col_list[col].last = TRUE;
33601
if (p_len != NULL) {
33602
*p_len = len;
33603
}
33604
return col_list;
33605
}
33606
33607
typedef struct bulkeditorrow {
33608
ValNodePtr values_list;
33609
ValNodePtr object_list;
33610
struct bulkeditorrow PNTR subrows;
33611
Int4 copied_to_meta;
33612
Int4 copied_to_sub;
33613
Boolean expanded;
33614
Boolean selected;
33615
} BulkEditorRowData, PNTR BulkEditorRowPtr;
33616
33617
static ValNodePtr FreeBulkEditorValues (ValNodePtr values, BulkEdFieldPtr field_list)
33618
{
33619
ValNodePtr vnp;
33620
Int4 col;
33621
33622
for (col = 0, vnp = values;
33623
vnp != NULL;
33624
col++, vnp = vnp->next) {
33625
if (field_list[col].free_func == NULL) {
33626
vnp->data.ptrvalue = MemFree (vnp->data.ptrvalue);
33627
} else {
33628
(field_list[col].free_func) (vnp->data.ptrvalue);
33629
vnp->data.ptrvalue = NULL;
33630
}
33631
}
33632
values = ValNodeFree (values);
33633
return values;
33634
}
33635
33636
static void FreeBulkEditorValuesList (ValNodePtr PNTR values_list, Int4 num_rows, BulkEdFieldPtr field_list)
33637
{
33638
Int4 i;
33639
33640
if (values_list == NULL || field_list == NULL) return;
33641
for (i = 0; i < num_rows; i++) {
33642
values_list[i] = FreeBulkEditorValues (values_list[i], field_list);
33643
}
33644
values_list = MemFree (values_list);
33645
}
33646
33647
static BulkEditorRowPtr FreeBulkEditorRows (BulkEditorRowPtr rows, BulkEdFieldPtr field_list)
33648
{
33649
Int4 row_num;
33650
33651
if (rows == NULL) return NULL;
33652
for (row_num = 0; rows[row_num].object_list != NULL; row_num++) {
33653
rows[row_num].values_list = FreeBulkEditorValues (rows[row_num].values_list, field_list);
33654
rows[row_num].object_list = ValNodeFree (rows[row_num].object_list);
33655
FreeBulkEditorRows (rows[row_num].subrows, field_list);
33656
rows[row_num].subrows = NULL;
33657
}
33658
rows = MemFree (rows);
33659
return rows;
33660
}
33661
33662
static void CopyToSingleBulkEditRow (BulkEditorRowPtr dst, BulkEditorRowPtr src, BulkEdFieldPtr field_list)
33663
{
33664
ValNodePtr vnp;
33665
Int4 col;
33666
33667
if (dst == NULL || src == NULL) return;
33668
33669
/* copy values */
33670
dst->values_list = NULL;
33671
for (vnp = src->values_list, col = 0; vnp != NULL; vnp = vnp->next, col++) {
33672
ValNodeAddPointer (&(dst->values_list), vnp->choice, field_list[col].copy_func(vnp->data.ptrvalue));
33673
}
33674
33675
/* copy object */
33676
dst->object_list = NULL;
33677
ValNodeAddPointer (&(dst->object_list), src->object_list->choice, src->object_list->data.ptrvalue);
33678
33679
/* copy selection */
33680
dst->selected = src->selected;
33681
}
33682
33683
static void ExpandAllBulkEditRows (BulkEditorRowPtr row_list)
33684
{
33685
Int4 row_num;
33686
33687
if (row_list == NULL) return;
33688
for (row_num = 0; row_list[row_num].object_list != NULL; row_num++) {
33689
if (row_list[row_num].subrows != NULL) {
33690
row_list[row_num].expanded = TRUE;
33691
}
33692
}
33693
}
33694
33695
static void CollapseAllBulkEditRows (BulkEditorRowPtr row_list)
33696
{
33697
Int4 row_num;
33698
33699
if (row_list == NULL) return;
33700
for (row_num = 0; row_list[row_num].object_list != NULL; row_num++) {
33701
if (row_list[row_num].subrows != NULL) {
33702
row_list[row_num].expanded = FALSE;
33703
}
33704
}
33705
}
33706
33707
33708
/* sort_col is zero-based data column, already corrected for selection and expansion columns */
33709
static CharPtr GetTextForBulkEditorRow (BulkEditorRowPtr berp, BulkEdFieldPtr field_list, Int4 sort_col)
33710
{
33711
ValNodePtr column_values = NULL, vnp;
33712
Int4 text_len = 6, col;
33713
CharPtr str, line_text = NULL, tmp_str;
33714
33715
if (berp == NULL) return NULL;
33716
for (vnp = berp->values_list, col = 0; vnp != NULL; vnp = vnp->next, col++) {
33717
if (field_list[col].display_func == NULL) {
33718
str = NULL;
33719
} else {
33720
str = (field_list[col].display_func)(vnp->data.ptrvalue);
33721
}
33722
if (str == NULL) {
33723
str = StringSave ("");
33724
}
33725
if (berp->subrows != NULL && col == sort_col) {
33726
tmp_str = (CharPtr) MemNew (sizeof (Char) * (18 + StringLen (str)));
33727
sprintf (tmp_str, "%s%s(%d)", field_list[col].draw_col_func == NULL ? "" : " ",
33728
str, ValNodeLen (berp->object_list));
33729
str = MemFree (str);
33730
str = tmp_str;
33731
}
33732
ValNodeAddPointer (&column_values, 0, str);
33733
text_len += StringLen (str) + 1;
33734
}
33735
line_text = (CharPtr) MemNew (text_len * sizeof (Char));
33736
line_text[0] = 0;
33737
/* add blank column for row selector */
33738
StringCat (line_text, "\t");
33739
for (vnp = column_values, col = 0; vnp != NULL; vnp = vnp->next, col++) {
33740
if (col == sort_col) {
33741
/* add blank column for expand/collapse */
33742
StringCat (line_text, "\t");
33743
}
33744
StringCat (line_text, vnp->data.ptrvalue);
33745
StringCat (line_text, "\t");
33746
}
33747
column_values = ValNodeFreeData (column_values);
33748
/* add blank column at end, to allow last real column to be highlighted when blank */
33749
StringCat (line_text, "\t\n");
33750
return line_text;
33751
}
33752
33753
33754
static Boolean DataPosFromBulkEdDlgRow (Int2 row, BulkEditorRowPtr row_list, Int4Ptr pRowNum, Int4Ptr pSubNum)
33755
{
33756
Int4 row_num = 0, sub_num;
33757
Int2 display_row = 1;
33758
33759
if (row < 1 || row_list == NULL || pRowNum == NULL || pSubNum == NULL) return FALSE;
33760
33761
while (row_list[row_num].object_list != NULL) {
33762
if (display_row == row) {
33763
*pRowNum = row_num;
33764
*pSubNum = -1;
33765
return TRUE;
33766
}
33767
display_row++;
33768
if (row_list[row_num].subrows != NULL && row_list[row_num].expanded) {
33769
sub_num = 0;
33770
while (display_row != row && row_list[row_num].subrows[sub_num].object_list != NULL) {
33771
display_row++;
33772
sub_num++;
33773
}
33774
if (row_list[row_num].subrows[sub_num].object_list == NULL) {
33775
sub_num = -1;
33776
} else {
33777
if (display_row == row) {
33778
*pRowNum = row_num;
33779
*pSubNum = sub_num;
33780
return TRUE;
33781
}
33782
}
33783
}
33784
row_num++;
33785
}
33786
*pRowNum = -1;
33787
*pSubNum = -1;
33788
return FALSE;
33789
}
33790
33791
33792
static Int4 BulkEdDlgRowFromDataPos (Int4 row_num, Int4 sub_num, BulkEditorRowPtr row_list)
33793
{
33794
Int4 i, j, display_row = 1;
33795
33796
if (row_list == NULL) return 0;
33797
/* count subrows also passed */
33798
for (i = 0; row_list[i].object_list != NULL && i < row_num; i++) {
33799
display_row++;
33800
if (row_list[i].subrows != NULL && row_list[i].expanded) {
33801
for (j = 0; row_list[i].subrows[j].object_list != NULL; j++) {
33802
display_row++;
33803
}
33804
}
33805
}
33806
if (sub_num > -1) {
33807
display_row += sub_num + 1;
33808
}
33809
return display_row;
33810
}
33811
33812
33813
static Int4 BulkEdDataColumnFromDocColumn (Int4 doc_col, Int4 sort_col)
33814
{
33815
/* subtract offset (document maps first column to 1) */
33816
doc_col--;
33817
/* subtract selection column */
33818
doc_col--;
33819
33820
/* subtract expand/collapse column */
33821
if (doc_col > sort_col && sort_col > -1) {
33822
doc_col--;
33823
}
33824
return doc_col;
33825
}
33826
33827
33828
static ValNodePtr GetBulkEditorRowValueByColumn (BulkEditorRowPtr berp, Int4 col)
33829
{
33830
Int4 i;
33831
ValNodePtr vnp;
33832
33833
if (col < 0) return NULL;
33834
33835
for (i = 0, vnp = berp->values_list;
33836
i < col && vnp != NULL;
33837
i++, vnp = vnp->next) {}
33838
return vnp;
33839
}
33840
33841
33842
static void SelectBulkEditorRows (BulkEditorRowPtr berp, Boolean val)
33843
{
33844
if (berp == NULL) return;
33845
33846
while (berp->object_list != NULL) {
33847
berp->selected = val;
33848
SelectBulkEditorRows (berp->subrows, val);
33849
berp++;
33850
}
33851
}
33852
33853
33854
static Int4 CountBulkEditorRowsSelected (BulkEditorRowPtr berp)
33855
{
33856
Int4 num = 0;
33857
if (berp == NULL) return 0;
33858
33859
while (berp->object_list != NULL) {
33860
if (berp->subrows == NULL) {
33861
if (berp->selected) {
33862
num++;
33863
}
33864
} else {
33865
num+= CountBulkEditorRowsSelected (berp->subrows);
33866
}
33867
berp++;
33868
}
33869
return num;
33870
}
33871
33872
33873
static void GetBulkEditorSelectedObjects (BulkEditorRowPtr berp, ValNodePtr PNTR object_list)
33874
{
33875
ValNodePtr vnp;
33876
if (berp == NULL || object_list == NULL) return;
33877
33878
while (berp->object_list != NULL) {
33879
if (berp->subrows == NULL) {
33880
if (berp->selected) {
33881
for (vnp = berp->object_list; vnp != NULL; vnp = vnp->next) {
33882
ValNodeAddPointer (object_list, vnp->choice, vnp->data.ptrvalue);
33883
}
33884
}
33885
} else {
33886
GetBulkEditorSelectedObjects (berp->subrows, object_list);
33887
}
33888
berp++;
33889
}
33890
}
33891
33892
33893
static Boolean AllBulkEditorRowsSelected (BulkEditorRowPtr berp)
33894
{
33895
if (berp == NULL) return FALSE;
33896
33897
while (berp->object_list != NULL) {
33898
/* note - don't need to check subrows, because metarow would
33899
* have been unselected if any subrows were unselected */
33900
if (!berp->selected) {
33901
return FALSE;
33902
}
33903
berp++;
33904
}
33905
return TRUE;
33906
}
33907
33908
33909
static void SelectBulkEditorRowsByStringConstraint (BulkEditorRowPtr berp, BulkEdFieldPtr field_list, Int4 col, StringConstraintXPtr scp, Boolean val)
33910
{
33911
ValNodePtr vnp;
33912
CharPtr str = NULL;
33913
Boolean match;
33914
33915
if (berp == NULL || field_list == NULL || col < 0 || field_list[col].display_func == NULL) return;
33916
33917
while (berp->object_list != NULL) {
33918
if (berp->subrows == NULL) {
33919
vnp = GetBulkEditorRowValueByColumn (berp, col);
33920
if (vnp != NULL) {
33921
str = field_list[col].display_func(vnp->data.ptrvalue);
33922
}
33923
match = DoesStringMatchConstraintX (str, scp);
33924
str = MemFree (str);
33925
if (scp != NULL && scp->not_present) {
33926
match = !match;
33927
}
33928
if (match) {
33929
berp->selected = val;
33930
}
33931
} else {
33932
SelectBulkEditorRowsByStringConstraint (berp->subrows, field_list, col, scp, val);
33933
berp->selected = AllBulkEditorRowsSelected (berp->subrows);
33934
}
33935
berp++;
33936
}
33937
}
33938
33939
33940
/* call nulls and null values bigger */
33941
/* return 0 if a and b are equal, -1 if a is smaller, and 1 if b is smaller */
33942
static Int4 CompareBulkRowValues (Pointer val_a, Pointer val_b, BulkDisplayFieldFunc display_func)
33943
{
33944
CharPtr str_a, str_b;
33945
Int4 rval = 0;
33946
33947
if (val_a == NULL && val_b == NULL) {
33948
rval = 0;
33949
} else if (val_a == NULL) {
33950
rval = 1;
33951
} else if (val_b == NULL) {
33952
rval = -1;
33953
} else if (display_func == NULL) {
33954
rval = 0;
33955
} else {
33956
str_a = display_func(val_a);
33957
str_b = display_func(val_b);
33958
rval = StringCmp (str_a, str_b);
33959
}
33960
return rval;
33961
}
33962
33963
/* call nulls and null values bigger */
33964
/* return 0 if a and b are equal, -1 if a is smaller, and 1 if b is smaller */
33965
static Int4 CompareBulkRows (BulkEditorRowPtr row_a, BulkEditorRowPtr row_b, Int4 sort_column, BulkEdFieldPtr field_list)
33966
{
33967
Int4 col;
33968
ValNodePtr vnp_a, vnp_b;
33969
Int4 rval = 0;
33970
33971
if (row_a == NULL && row_b == NULL) {
33972
rval = 0;
33973
} else if (row_a == NULL) {
33974
rval = 1;
33975
} else if (row_b == NULL) {
33976
rval = -1;
33977
} else if (row_a->values_list == NULL && row_b->values_list == NULL) {
33978
rval = 0;
33979
} else if (row_a->values_list == NULL) {
33980
rval = 1;
33981
} else if (row_b->values_list == NULL) {
33982
rval = -1;
33983
} else {
33984
col = 0;
33985
vnp_a = GetBulkEditorRowValueByColumn (row_a, sort_column);
33986
vnp_b = GetBulkEditorRowValueByColumn (row_b, sort_column);
33987
33988
if (vnp_a == NULL && vnp_b == NULL) {
33989
rval = 0;
33990
} else if (vnp_a == NULL) {
33991
rval = 1;
33992
} else if (vnp_b == NULL) {
33993
rval = -1;
33994
} else {
33995
rval = CompareBulkRowValues (vnp_a->data.ptrvalue, vnp_b->data.ptrvalue, field_list[sort_column].display_func);
33996
}
33997
}
33998
return rval;
33999
}
34000
34001
static Int4 CountIndividualRows (BulkEditorRowPtr row_list)
34002
{
34003
Int4 num_rows = 0, row_num;
34004
34005
if (row_list == NULL) return 0;
34006
34007
for (row_num = 0; row_list[row_num].object_list != NULL; row_num++) {
34008
if (row_list[row_num].subrows == NULL) {
34009
num_rows++;
34010
} else {
34011
num_rows += CountIndividualRows(row_list[row_num].subrows);
34012
}
34013
}
34014
return num_rows;
34015
}
34016
34017
34018
static void SetDefaultCopiedToValues (BulkEditorRowPtr row_list)
34019
{
34020
Int4 row_num;
34021
34022
if (row_list == NULL) return;
34023
34024
for (row_num = 0; row_list[row_num].object_list != NULL; row_num++) {
34025
row_list[row_num].copied_to_meta = -1;
34026
row_list[row_num].copied_to_sub = -1;
34027
if (row_list[row_num].subrows != NULL) {
34028
SetDefaultCopiedToValues(row_list[row_num].subrows);
34029
}
34030
}
34031
}
34032
34033
34034
static BulkEditorRowPtr ResortBulkEditorRows (BulkEditorRowPtr orig_rows, BulkEdFieldPtr field_list, Int4 new_sort_column)
34035
{
34036
Int4 num_individual_rows = 0;
34037
Int4 row_num, sub_num, last_inserted = 0, comp, col;
34038
BulkEditorRowPtr new_rows = NULL, smallest, berp;
34039
ValNodePtr matches, vnp;
34040
Boolean any_left, all_selected;
34041
34042
/* count individual rows (will need this many or fewer) */
34043
num_individual_rows = CountIndividualRows(orig_rows);
34044
34045
/* set default copied_to values */
34046
SetDefaultCopiedToValues (orig_rows);
34047
34048
new_rows = (BulkEditorRowPtr) MemNew (sizeof (BulkEditorRowData) * (num_individual_rows + 1));
34049
MemSet (new_rows, 0, sizeof (BulkEditorRowData) * (num_individual_rows + 1));
34050
any_left = TRUE;
34051
while (any_left) {
34052
smallest = NULL;
34053
matches = NULL;
34054
for (row_num = 0; orig_rows[row_num].object_list != NULL; row_num++) {
34055
if (orig_rows[row_num].subrows != NULL) {
34056
/* look in subrows */
34057
for (sub_num = 0; orig_rows[row_num].subrows[sub_num].object_list != NULL; sub_num++) {
34058
if (orig_rows[row_num].subrows[sub_num].copied_to_meta > -1) continue; /* already copied to other list */
34059
if (smallest == NULL) {
34060
smallest = orig_rows[row_num].subrows + sub_num;
34061
ValNodeAddPointer (&matches, 0, orig_rows[row_num].subrows + sub_num);
34062
} else {
34063
comp = CompareBulkRows (orig_rows[row_num].subrows + sub_num, smallest, new_sort_column, field_list);
34064
if (comp == 0) {
34065
/* equal - add to list of matches */
34066
ValNodeAddPointer (&matches, 0, orig_rows[row_num].subrows + sub_num);
34067
} else if (comp < 0) {
34068
/* smaller - make new smallest and list of matches */
34069
smallest = orig_rows[row_num].subrows + sub_num;
34070
matches = ValNodeFree (matches);
34071
ValNodeAddPointer (&matches, 0, orig_rows[row_num].subrows + sub_num);
34072
}
34073
/* if it's bigger, leave it alone for now */
34074
}
34075
}
34076
} else {
34077
/* look at just this row */
34078
if (orig_rows[row_num].copied_to_meta > -1) continue; /* already copied to other list */
34079
if (smallest == NULL) {
34080
smallest = orig_rows + row_num;
34081
ValNodeAddPointer (&matches, 0, orig_rows + row_num);
34082
} else {
34083
comp = CompareBulkRows (orig_rows + row_num, smallest, new_sort_column, field_list);
34084
if (comp == 0) {
34085
/* equal - add to list of matches */
34086
ValNodeAddPointer (&matches, 0, orig_rows + row_num);
34087
} else if (comp < 0) {
34088
/* smaller - make new smallest and list of matches */
34089
smallest = orig_rows + row_num;
34090
matches = ValNodeFree (matches);
34091
ValNodeAddPointer (&matches, 0, orig_rows + row_num);
34092
}
34093
/* if it's bigger, leave it alone for now */
34094
}
34095
}
34096
}
34097
if (smallest == NULL) {
34098
any_left = FALSE;
34099
} else {
34100
if (ValNodeLen (matches) > 1) {
34101
/* make metarow */
34102
/* add value for only sort column */
34103
for (col = 0, vnp = smallest->values_list; vnp != NULL; col++, vnp = vnp->next) {
34104
if (col == new_sort_column) {
34105
ValNodeAddPointer (&(new_rows[last_inserted].values_list), vnp->choice, field_list[col].copy_func(vnp->data.ptrvalue));
34106
} else {
34107
ValNodeAddPointer (&(new_rows[last_inserted].values_list), 0, NULL);
34108
}
34109
}
34110
/* add features and subrows */
34111
new_rows[last_inserted].subrows = (BulkEditorRowPtr) MemNew (sizeof(BulkEditorRowData) * (ValNodeLen(matches) + 1));
34112
MemSet (new_rows[last_inserted].subrows, 0, sizeof(BulkEditorRowData) * (ValNodeLen(matches) + 1));
34113
all_selected = TRUE;
34114
for (vnp = matches, sub_num = 0; vnp != NULL; vnp = vnp->next, sub_num++) {
34115
berp = (vnp->data.ptrvalue);
34116
ValNodeAddPointer (&(new_rows[last_inserted].object_list), berp->object_list->choice, berp->object_list->data.ptrvalue);
34117
CopyToSingleBulkEditRow (new_rows[last_inserted].subrows + sub_num, berp, field_list);
34118
berp->copied_to_meta = last_inserted;
34119
berp->copied_to_sub = sub_num;
34120
if (!berp->selected) {
34121
all_selected = FALSE;
34122
}
34123
}
34124
new_rows[last_inserted].selected = all_selected;
34125
} else {
34126
CopyToSingleBulkEditRow (new_rows + last_inserted, smallest, field_list);
34127
smallest->copied_to_meta = last_inserted;
34128
smallest->copied_to_sub = 0;
34129
}
34130
last_inserted++;
34131
matches = ValNodeFree (matches);
34132
}
34133
}
34134
return new_rows;
34135
}
34136
34137
34138
/* sort_column is zero-based data column, already corrected for selection and expansion columns */
34139
static Boolean AllSubrowsSameValue (BulkEditorRowPtr berp, BulkEdFieldPtr field_list, Int4 sort_column)
34140
{
34141
Int4 i;
34142
Boolean all_same = TRUE;
34143
34144
if (berp == NULL || berp->subrows == NULL || berp->subrows[0].object_list == NULL) {
34145
return TRUE;
34146
}
34147
34148
for (i = 1; berp->subrows[i].object_list != NULL && all_same; i++) {
34149
if (CompareBulkRows (berp->subrows + i - 1, berp->subrows + i, sort_column, field_list) != 0) {
34150
all_same = FALSE;
34151
}
34152
}
34153
34154
return all_same;
34155
}
34156
34157
34158
/* sort_column is zero-based data column, already corrected for selection and expansion columns */
34159
/* look to see if data in columns is different from data in editor */
34160
static Boolean AnyChangeInBulkFields (BulkEditorRowPtr berp, BulkEdFieldPtr field_list, DialoG editor, Int4 sort_column)
34161
{
34162
Pointer m_data;
34163
ValNodePtr vnp;
34164
Int4 comp;
34165
34166
if (berp == NULL || berp->subrows == NULL || berp->subrows[0].object_list == NULL) return FALSE;
34167
if (field_list == NULL || editor == NULL) return FALSE;
34168
34169
if (!AllSubrowsSameValue (berp, field_list, sort_column)) {
34170
return TRUE;
34171
}
34172
34173
/* find value for sort_column from first subrow */
34174
vnp = GetBulkEditorRowValueByColumn (berp, sort_column);
34175
34176
if (vnp == NULL) return TRUE;
34177
34178
/* compare with data from editor */
34179
m_data = DialogToPointer (editor);
34180
34181
comp = CompareBulkRowValues (m_data, vnp->data.ptrvalue, field_list[sort_column].display_func);
34182
34183
/* free data from editor */
34184
if (field_list[sort_column].free_func) {
34185
(field_list[sort_column].free_func)(m_data);
34186
}
34187
34188
if (comp == 0) {
34189
return FALSE;
34190
} else {
34191
return TRUE;
34192
}
34193
}
34194
34195
34196
/* col is zero-based data column, already corrected for selection and expansion columns */
34197
static void ApplyValueToOneBulkEditorRow (BulkEditorRowPtr berp, Int2 col, BulkEdFieldPtr field_list, DialoG editor)
34198
{
34199
ValNodePtr vnp;
34200
34201
if (berp == NULL || field_list == NULL || editor == NULL) return;
34202
34203
vnp = GetBulkEditorRowValueByColumn (berp, col);
34204
34205
if (vnp != NULL) {
34206
if (field_list[col].free_func == NULL) {
34207
vnp->data.ptrvalue = MemFree (vnp->data.ptrvalue);
34208
} else {
34209
(field_list[col].free_func) (vnp->data.ptrvalue);
34210
vnp->data.ptrvalue = NULL;
34211
}
34212
vnp->data.ptrvalue = DialogToPointer (editor);
34213
}
34214
}
34215
34216
34217
static void PopulateSingleBulkEditRowFromData (BulkEditorRowPtr berp, Uint1 data_choice, Pointer data, BulkEdFieldPtr field_list, Pointer metadata)
34218
{
34219
Int4 col;
34220
34221
/* add values for all columns */
34222
for (col = 0; field_list[col].name != NULL; col++) {
34223
ValNodeAddPointer (&(berp->values_list), 0, (field_list[col].get_func (data_choice, data, metadata)));
34224
}
34225
/* add feature */
34226
ValNodeAddPointer (&(berp->object_list), data_choice, data);
34227
}
34228
34229
static BulkEditorRowPtr MakeBulkEditorRowsFromObjectList (ValNodePtr object_list, BulkEdFieldPtr field_list, Int4 sort_column, Pointer metadata)
34230
{
34231
ValNodePtr vnp;
34232
BulkEditorRowPtr bulk_ed_rows = NULL, sorted_rows = NULL;
34233
Int4 num_rows, row_num;
34234
34235
if (object_list == NULL || field_list == NULL) return NULL;
34236
34237
/* first, create list with one row per object */
34238
num_rows = ValNodeLen (object_list);
34239
34240
bulk_ed_rows = (BulkEditorRowPtr) MemNew (sizeof (BulkEditorRowData) * (num_rows + 1));
34241
MemSet (bulk_ed_rows, 0, sizeof (BulkEditorRowData) * (num_rows + 1));
34242
34243
for (vnp = object_list, row_num = 0; vnp != NULL; vnp = vnp->next, row_num++)
34244
{
34245
PopulateSingleBulkEditRowFromData (bulk_ed_rows + row_num, vnp->choice, vnp->data.ptrvalue, field_list, metadata);
34246
}
34247
34248
if (sort_column >= 0)
34249
{
34250
/* Now resort rows for column */
34251
sorted_rows = ResortBulkEditorRows (bulk_ed_rows, field_list, sort_column);
34252
bulk_ed_rows = FreeBulkEditorRows (bulk_ed_rows, field_list);
34253
bulk_ed_rows = sorted_rows;
34254
}
34255
return bulk_ed_rows;
34256
}
34257
34258
34259
static Int4
34260
AddRowsToListBySelection
34261
(BulkEditorRowPtr dest,
34262
BulkEditorRowPtr src,
34263
BulkEdFieldPtr field_list,
34264
Int4 last_inserted,
34265
Boolean selected)
34266
{
34267
Int4 row_num;
34268
34269
if (dest == NULL || src == NULL) return last_inserted;
34270
34271
for (row_num = 0; src[row_num].object_list != NULL; row_num++) {
34272
if (src[row_num].subrows == NULL) {
34273
if ((src[row_num].selected && selected)
34274
|| (!src[row_num].selected && !selected)) {
34275
CopyToSingleBulkEditRow (dest + last_inserted, src + row_num, field_list);
34276
src[row_num].copied_to_meta = last_inserted;
34277
src[row_num].copied_to_sub = 0;
34278
last_inserted++;
34279
}
34280
} else {
34281
last_inserted = AddRowsToListBySelection(dest, src[row_num].subrows, field_list, last_inserted, selected);
34282
}
34283
}
34284
return last_inserted;
34285
}
34286
34287
static BulkEditorRowPtr ResortBulkEditorRowsBySelected (BulkEditorRowPtr orig_rows, BulkEdFieldPtr field_list)
34288
{
34289
Int4 num_individual_rows;
34290
Int4 last_inserted = 0;
34291
BulkEditorRowPtr new_rows = NULL;
34292
34293
/* count individual rows (will need this many or fewer) */
34294
num_individual_rows = CountIndividualRows(orig_rows);
34295
34296
/* set default copied_to values */
34297
SetDefaultCopiedToValues (orig_rows);
34298
34299
new_rows = (BulkEditorRowPtr) MemNew (sizeof (BulkEditorRowData) * (num_individual_rows + 1));
34300
MemSet (new_rows, 0, sizeof (BulkEditorRowData) * (num_individual_rows + 1));
34301
34302
/* add selected rows first */
34303
last_inserted = AddRowsToListBySelection(new_rows, orig_rows, field_list, last_inserted, TRUE);
34304
34305
/* add unselected rows */
34306
last_inserted = AddRowsToListBySelection(new_rows, orig_rows, field_list, last_inserted, FALSE);
34307
34308
return new_rows;
34309
}
34310
34311
34312
34313
34314
34315
typedef enum {
34316
eBulkApplyField = 1,
34317
eBulkEditField,
34318
eBulkConvertField,
34319
eBulkParseField,
34320
eBulkSwapField,
34321
eBulkRemoveField,
34322
eBulkCapitalizeField
34323
} EBulkAction;
34324
34325
static Int4 GetFieldNumFromPopupValue (Int4 popup_val, BulkEdFieldPtr field_list, Boolean edit_only)
34326
{
34327
Int4 i, pval = 1;
34328
34329
for (i = 0; field_list[i].name != NULL; i++) {
34330
if (field_list[i].create_dlg_func != NULL || (!edit_only && field_list[i].display_func != NULL)) {
34331
if (pval == popup_val) {
34332
return i;
34333
} else {
34334
pval++;
34335
}
34336
}
34337
}
34338
return -1;
34339
}
34340
34341
static Int4 GetPopupValueFromFieldNum (Int4 field_num, BulkEdFieldPtr field_list, Boolean edit_only)
34342
{
34343
Int4 i, pval = 1;
34344
34345
for (i = 0; field_list[i].name != NULL; i++) {
34346
if (field_list[i].create_dlg_func != NULL || (!edit_only && field_list[i].display_func != NULL)) {
34347
if (i == field_num) {
34348
return pval;
34349
} else {
34350
pval++;
34351
}
34352
}
34353
}
34354
return 0;
34355
}
34356
34357
34358
static PopuP MakeBulkEditorFieldListPopup (GrouP g, BulkEdFieldPtr field_list, Boolean edit_only)
34359
{
34360
PopuP p;
34361
Int4 i;
34362
34363
if (field_list == NULL) return NULL;
34364
34365
p = PopupList (g, TRUE, NULL);
34366
for (i = 0; field_list[i].name != NULL; i++) {
34367
if (field_list[i].create_dlg_func != NULL || (!edit_only && field_list[i].display_func != NULL)) {
34368
PopupItem (p, field_list[i].name);
34369
}
34370
}
34371
return p;
34372
}
34373
34374
34375
typedef struct onefieldbulkedit
34376
{
34377
Int4 field;
34378
EditApplyPtr edit_apply;
34379
ChangeCasePtr capitalization;
34380
} OneFieldBulkEditData, PNTR OneFieldBulkEditPtr;
34381
34382
static OneFieldBulkEditPtr OneFieldBulkEditFree (OneFieldBulkEditPtr ofp)
34383
{
34384
if (ofp != NULL) {
34385
ofp->edit_apply = EditApplyFree (ofp->edit_apply);
34386
ofp->capitalization = MemFree (ofp->capitalization);
34387
ofp = MemFree (ofp);
34388
}
34389
return ofp;
34390
}
34391
34392
typedef struct onefieldbulkeditdlg
34393
{
34394
DIALOG_MESSAGE_BLOCK
34395
Nlm_ChangeNotifyProc change_notify;
34396
Pointer change_userdata;
34397
BulkEdFieldPtr field_list;
34398
DialoG edit_apply;
34399
DialoG capitalization;
34400
PopuP field;
34401
34402
} OneFieldBulkEditDialogData, PNTR OneFieldBulkEditDialogPtr;
34403
34404
34405
static void OneFieldBulkEditToDialog (DialoG d, Pointer data)
34406
{
34407
OneFieldBulkEditDialogPtr dlg;
34408
OneFieldBulkEditPtr dlg_data;
34409
34410
dlg = (OneFieldBulkEditDialogPtr) GetObjectExtra (d);
34411
if (dlg == NULL) return;
34412
34413
dlg_data = (OneFieldBulkEditPtr) data;
34414
if (dlg_data == NULL) {
34415
SetValue (dlg->field, 1);
34416
PointerToDialog (dlg->edit_apply, NULL);
34417
PointerToDialog (dlg->capitalization, NULL);
34418
} else {
34419
SetValue (dlg->field, GetPopupValueFromFieldNum(dlg_data->field, dlg->field_list, TRUE));
34420
PointerToDialog (dlg->edit_apply, dlg_data->edit_apply);
34421
PointerToDialog (dlg->capitalization, dlg_data->capitalization);
34422
}
34423
if (dlg->change_notify != NULL) {
34424
(dlg->change_notify) (dlg->change_userdata);
34425
}
34426
}
34427
34428
34429
static Pointer OneFieldBulkEditDialogToPointer (DialoG d)
34430
{
34431
OneFieldBulkEditDialogPtr dlg;
34432
OneFieldBulkEditPtr dlg_data;
34433
34434
dlg = (OneFieldBulkEditDialogPtr) GetObjectExtra (d);
34435
if (dlg == NULL) return NULL;
34436
34437
dlg_data = (OneFieldBulkEditPtr) MemNew (sizeof (OneFieldBulkEditData));
34438
dlg_data->field = GetFieldNumFromPopupValue(GetValue (dlg->field), dlg->field_list, TRUE);
34439
dlg_data->edit_apply = DialogToPointer (dlg->edit_apply);
34440
dlg_data->capitalization = DialogToPointer (dlg->capitalization);
34441
34442
return dlg_data;
34443
}
34444
34445
static DialoG OneFieldBulkEditDialog
34446
(GrouP h,
34447
EBulkAction action_choice,
34448
Nlm_ChangeNotifyProc change_notify,
34449
Pointer change_userdata,
34450
BulkEdFieldPtr field_list)
34451
34452
{
34453
OneFieldBulkEditDialogPtr dlg;
34454
GrouP p;
34455
34456
dlg = (OneFieldBulkEditDialogPtr) MemNew (sizeof (OneFieldBulkEditDialogData));
34457
if (dlg == NULL)
34458
{
34459
return NULL;
34460
}
34461
34462
p = HiddenGroup (h, 2, 0, NULL);
34463
SetObjectExtra (p, dlg, StdCleanupExtraProc);
34464
SetGroupSpacing (p, 10, 10);
34465
34466
dlg->dialog = (DialoG) p;
34467
dlg->todialog = OneFieldBulkEditToDialog;
34468
dlg->fromdialog = OneFieldBulkEditDialogToPointer;
34469
dlg->dialogmessage = NULL;
34470
dlg->testdialog = NULL;
34471
34472
dlg->field_list = field_list;
34473
34474
dlg->field = MakeBulkEditorFieldListPopup (p, field_list, TRUE);
34475
SetValue (dlg->field, 1);
34476
34477
if (action_choice == eBulkApplyField)
34478
{
34479
dlg->edit_apply = EditApplyDialog (p, eEditApplyChoice_Apply, NULL, NULL, NULL, NULL);
34480
}
34481
else if (action_choice == eBulkEditField)
34482
{
34483
dlg->edit_apply = EditApplyDialog (p, eEditApplyChoice_Edit, NULL, NULL, NULL, NULL);
34484
}
34485
else if (action_choice == eBulkCapitalizeField)
34486
{
34487
dlg->capitalization = ChangeCaseDialog (p);
34488
}
34489
34490
return (DialoG) p;
34491
}
34492
34493
34494
typedef struct twofieldbulkedit
34495
{
34496
Int4 field_from;
34497
Int4 field_to;
34498
Boolean strip_name;
34499
Boolean leave_on_original;
34500
Boolean remove_parsed;
34501
TextPortionXPtr text_portion;
34502
} TwoFieldBulkEditData, PNTR TwoFieldBulkEditPtr;
34503
34504
34505
static TwoFieldBulkEditPtr TwoFieldBulkEditFree (TwoFieldBulkEditPtr tfp)
34506
{
34507
if (tfp != NULL) {
34508
tfp->text_portion = TextPortionXFree (tfp->text_portion);
34509
tfp = MemFree (tfp);
34510
}
34511
return tfp;
34512
}
34513
34514
34515
typedef struct twofieldbulkeditdlg
34516
{
34517
DIALOG_MESSAGE_BLOCK
34518
Nlm_ChangeNotifyProc change_notify;
34519
Pointer change_userdata;
34520
BulkEdFieldPtr field_list;
34521
ButtoN strip_name;
34522
ButtoN leave_on_original;
34523
ButtoN remove_parsed;
34524
DialoG text_portion;
34525
PopuP field_from;
34526
PopuP field_to;
34527
34528
} TwoFieldBulkEditDialogData, PNTR TwoFieldBulkEditDialogPtr;
34529
34530
34531
static void TwoFieldBulkEditToDialog (DialoG d, Pointer data)
34532
{
34533
TwoFieldBulkEditDialogPtr dlg;
34534
TwoFieldBulkEditPtr dlg_data;
34535
34536
dlg = (TwoFieldBulkEditDialogPtr) GetObjectExtra (d);
34537
if (dlg == NULL) return;
34538
34539
dlg_data = (TwoFieldBulkEditPtr) data;
34540
if (dlg_data == NULL) {
34541
SetValue (dlg->field_from, 1);
34542
SetValue (dlg->field_to, 1);
34543
if (dlg->leave_on_original != NULL) {
34544
SetStatus (dlg->leave_on_original, FALSE);
34545
}
34546
if (dlg->strip_name != NULL) {
34547
SetStatus (dlg->strip_name, FALSE);
34548
}
34549
if (dlg->remove_parsed != NULL) {
34550
SetStatus (dlg->remove_parsed, FALSE);
34551
}
34552
PointerToDialog (dlg->text_portion, NULL);
34553
} else {
34554
SetValue (dlg->field_from, GetPopupValueFromFieldNum(dlg_data->field_from, dlg->field_list, TRUE));
34555
SetValue (dlg->field_to, GetPopupValueFromFieldNum(dlg_data->field_to, dlg->field_list, TRUE));
34556
if (dlg->leave_on_original != NULL) {
34557
SetStatus (dlg->leave_on_original, dlg_data->leave_on_original);
34558
}
34559
if (dlg->strip_name != NULL) {
34560
SetStatus (dlg->strip_name, dlg_data->strip_name);
34561
}
34562
if (dlg->remove_parsed != NULL) {
34563
SetStatus (dlg->remove_parsed, dlg_data->remove_parsed);
34564
}
34565
PointerToDialog (dlg->text_portion, dlg_data->text_portion);
34566
}
34567
if (dlg->change_notify != NULL) {
34568
(dlg->change_notify) (dlg->change_userdata);
34569
}
34570
}
34571
34572
34573
static Pointer TwoFieldBulkEditDialogToPointer (DialoG d)
34574
{
34575
TwoFieldBulkEditDialogPtr dlg;
34576
TwoFieldBulkEditPtr dlg_data;
34577
34578
dlg = (TwoFieldBulkEditDialogPtr) GetObjectExtra (d);
34579
if (dlg == NULL) return NULL;
34580
34581
dlg_data = (TwoFieldBulkEditPtr) MemNew (sizeof (TwoFieldBulkEditData));
34582
dlg_data->field_from = GetFieldNumFromPopupValue(GetValue (dlg->field_from), dlg->field_list, TRUE);
34583
dlg_data->field_to = GetFieldNumFromPopupValue(GetValue (dlg->field_to), dlg->field_list, TRUE);
34584
dlg_data->leave_on_original = dlg->leave_on_original == NULL ? FALSE : GetStatus (dlg->leave_on_original);
34585
dlg_data->strip_name = dlg->strip_name == NULL ? FALSE : GetStatus (dlg->strip_name);
34586
dlg_data->remove_parsed = dlg->remove_parsed == NULL ? FALSE : GetStatus (dlg->remove_parsed);
34587
dlg_data->text_portion = DialogToPointer (dlg->text_portion);
34588
34589
return dlg_data;
34590
}
34591
34592
static DialoG TwoFieldBulkEditDialog
34593
(GrouP h,
34594
EBulkAction action_choice,
34595
Nlm_ChangeNotifyProc change_notify,
34596
Pointer change_userdata,
34597
BulkEdFieldPtr field_list,
34598
Boolean strip_name)
34599
34600
{
34601
TwoFieldBulkEditDialogPtr dlg;
34602
GrouP p, g1, g2;
34603
34604
dlg = (TwoFieldBulkEditDialogPtr) MemNew (sizeof (TwoFieldBulkEditDialogData));
34605
if (dlg == NULL)
34606
{
34607
return NULL;
34608
}
34609
34610
p = HiddenGroup (h, -1, 0, NULL);
34611
SetObjectExtra (p, dlg, StdCleanupExtraProc);
34612
SetGroupSpacing (p, 10, 10);
34613
34614
dlg->dialog = (DialoG) p;
34615
dlg->todialog = TwoFieldBulkEditToDialog;
34616
dlg->fromdialog = TwoFieldBulkEditDialogToPointer;
34617
dlg->dialogmessage = NULL;
34618
dlg->testdialog = NULL;
34619
34620
dlg->field_list = field_list;
34621
34622
g1 = HiddenGroup (p, 2, 0, NULL);
34623
StaticPrompt (g1, "From", 0, dialogTextHeight, systemFont, 'l');
34624
StaticPrompt (g1, "To", 0, dialogTextHeight, systemFont, 'l');
34625
34626
dlg->field_from = MakeBulkEditorFieldListPopup (g1, field_list, TRUE);
34627
SetValue (dlg->field_from, 1);
34628
dlg->field_to = MakeBulkEditorFieldListPopup (g1, field_list, TRUE);
34629
SetValue (dlg->field_to, 1);
34630
34631
if (action_choice == eBulkParseField)
34632
{
34633
dlg->text_portion = TextPortionXDialog(p);
34634
}
34635
34636
g2 = HiddenGroup (p, 3, 0, NULL);
34637
34638
if (action_choice == eBulkParseField)
34639
{
34640
dlg->remove_parsed = CheckBox (g2, "Remove from parsed field", NULL);
34641
}
34642
34643
if (action_choice == eBulkConvertField)
34644
{
34645
dlg->leave_on_original = CheckBox (g2, "Leave on original", NULL);
34646
}
34647
if (strip_name)
34648
{
34649
dlg->strip_name = CheckBox (g2, "Strip name from text", NULL);
34650
}
34651
34652
AlignObjects (ALIGN_CENTER, (HANDLE) g1, (HANDLE)g2, (HANDLE) dlg->text_portion, NULL);
34653
return (DialoG) p;
34654
}
34655
34656
34657
static void BulkDrawCollapseExpand (Boolean val, RectPtr r)
34658
{
34659
RecT rct;
34660
34661
if (r == NULL) return;
34662
34663
rct = *r;
34664
rct.bottom = rct.top + stdLineHeight - 4;
34665
rct.right = rct.left + stdLineHeight - 4;
34666
InsetRect (&rct, 2, 2);
34667
FrameRect (&rct);
34668
34669
if (val) {
34670
/* draw minus */
34671
MoveTo (rct.left, (rct.top + rct.bottom) / 2);
34672
LineTo (rct.right - 1, (rct.top + rct.bottom) / 2);
34673
} else {
34674
/* draw plus */
34675
MoveTo (rct.left, (rct.top + rct.bottom) / 2);
34676
LineTo (rct.right - 1, (rct.top + rct.bottom) / 2);
34677
MoveTo ((rct.left + rct.right) / 2, rct.top);
34678
LineTo ((rct.left + rct.right) / 2, rct.bottom);
34679
}
34680
}
34681
34682
34683
static void BulkDrawSelect (Boolean val, RectPtr r)
34684
{
34685
RecT rct;
34686
34687
if (r == NULL) return;
34688
34689
rct = *r;
34690
rct.bottom = rct.top + stdLineHeight - 4;
34691
rct.right = rct.left + stdLineHeight - 4;
34692
InsetRect (&rct, 2, 2);
34693
FrameRect (&rct);
34694
34695
if (val) {
34696
/* draw X */
34697
MoveTo (rct.left, rct.top);
34698
LineTo (rct.right - 1, rct.bottom - 1);
34699
MoveTo (rct.right, rct.top);
34700
LineTo (rct.left, rct.bottom - 1);
34701
}
34702
}
34703
34704
34705
typedef struct bulkeditordlg {
34706
DIALOG_MESSAGE_BLOCK
34707
DoC title_doc;
34708
DoC doc;
34709
BulkEdFieldPtr field_list;
34710
ColPtr col_list;
34711
ParData par_fmt;
34712
BulkEditorRowPtr row_list;
34713
DialoG PNTR editor_list;
34714
Int4 num_columns;
34715
Int2 last_viewed_row;
34716
Int2 last_viewed_col; /* this will always refer to the data column */
34717
Int2 last_sorted_col; /* this will always refer to the data column */
34718
34719
/* These are for the bulk edit actions */
34720
PopuP bulk_action;
34721
GrouP action_pages[8];
34722
34723
DialoG bulk_apply;
34724
DialoG bulk_edit;
34725
DialoG bulk_convert;
34726
DialoG bulk_parse;
34727
DialoG bulk_swap;
34728
DialoG bulk_remove;
34729
DialoG bulk_capitalize;
34730
34731
GrouP sel_unsel_grp;
34732
PopuP check_constraint_field;
34733
DialoG check_constraint;
34734
PrompT check_status;
34735
34736
Boolean any_editing;
34737
Boolean collapse_by_default;
34738
ClickableCallback single_click_func;
34739
ClickableCallback double_click_func;
34740
Pointer metadata;
34741
} BulkEditorDlgData, PNTR BulkEditorDlgPtr;
34742
34743
34744
static void InitBulkEdTitleDoc (BulkEditorDlgPtr dlg, DoC doc)
34745
{
34746
Int4 i, text_len = 5;
34747
CharPtr line_text;
34748
34749
if (dlg == NULL || doc == NULL) {
34750
return;
34751
}
34752
34753
Reset (doc);
34754
for (i = 0; i < dlg->num_columns; i++) {
34755
text_len += StringLen (dlg->field_list[i].name) + 1;
34756
}
34757
34758
line_text = (CharPtr) MemNew (text_len * sizeof (Char));
34759
line_text[0] = 0;
34760
/* add blank column for row selection */
34761
StringCat (line_text, "\t");
34762
34763
for (i = 0; i < dlg->num_columns - 1; i++) {
34764
if (i == dlg->last_sorted_col) {
34765
/* add blank column for expand/collapse */
34766
StringCat (line_text, "\t");
34767
}
34768
StringCat (line_text, dlg->field_list[i].name);
34769
StringCat (line_text, "\t");
34770
}
34771
if (i == dlg->last_sorted_col) {
34772
/* add blank column for expand/collapse */
34773
StringCat (line_text, "\t");
34774
}
34775
StringCat (line_text, dlg->field_list[i].name);
34776
/* add blank column at end */
34777
StringCat (line_text, "\t\n");
34778
34779
AppendText (doc, line_text, &(dlg->par_fmt), dlg->col_list, programFont);
34780
line_text = MemFree (line_text);
34781
}
34782
34783
34784
/* redraw, set scroll position */
34785
static void UpdateBulkEdDisplay (BulkEditorDlgPtr dlg)
34786
{
34787
Int4 i, text_len = 0, sub_num;
34788
CharPtr line_text;
34789
BaR sb;
34790
Int4 offset = 0;
34791
Int2 first_shown = 0;
34792
34793
if (dlg == NULL) {
34794
return;
34795
}
34796
34797
/* Get original scroll position */
34798
sb = GetSlateVScrollBar ((SlatE)dlg->doc);
34799
offset = 0;
34800
GetScrlParams4 (dlg->doc, &offset, &first_shown, NULL);
34801
34802
Reset (dlg->doc);
34803
34804
if (dlg->row_list == NULL) {
34805
return;
34806
}
34807
34808
for (i = 0; dlg->row_list[i].object_list != NULL; i++) {
34809
line_text = GetTextForBulkEditorRow(dlg->row_list + i, dlg->field_list, dlg->last_sorted_col);
34810
AppendText (dlg->doc, line_text, &(dlg->par_fmt), dlg->col_list, programFont);
34811
line_text = MemFree (line_text);
34812
if (dlg->row_list[i].subrows != NULL && dlg->row_list[i].expanded) {
34813
for (sub_num = 0; dlg->row_list[i].subrows[sub_num].object_list != NULL; sub_num++) {
34814
line_text = GetTextForBulkEditorRow(dlg->row_list[i].subrows + sub_num, dlg->field_list, dlg->last_sorted_col);
34815
AppendText (dlg->doc, line_text, &(dlg->par_fmt), dlg->col_list, programFont);
34816
line_text = MemFree (line_text);
34817
}
34818
}
34819
}
34820
34821
/* restore original scroll position */
34822
GetItemParams4 (dlg->doc, first_shown, &offset, NULL, NULL, NULL, NULL);
34823
offset = MIN (offset, GetBarMax (sb));
34824
SetScrlParams4 (dlg->doc, offset);
34825
}
34826
34827
/* col is zero-based data column, already corrected for selection and expansion columns */
34828
static void BulkEdDlgToField (Int2 row, Int2 col, BulkEditorDlgPtr dlg)
34829
{
34830
Int4 i;
34831
Int4 bulk_row, sub_num;
34832
34833
if (row < 1 || col < 0 || dlg == NULL) return;
34834
if (dlg->editor_list[col] == NULL) return;
34835
34836
if (!DataPosFromBulkEdDlgRow (row, dlg->row_list, &bulk_row, &sub_num)) return;
34837
34838
/* don't apply values if editing master row and column other than sort */
34839
if (sub_num < 0 && col != dlg->last_sorted_col && dlg->row_list[bulk_row].subrows != NULL) return;
34840
34841
if (sub_num < 0) {
34842
/* if applying to all, get confirmation */
34843
if (dlg->row_list[bulk_row].subrows != NULL) {
34844
/* if nothing changed, no need to ask, nothing to do */
34845
if (!AnyChangeInBulkFields(dlg->row_list + bulk_row, dlg->field_list, dlg->editor_list[dlg->last_sorted_col], dlg->last_sorted_col)) {
34846
return;
34847
} else if (ANS_CANCEL == Message (MSG_OKC, "Apply value to all features in collapsible group?")) {
34848
return;
34849
}
34850
}
34851
ApplyValueToOneBulkEditorRow (dlg->row_list + bulk_row, col, dlg->field_list, dlg->editor_list[col]);
34852
if (dlg->row_list[bulk_row].subrows != NULL) {
34853
for (i = 0; dlg->row_list[bulk_row].subrows[i].object_list != NULL; i++) {
34854
ApplyValueToOneBulkEditorRow (dlg->row_list[bulk_row].subrows + i, col, dlg->field_list, dlg->editor_list[col]);
34855
}
34856
}
34857
} else {
34858
ApplyValueToOneBulkEditorRow (dlg->row_list[bulk_row].subrows + sub_num, col, dlg->field_list, dlg->editor_list[col]);
34859
}
34860
UpdateBulkEdDisplay (dlg);
34861
}
34862
34863
34864
/* col is zero-based data column, already corrected for selection and expansion columns */
34865
/* if col is -1, hide everything (sorted by selection) */
34866
static void ShowBulkFieldEditor (BulkEditorDlgPtr dlg, Int4 bulk_row, Int4 sub_num, Int2 col)
34867
{
34868
BulkEditorRowPtr berp;
34869
ValNodePtr vnp;
34870
Int2 i;
34871
34872
for (i = 0; i < dlg->num_columns; i++) {
34873
SafeHide (dlg->editor_list[i]);
34874
}
34875
34876
if (col < 0) return;
34877
34878
if (sub_num < 0) {
34879
berp = dlg->row_list + bulk_row;
34880
} else {
34881
berp = dlg->row_list[bulk_row].subrows + sub_num;
34882
}
34883
34884
/* only show editor dialog if sorted column or not master row */
34885
if (col == dlg->last_sorted_col || berp->subrows == NULL) {
34886
vnp = GetBulkEditorRowValueByColumn (berp, col);
34887
34888
if (vnp == NULL) {
34889
PointerToDialog (dlg->editor_list[col], NULL);
34890
} else {
34891
PointerToDialog (dlg->editor_list[col], vnp->data.ptrvalue);
34892
}
34893
34894
SafeShow (dlg->editor_list[col]);
34895
}
34896
}
34897
34898
34899
/* clicking on a column in the title indicates that we should sort by this column. */
34900
static void ClickBulkTitle (DoC d, PoinT pt)
34901
{
34902
BulkEditorDlgPtr dlg;
34903
Int2 item;
34904
Int2 row;
34905
Int2 col;
34906
Int4 bulk_row_num = -1, bulk_sub_num = -1;
34907
RecT r;
34908
Int4 offset = 0, i;
34909
BulkEditorRowPtr sorted_rows;
34910
34911
dlg = (BulkEditorDlgPtr) GetObjectExtra (d);
34912
if (dlg == NULL) return;
34913
34914
MapDocPoint (d, pt, &item, &row, &col, NULL);
34915
34916
if (col - 2 == dlg->last_sorted_col) {
34917
/* clicked on checkbox column */
34918
col = -1;
34919
} else {
34920
col = BulkEdDataColumnFromDocColumn(col, dlg->last_sorted_col);
34921
}
34922
34923
if (item < 1 || col < -1 || col >= dlg->num_columns) return;
34924
BulkEdDlgToField (dlg->last_viewed_row, dlg->last_viewed_col, dlg);
34925
ResetClip();
34926
34927
/* save value of column listed */
34928
dlg->last_sorted_col = col;
34929
34930
if (col < 0) {
34931
sorted_rows = ResortBulkEditorRowsBySelected (dlg->row_list, dlg->field_list);
34932
} else {
34933
sorted_rows = ResortBulkEditorRows (dlg->row_list, dlg->field_list, dlg->last_sorted_col);
34934
if (dlg->collapse_by_default) {
34935
CollapseAllBulkEditRows (sorted_rows);
34936
} else {
34937
ExpandAllBulkEditRows (sorted_rows);
34938
}
34939
}
34940
/* get new position from old row */
34941
if (DataPosFromBulkEdDlgRow (dlg->last_viewed_row, dlg->row_list, &bulk_row_num, &bulk_sub_num)) {
34942
if (bulk_sub_num > -1) {
34943
dlg->last_viewed_row = BulkEdDlgRowFromDataPos (dlg->row_list[bulk_row_num].subrows[bulk_sub_num].copied_to_meta,
34944
dlg->row_list[bulk_row_num].subrows[bulk_sub_num].copied_to_sub,
34945
sorted_rows);
34946
} else {
34947
dlg->last_viewed_row = BulkEdDlgRowFromDataPos (dlg->row_list[bulk_row_num].copied_to_meta,
34948
dlg->row_list[bulk_row_num].copied_to_sub,
34949
sorted_rows);
34950
}
34951
dlg->last_viewed_col = dlg->last_sorted_col;
34952
}
34953
34954
dlg->row_list = FreeBulkEditorRows (dlg->row_list, dlg->field_list);
34955
dlg->row_list = sorted_rows;
34956
34957
34958
/* reformat the columns */
34959
dlg->col_list = AllocateDocColumnsForFieldList (dlg->field_list, NULL, dlg->last_sorted_col);
34960
ResetClip();
34961
InitBulkEdTitleDoc (dlg, dlg->title_doc);
34962
ObjectRect (dlg->title_doc, &r);
34963
InvalRect (&r);
34964
34965
UpdateBulkEdDisplay (dlg);
34966
34967
if (dlg->last_viewed_row > 0) {
34968
/* show appropriate editor for highlighted item */
34969
if (DataPosFromBulkEdDlgRow (dlg->last_viewed_row, dlg->row_list, &bulk_row_num, &bulk_sub_num)) {
34970
ShowBulkFieldEditor (dlg, bulk_row_num, bulk_sub_num, dlg->last_sorted_col);
34971
} else {
34972
dlg->last_viewed_row = 0;
34973
dlg->last_viewed_col = 0;
34974
for (i = 0; i < dlg->num_columns; i++) {
34975
SafeHide (dlg->editor_list[i]);
34976
}
34977
}
34978
34979
/* scroll to new position of last_viewed */
34980
GetItemParams4 (dlg->doc, dlg->last_viewed_row, &offset, NULL, NULL, NULL, NULL);
34981
SetScrlParams4 (dlg->doc, offset);
34982
}
34983
34984
/* redraw highlight etc. */
34985
ObjectRect (dlg->title_doc, &r);
34986
InvalRect (&r);
34987
ObjectRect (dlg->doc, &r);
34988
InvalRect (&r);
34989
Update ();
34990
}
34991
34992
static void UpdateCheckStatus (BulkEditorDlgPtr dlg)
34993
{
34994
Int4 num_selected;
34995
CharPtr status_fmt = "%d feature%s currently checked";
34996
Char status_str[50];
34997
34998
if (dlg == NULL) return;
34999
35000
num_selected = CountBulkEditorRowsSelected (dlg->row_list);
35001
sprintf (status_str, status_fmt, num_selected, num_selected == 1 ? "" : "s");
35002
SetTitle (dlg->check_status, status_str);
35003
}
35004
35005
35006
/* when clicking on field, show editor (if available), change selection, collapse/expand,
35007
* set last viewed row, populate data from previously displayed editor
35008
*/
35009
static void ClickBulkEdField (DoC d, PoinT pt)
35010
{
35011
BulkEditorDlgPtr dlg;
35012
BulkEditorRowPtr berp;
35013
Int2 item;
35014
Int2 row;
35015
Int2 col;
35016
RecT r;
35017
ValNodePtr vnp;
35018
Int4 bulk_row = -1, sub_num = -1;
35019
Boolean dblclick = dblClick;
35020
35021
dlg = (BulkEditorDlgPtr) GetObjectExtra (d);
35022
if (dlg == NULL) return;
35023
35024
MapDocPoint (d, pt, &item, &row, &col, NULL);
35025
35026
if (!DataPosFromBulkEdDlgRow (item, dlg->row_list, &bulk_row, &sub_num)) {
35027
return;
35028
}
35029
35030
if (sub_num < 0) {
35031
berp = dlg->row_list + bulk_row;
35032
} else {
35033
berp = dlg->row_list[bulk_row].subrows + sub_num;
35034
}
35035
35036
if (col == 1) {
35037
/* do selection */
35038
berp->selected = !berp->selected;
35039
if (berp->subrows != NULL) {
35040
SelectBulkEditorRows (berp->subrows, berp->selected);
35041
} else if (sub_num > -1) {
35042
/* this is a subrow - metarow can no longer be selected
35043
* if this is not selected.
35044
*/
35045
if (dlg->row_list[bulk_row].selected && !berp->selected) {
35046
dlg->row_list[bulk_row].selected = FALSE;
35047
} else if (AllBulkEditorRowsSelected(dlg->row_list[bulk_row].subrows)) {
35048
/* all child rows are now selected, so select metarow */
35049
dlg->row_list[bulk_row].selected = TRUE;
35050
}
35051
}
35052
UpdateCheckStatus (dlg);
35053
ObjectRect (dlg->doc, &r);
35054
InvalRect (&r);
35055
Update ();
35056
return;
35057
} else if (col == dlg->last_sorted_col + 2) {
35058
/* do expand/collapse */
35059
if (berp->subrows != NULL) {
35060
berp->expanded = !berp->expanded;
35061
UpdateBulkEdDisplay (dlg);
35062
ObjectRect (dlg->doc, &r);
35063
InvalRect (&r);
35064
Update ();
35065
}
35066
return;
35067
} else {
35068
/* adjust to account for checkbox column */
35069
col = BulkEdDataColumnFromDocColumn(col, dlg->last_sorted_col);
35070
}
35071
if (item < 1 || col < 0 || col >= dlg->num_columns) return;
35072
BulkEdDlgToField (dlg->last_viewed_row, dlg->last_viewed_col, dlg);
35073
ResetClip();
35074
35075
ShowBulkFieldEditor (dlg, bulk_row, sub_num, col);
35076
35077
if (dlg->field_list[col].release_cell_func != NULL) {
35078
vnp = GetBulkEditorRowValueByColumn (berp, col);
35079
if (vnp != NULL) {
35080
vnp->data.ptrvalue = (dlg->field_list[col].release_cell_func) (vnp->data.ptrvalue);
35081
}
35082
}
35083
dlg->last_viewed_row = item;
35084
dlg->last_viewed_col = col;
35085
35086
/* redraw highlight etc. */
35087
ObjectRect (dlg->doc, &r);
35088
InvalRect (&r);
35089
Update ();
35090
35091
35092
if (dblclick) {
35093
if (dlg->double_click_func != NULL) {
35094
(dlg->double_click_func) (berp->object_list, NULL);
35095
}
35096
} else {
35097
if (dlg->single_click_func != NULL) {
35098
(dlg->single_click_func) (berp->object_list, NULL);
35099
}
35100
}
35101
}
35102
35103
static Boolean HighlightBulkEdField (DoC d, Int2 item, Int2 row, Int2 col)
35104
35105
{
35106
BulkEditorDlgPtr dlg;
35107
35108
dlg = (BulkEditorDlgPtr) GetObjectExtra (d);
35109
if (dlg == NULL) return FALSE;
35110
35111
if (col == 1 || col == dlg->last_sorted_col + 1) {
35112
/* don't highlight selection column or expansion column */
35113
return FALSE;
35114
}
35115
35116
col = BulkEdDataColumnFromDocColumn (col, dlg->last_sorted_col);
35117
35118
if (item == dlg->last_viewed_row && col == dlg->last_viewed_col) {
35119
return TRUE;
35120
} else {
35121
return FALSE;
35122
}
35123
}
35124
35125
static void DrawBulkEdCell (DoC d, RectPtr r, Int2 item, Int2 firstLine)
35126
35127
{
35128
Int2 lineHeight;
35129
RecT rct;
35130
Int2 format_col, data_col;
35131
BulkEditorDlgPtr dlg;
35132
BulkEditorRowPtr berp;
35133
ValNodePtr vnp;
35134
Int4 bulk_row_num = -1, bulk_sub_num = -1;
35135
35136
dlg = (BulkEditorDlgPtr) GetObjectExtra (d);
35137
if (dlg == NULL || r == NULL || item <= 0 || firstLine != 0) {
35138
return;
35139
}
35140
35141
GetItemParams (d, item, NULL, NULL, NULL, &lineHeight, NULL);
35142
rct = *r;
35143
35144
if (!DataPosFromBulkEdDlgRow (item, dlg->row_list, &bulk_row_num, &bulk_sub_num)) {
35145
return;
35146
}
35147
35148
/* draw lines at top of each row after the first that does not have subrows */
35149
if (bulk_row_num > 0 && bulk_sub_num < 0) {
35150
MoveTo (rct.left, rct.top);
35151
LineTo (rct.right, rct.top);
35152
}
35153
35154
if (bulk_sub_num < 0) {
35155
berp = dlg->row_list + bulk_row_num;
35156
} else {
35157
berp = dlg->row_list[bulk_row_num].subrows + bulk_sub_num;
35158
}
35159
35160
/* for column 0, draw selection box */
35161
format_col = 0;
35162
rct.right = rct.left + dlg->col_list[format_col].pixWidth - 1;
35163
BulkDrawSelect (berp->selected, &rct);
35164
rct.left = rct.right + 1;
35165
format_col++;
35166
35167
for (data_col = 0, vnp = berp->values_list;
35168
data_col < dlg->num_columns && vnp != NULL;
35169
data_col++, vnp = vnp->next) {
35170
rct.right = rct.left + dlg->col_list[format_col].pixWidth - 1;
35171
if (data_col == dlg->last_sorted_col) {
35172
/* draw box if expandable */
35173
if (bulk_sub_num == -1
35174
&& dlg->row_list[bulk_row_num].subrows != NULL) {
35175
BulkDrawCollapseExpand (dlg->row_list[bulk_row_num].expanded, &rct);
35176
}
35177
rct.left = rct.right + 1;
35178
format_col++;
35179
rct.right = rct.left + dlg->col_list[format_col].pixWidth - 1;
35180
}
35181
if (dlg->field_list[data_col].draw_col_func != NULL) {
35182
(dlg->field_list[data_col].draw_col_func)(vnp->data.ptrvalue, &rct);
35183
}
35184
rct.left = rct.right + 1;
35185
format_col++;
35186
}
35187
}
35188
35189
static void CleanupBulkEditorDialog (GraphiC g, VoidPtr data)
35190
{
35191
BulkEditorDlgPtr dlg;
35192
35193
dlg = (BulkEditorDlgPtr) data;
35194
if (dlg != NULL) {
35195
dlg->row_list = FreeBulkEditorRows(dlg->row_list, dlg->field_list);
35196
}
35197
StdCleanupExtraProc (g, data);
35198
}
35199
35200
static void ApplyBulkEditorRowToObject (BulkEditorRowPtr berp, Pointer target, BulkEdFieldPtr field_list)
35201
{
35202
ValNodePtr vnp_val;
35203
Int4 i;
35204
35205
if (berp == NULL || target == NULL || field_list == NULL) return;
35206
35207
for (i = 0, vnp_val = berp->values_list;
35208
vnp_val != NULL;
35209
i++, vnp_val = vnp_val->next) {
35210
if (field_list[i].set_func != NULL) {
35211
(field_list[i].set_func) (target, vnp_val->data.ptrvalue);
35212
}
35213
}
35214
}
35215
35216
static void ApplyBulkEditorToObjectList (DialoG d)
35217
{
35218
BulkEditorDlgPtr dlg;
35219
Int4 row, i;
35220
35221
dlg = (BulkEditorDlgPtr) GetObjectExtra (d);
35222
if (dlg == NULL) return;
35223
35224
BulkEdDlgToField (dlg->last_viewed_row, dlg->last_viewed_col, dlg);
35225
35226
for (row = 0; dlg->row_list[row].object_list != NULL; row++) {
35227
if (dlg->row_list[row].subrows == NULL) {
35228
ApplyBulkEditorRowToObject (dlg->row_list + row,
35229
dlg->row_list[row].object_list->data.ptrvalue,
35230
dlg->field_list);
35231
} else {
35232
for (i = 0; dlg->row_list[row].subrows[i].object_list != NULL; i++) {
35233
ApplyBulkEditorRowToObject (dlg->row_list[row].subrows + i,
35234
dlg->row_list[row].subrows[i].object_list->data.ptrvalue,
35235
dlg->field_list);
35236
}
35237
}
35238
}
35239
}
35240
35241
static void ChangeBulkEditorAction (PopuP p)
35242
{
35243
BulkEditorDlgPtr dlg;
35244
Int4 page_num;
35245
Int4 num_pages;
35246
35247
dlg = (BulkEditorDlgPtr) GetObjectExtra (p);
35248
if (dlg == NULL || !dlg->any_editing) return;
35249
35250
num_pages = sizeof (dlg->action_pages) / sizeof (GrouP);
35251
for (page_num = 0; page_num < num_pages; page_num++) {
35252
Hide (dlg->action_pages[page_num]);
35253
}
35254
page_num = GetValue (dlg->bulk_action) - 1;
35255
if (page_num > -1 && page_num < num_pages) {
35256
Show (dlg->action_pages[page_num]);
35257
}
35258
}
35259
35260
static void RemoveColumnFromSelectedBulkEditRows (BulkEditorRowPtr row_list, Int4 col, BulkEdFieldPtr field_list)
35261
{
35262
ValNodePtr vnp;
35263
35264
if (row_list == NULL || col < 0 || field_list == NULL) return;
35265
while (row_list->object_list != NULL) {
35266
if (row_list->selected) {
35267
if (row_list->subrows == NULL || AllBulkEditorRowsSelected(row_list->subrows)) {
35268
vnp = GetBulkEditorRowValueByColumn (row_list, col);
35269
if (vnp != NULL) {
35270
field_list[col].free_func(vnp->data.ptrvalue);
35271
vnp->data.ptrvalue = NULL;
35272
}
35273
}
35274
}
35275
RemoveColumnFromSelectedBulkEditRows (row_list->subrows, col, field_list);
35276
row_list++;
35277
}
35278
}
35279
35280
static void
35281
ApplyEditColumnFromSelectedBulkEditRows
35282
(BulkEditorRowPtr berp,
35283
BulkEdFieldPtr field_list,
35284
Int4 col,
35285
ApplyValuePtr avp)
35286
{
35287
ValNodePtr vnp;
35288
35289
if (berp == NULL) return;
35290
35291
while (berp->object_list != NULL) {
35292
if (berp->selected) {
35293
if (berp->subrows == NULL || AllBulkEditorRowsSelected(berp->subrows)) {
35294
vnp = GetBulkEditorRowValueByColumn (berp, col);
35295
if (vnp != NULL) {
35296
vnp->data.ptrvalue = (field_list[col].set_str_func) (vnp->data.ptrvalue, avp);
35297
}
35298
}
35299
}
35300
ApplyEditColumnFromSelectedBulkEditRows (berp->subrows, field_list, col, avp);
35301
berp++;
35302
}
35303
}
35304
35305
35306
static void
35307
CapitalizeColumnsForSelectedBulkEditRows
35308
(BulkEditorRowPtr berp,
35309
BulkEdFieldPtr field_list,
35310
Int4 col,
35311
ChangeCasePtr capitalization)
35312
{
35313
ValNodePtr vnp;
35314
CharPtr val_str;
35315
ApplyValueData avd;
35316
SeqFeatPtr sfp;
35317
SeqEntryPtr sep, last_sep = NULL;
35318
ValNodePtr orgname_list = NULL;
35319
35320
if (berp == NULL) return;
35321
35322
avd.field_list = NULL;
35323
avd.text_to_replace = NULL;
35324
avd.where_to_replace = EditApplyFindLocation_anywhere;
35325
avd.etp = NULL;
35326
35327
while (berp->object_list != NULL) {
35328
if (berp->selected) {
35329
if (berp->subrows == NULL || AllBulkEditorRowsSelected(berp->subrows)) {
35330
vnp = GetBulkEditorRowValueByColumn (berp, col);
35331
if (vnp != NULL) {
35332
val_str = (field_list[col].display_func)(vnp->data.ptrvalue);
35333
if (!StringHasNoText (val_str)) {
35334
if (berp->object_list->choice == OBJ_SEQFEAT && berp->object_list->data.ptrvalue != NULL) {
35335
sfp = (SeqFeatPtr) berp->object_list->data.ptrvalue;
35336
sep = GetTopSeqEntryForEntityID (sfp->idx.entityID);
35337
if (sep != last_sep) {
35338
orgname_list = ValNodeFree (orgname_list);
35339
/* get org names to use in fixes */
35340
VisitBioSourcesInSep (sep, &orgname_list, GetOrgNamesInRecordCallback);
35341
last_sep = sep;
35342
}
35343
}
35344
ChangeCase (&val_str, capitalization, orgname_list);
35345
avd.new_text = val_str;
35346
vnp->data.ptrvalue = (field_list[col].set_str_func) (vnp->data.ptrvalue, &avd);
35347
}
35348
val_str = MemFree (val_str);
35349
}
35350
}
35351
}
35352
CapitalizeColumnsForSelectedBulkEditRows (berp->subrows, field_list, col, capitalization);
35353
berp++;
35354
}
35355
orgname_list = ValNodeFree (orgname_list);
35356
}
35357
35358
static void RemoveNameFromText (CharPtr orig, CharPtr remove)
35359
{
35360
CharPtr cp, cp_dst;
35361
Int4 len;
35362
35363
if (StringHasNoText (orig) || StringHasNoText (remove)) {
35364
return;
35365
}
35366
cp = StringISearch (orig, remove);
35367
if (cp != NULL) {
35368
len = StringLen (remove);
35369
cp_dst = cp;
35370
cp = cp + len;
35371
while (*cp != 0 && len > 0) {
35372
*cp_dst = *cp;
35373
cp_dst++;
35374
cp++;
35375
len--;
35376
}
35377
*cp_dst = 0;
35378
}
35379
}
35380
35381
static void ConvertColumnsForSelectedBulkEditRows
35382
(BulkEditorRowPtr berp,
35383
BulkEdFieldPtr field_list,
35384
TwoFieldBulkEditPtr tfp,
35385
ExistingTextPtr etp)
35386
{
35387
ValNodePtr vnp_from, vnp_to;
35388
CharPtr val_from;
35389
ApplyValueData avd;
35390
if (berp == NULL || tfp == NULL) return;
35391
35392
avd.field_list = NULL;
35393
avd.text_to_replace = NULL;
35394
avd.where_to_replace = EditApplyFindLocation_anywhere;
35395
avd.etp = etp;
35396
35397
while (berp->object_list != NULL) {
35398
if (berp->selected && berp->subrows == NULL) {
35399
vnp_from = GetBulkEditorRowValueByColumn (berp, tfp->field_from);
35400
vnp_to = GetBulkEditorRowValueByColumn (berp, tfp->field_to);
35401
if (vnp_from != NULL && vnp_to != NULL) {
35402
val_from = (field_list[tfp->field_from].display_func)(vnp_from->data.ptrvalue);
35403
if (StringDoesHaveText (val_from)) {
35404
if (tfp->strip_name) {
35405
RemoveNameFromText (val_from, field_list[tfp->field_to].name);
35406
}
35407
35408
avd.new_text = val_from;
35409
vnp_to->data.ptrvalue = (field_list[tfp->field_to].set_str_func) (vnp_to->data.ptrvalue, &avd);
35410
35411
if (!tfp->leave_on_original) {
35412
(field_list[tfp->field_from].free_func)(vnp_from->data.ptrvalue);
35413
vnp_from->data.ptrvalue = NULL;
35414
}
35415
35416
}
35417
val_from = MemFree (val_from);
35418
}
35419
}
35420
ConvertColumnsForSelectedBulkEditRows (berp->subrows, field_list, tfp, etp);
35421
berp++;
35422
}
35423
}
35424
35425
35426
static void ParseColumnsForSelectedBulkEditRows
35427
(BulkEditorRowPtr berp,
35428
BulkEdFieldPtr field_list,
35429
TwoFieldBulkEditPtr tfp,
35430
ExistingTextPtr etp)
35431
{
35432
ValNodePtr vnp_from, vnp_to;
35433
CharPtr val_from, val_to;
35434
ApplyValueData avd;
35435
if (berp == NULL || tfp == NULL) return;
35436
35437
avd.field_list = NULL;
35438
avd.text_to_replace = NULL;
35439
avd.where_to_replace = EditApplyFindLocation_anywhere;
35440
avd.etp = etp;
35441
35442
while (berp->object_list != NULL) {
35443
if (berp->selected && berp->subrows == NULL) {
35444
vnp_from = GetBulkEditorRowValueByColumn (berp, tfp->field_from);
35445
vnp_to = GetBulkEditorRowValueByColumn (berp, tfp->field_to);
35446
if (vnp_from != NULL && vnp_to != NULL) {
35447
val_from = (field_list[tfp->field_from].display_func)(vnp_from->data.ptrvalue);
35448
val_to = NULL;
35449
if (StringDoesHaveText (val_from)) {
35450
val_to = ReplaceStringForParse(val_from, tfp->text_portion);
35451
if (StringDoesHaveText (val_to)) {
35452
avd.new_text = val_to;
35453
vnp_to->data.ptrvalue = (field_list[tfp->field_to].set_str_func) (vnp_to->data.ptrvalue, &avd);
35454
}
35455
if (tfp->remove_parsed) {
35456
avd.new_text = val_from;
35457
avd.etp = NULL;
35458
vnp_from->data.ptrvalue = (field_list[tfp->field_from].set_str_func) (vnp_from->data.ptrvalue, &avd);
35459
avd.etp = etp;
35460
}
35461
}
35462
val_from = MemFree (val_from);
35463
val_to = MemFree (val_to);
35464
}
35465
}
35466
ParseColumnsForSelectedBulkEditRows (berp->subrows, field_list, tfp, etp);
35467
berp++;
35468
}
35469
}
35470
35471
35472
static void SwapColumnsForSelectedBulkEditRows
35473
(BulkEditorRowPtr berp,
35474
BulkEdFieldPtr field_list,
35475
Int4 col_from,
35476
Int4 col_to)
35477
{
35478
ValNodePtr vnp_from, vnp_to;
35479
CharPtr val_from, val_to;
35480
ApplyValueData avd;
35481
if (berp == NULL) return;
35482
35483
avd.etp = NULL;
35484
avd.field_list = NULL;
35485
avd.text_to_replace = NULL;
35486
avd.where_to_replace = EditApplyFindLocation_anywhere;
35487
35488
while (berp->object_list != NULL) {
35489
if (berp->selected && berp->subrows == NULL) {
35490
vnp_from = GetBulkEditorRowValueByColumn (berp, col_from);
35491
vnp_to = GetBulkEditorRowValueByColumn (berp, col_to);
35492
if (vnp_from != NULL && vnp_to != NULL) {
35493
val_from = (field_list[col_from].display_func)(vnp_from->data.ptrvalue);
35494
val_to = (field_list[col_to].display_func)(vnp_to->data.ptrvalue);
35495
if (StringDoesHaveText (val_from) || StringDoesHaveText (val_to)) {
35496
avd.new_text = val_to;
35497
vnp_from->data.ptrvalue = (field_list[col_from].set_str_func) (vnp_from->data.ptrvalue, &avd);
35498
35499
avd.new_text = val_from;
35500
vnp_to->data.ptrvalue = (field_list[col_to].set_str_func) (vnp_to->data.ptrvalue, &avd);
35501
}
35502
val_from = MemFree (val_from);
35503
val_to = MemFree (val_to);
35504
}
35505
}
35506
SwapColumnsForSelectedBulkEditRows (berp->subrows, field_list, col_from, col_to);
35507
berp++;
35508
}
35509
}
35510
35511
35512
35513
static void
35514
AddSampleDataForBulkEditorSelectedFeatures
35515
(BulkEditorRowPtr berp,
35516
BulkEdFieldPtr field_list,
35517
Int4 col,
35518
Int4 col_src,
35519
GetSamplePtr gsp,
35520
TextPortionXPtr text_portion)
35521
{
35522
CharPtr str, str_src, str_parse;
35523
ValNodePtr vnp, vnp_src;
35524
Boolean skip;
35525
35526
if (berp == NULL || field_list == NULL || col < 0 || field_list[col].display_func == NULL || gsp == NULL) return;
35527
35528
while (berp->object_list != NULL) {
35529
if (berp->subrows == NULL && berp->selected) {
35530
vnp = GetBulkEditorRowValueByColumn (berp, col);
35531
if (vnp != NULL) {
35532
str = (field_list[col]).display_func (vnp->data.ptrvalue);
35533
if (!StringHasNoText (str)) {
35534
skip = FALSE;
35535
/* only add values if col_src < 0 or data in col_src is not blank */
35536
if (col_src >= 0) {
35537
skip = TRUE;
35538
vnp_src = GetBulkEditorRowValueByColumn (berp, col_src);
35539
if (vnp_src != NULL) {
35540
str_src = (field_list[col_src]).display_func(vnp_src->data.ptrvalue);
35541
if (StringDoesHaveText (str_src)) {
35542
if (text_portion == NULL) {
35543
skip = FALSE;
35544
} else {
35545
str_parse = ReplaceStringForParse(str_src, text_portion);
35546
if (StringDoesHaveText (str_parse)) {
35547
skip = FALSE;
35548
}
35549
str_parse = MemFree (str_parse);
35550
}
35551
}
35552
str_src = MemFree (str_src);
35553
}
35554
}
35555
if (!skip) {
35556
gsp->num_found++;
35557
if (gsp->sample_text == NULL) {
35558
gsp->sample_text = str;
35559
str = NULL;
35560
} else if (StringCmp (str, gsp->sample_text) != 0) {
35561
gsp->all_same = FALSE;
35562
}
35563
}
35564
}
35565
str = MemFree (str);
35566
}
35567
}
35568
AddSampleDataForBulkEditorSelectedFeatures (berp->subrows, field_list, col, col_src, gsp, text_portion);
35569
berp++;
35570
}
35571
}
35572
35573
35574
static GetSamplePtr
35575
GetSampleDataForBulkEditorSelectedFeatures
35576
(BulkEditorRowPtr berp,
35577
BulkEdFieldPtr field_list,
35578
Int4 col,
35579
Int4 col_src,
35580
TextPortionXPtr text_portion)
35581
{
35582
GetSamplePtr gsp;
35583
35584
if (berp == NULL || field_list == NULL || col < 0) return NULL;
35585
35586
gsp = GetSampleNew ();
35587
35588
AddSampleDataForBulkEditorSelectedFeatures(berp, field_list, col, col_src, gsp, text_portion);
35589
35590
return gsp;
35591
}
35592
35593
35594
static void ApplyBulkEdit (ButtoN b)
35595
{
35596
BulkEditorDlgPtr dlg;
35597
RecT r;
35598
GetSamplePtr gsp = NULL;
35599
ExistingTextPtr etp = NULL;
35600
ApplyValueData avd;
35601
OneFieldBulkEditPtr ofp = NULL;
35602
TwoFieldBulkEditPtr tfp = NULL;
35603
35604
dlg = (BulkEditorDlgPtr) GetObjectExtra (b);
35605
if (dlg == NULL) return;
35606
35607
switch (GetValue (dlg->bulk_action)) {
35608
case eBulkRemoveField:
35609
ofp = (OneFieldBulkEditPtr) DialogToPointer (dlg->bulk_remove);
35610
if (ofp != NULL) {
35611
RemoveColumnFromSelectedBulkEditRows (dlg->row_list, ofp->field, dlg->field_list);
35612
}
35613
break;
35614
case eBulkApplyField:
35615
ofp = (OneFieldBulkEditPtr) DialogToPointer (dlg->bulk_apply);
35616
if (ofp != NULL) {
35617
gsp = GetSampleDataForBulkEditorSelectedFeatures (dlg->row_list, dlg->field_list, ofp->field, -1, NULL);
35618
etp = GetExistingTextHandlerInfo (gsp == NULL ? 0 : gsp->num_found, FALSE);
35619
if (etp == NULL || etp->existing_text_choice != eExistingTextChoiceCancel) {
35620
avd.etp = etp;
35621
avd.field_list = NULL;
35622
AddEditApplyDataToApplyValue (AECR_APPLY, ofp->edit_apply, &avd);
35623
ApplyEditColumnFromSelectedBulkEditRows (dlg->row_list, dlg->field_list, ofp->field, &avd);
35624
}
35625
}
35626
break;
35627
case eBulkEditField:
35628
ofp = (OneFieldBulkEditPtr) DialogToPointer (dlg->bulk_edit);
35629
if (ofp != NULL) {
35630
avd.etp = NULL;
35631
avd.field_list = NULL;
35632
AddEditApplyDataToApplyValue (AECR_EDIT, ofp->edit_apply, &avd);
35633
ApplyEditColumnFromSelectedBulkEditRows (dlg->row_list, dlg->field_list, ofp->field, &avd);
35634
}
35635
break;
35636
case eBulkConvertField:
35637
tfp = (TwoFieldBulkEditPtr) DialogToPointer (dlg->bulk_convert);
35638
if (tfp != NULL) {
35639
gsp = GetSampleDataForBulkEditorSelectedFeatures (dlg->row_list, dlg->field_list, tfp->field_to, tfp->field_from, NULL);
35640
etp = GetExistingTextHandlerInfo (gsp == NULL ? 0 : gsp->num_found, FALSE);
35641
if (etp == NULL || etp->existing_text_choice != eExistingTextChoiceCancel) {
35642
ConvertColumnsForSelectedBulkEditRows (dlg->row_list, dlg->field_list, tfp, etp);
35643
}
35644
}
35645
break;
35646
case eBulkParseField:
35647
tfp = (TwoFieldBulkEditPtr) DialogToPointer (dlg->bulk_parse);
35648
if (tfp != NULL) {
35649
gsp = GetSampleDataForBulkEditorSelectedFeatures (dlg->row_list, dlg->field_list, tfp->field_to, tfp->field_from, tfp->text_portion);
35650
etp = GetExistingTextHandlerInfo (gsp == NULL ? 0 : gsp->num_found, FALSE);
35651
if (etp == NULL || etp->existing_text_choice != eExistingTextChoiceCancel) {
35652
ParseColumnsForSelectedBulkEditRows (dlg->row_list, dlg->field_list, tfp, etp);
35653
}
35654
}
35655
break;
35656
case eBulkSwapField:
35657
tfp = (TwoFieldBulkEditPtr) DialogToPointer (dlg->bulk_swap);
35658
if (tfp != NULL) {
35659
SwapColumnsForSelectedBulkEditRows (dlg->row_list, dlg->field_list, tfp->field_from, tfp->field_to);
35660
}
35661
break;
35662
case eBulkCapitalizeField:
35663
ofp = (OneFieldBulkEditPtr) DialogToPointer (dlg->bulk_capitalize);
35664
if (ofp != NULL && ofp->capitalization != NULL && ofp->capitalization->change != eChangeCaseNone) {
35665
CapitalizeColumnsForSelectedBulkEditRows (dlg->row_list, dlg->field_list, ofp->field, ofp->capitalization);
35666
}
35667
break;
35668
}
35669
35670
ofp = OneFieldBulkEditFree (ofp);
35671
tfp = TwoFieldBulkEditFree (tfp);
35672
gsp = GetSampleFree (gsp);
35673
etp = MemFree (etp);
35674
35675
UpdateBulkEdDisplay (dlg);
35676
ObjectRect (dlg->doc, &r);
35677
InvalRect (&r);
35678
Update ();
35679
}
35680
35681
35682
static void BulkEditorCheckAll (ButtoN b)
35683
{
35684
BulkEditorDlgPtr dlg;
35685
RecT r;
35686
35687
dlg = (BulkEditorDlgPtr) GetObjectExtra (b);
35688
if (dlg == NULL) return;
35689
35690
SelectBulkEditorRows (dlg->row_list, TRUE);
35691
UpdateCheckStatus (dlg);
35692
ObjectRect (dlg->doc, &r);
35693
InvalRect (&r);
35694
Update ();
35695
}
35696
35697
35698
static void BulkEditorUncheckAll (ButtoN b)
35699
{
35700
BulkEditorDlgPtr dlg;
35701
RecT r;
35702
35703
dlg = (BulkEditorDlgPtr) GetObjectExtra (b);
35704
if (dlg == NULL) return;
35705
35706
SelectBulkEditorRows (dlg->row_list, FALSE);
35707
UpdateCheckStatus (dlg);
35708
ObjectRect (dlg->doc, &r);
35709
InvalRect (&r);
35710
Update ();
35711
}
35712
35713
static void BulkEditorStringConstraintCheck (ButtoN b)
35714
{
35715
BulkEditorDlgPtr dlg;
35716
RecT r;
35717
Int4 field_num;
35718
StringConstraintXPtr scp;
35719
Boolean val;
35720
35721
dlg = (BulkEditorDlgPtr) GetObjectExtra (b);
35722
if (dlg == NULL) return;
35723
35724
field_num = GetFieldNumFromPopupValue(GetValue (dlg->check_constraint_field), dlg->field_list, FALSE);
35725
scp = DialogToPointer (dlg->check_constraint);
35726
35727
if (GetValue (dlg->sel_unsel_grp) == 1) {
35728
val = TRUE;
35729
} else {
35730
val = FALSE;
35731
}
35732
35733
SelectBulkEditorRowsByStringConstraint (dlg->row_list, dlg->field_list, field_num, scp, val);
35734
35735
scp = StringConstraintXFree (scp);
35736
UpdateCheckStatus (dlg);
35737
35738
ObjectRect (dlg->doc, &r);
35739
InvalRect (&r);
35740
Update ();
35741
}
35742
35743
35744
static void ObjectListToBulkEditorDialog (DialoG d, Pointer data)
35745
{
35746
BulkEditorDlgPtr dlg;
35747
ValNodePtr object_list;
35748
35749
dlg = (BulkEditorDlgPtr) GetObjectExtra (d);
35750
if (dlg == NULL) return;
35751
object_list = (ValNodePtr) data;
35752
35753
dlg->row_list = FreeBulkEditorRows(dlg->row_list, dlg->field_list);
35754
dlg->row_list = MakeBulkEditorRowsFromObjectList (object_list, dlg->field_list, dlg->last_sorted_col, dlg->metadata);
35755
if (dlg->collapse_by_default) {
35756
CollapseAllBulkEditRows (dlg->row_list);
35757
} else {
35758
ExpandAllBulkEditRows (dlg->row_list);
35759
}
35760
ResetClip();
35761
UpdateBulkEdDisplay (dlg);
35762
UpdateCheckStatus (dlg);
35763
}
35764
35765
35766
static Pointer GetSelectedObjectsFromBulkEditorDialog (DialoG d)
35767
{
35768
BulkEditorDlgPtr dlg;
35769
ValNodePtr object_list = NULL;
35770
35771
dlg = (BulkEditorDlgPtr) GetObjectExtra (d);
35772
if (dlg == NULL) return NULL;
35773
35774
GetBulkEditorSelectedObjects (dlg->row_list, &object_list);
35775
return (Pointer) object_list;
35776
}
35777
35778
35779
static DialoG
35780
CreateBulkEditorDialogEx
35781
(GrouP h,
35782
BulkEdFieldPtr field_list,
35783
ValNodePtr feat_list,
35784
SeqEntryPtr sep,
35785
Boolean collapse_by_default,
35786
ClickableCallback single_click_func,
35787
ClickableCallback double_click_func,
35788
Pointer metadata)
35789
{
35790
GrouP p;
35791
BulkEditorDlgPtr dlg;
35792
Int4 width, num_columns = 0;
35793
Int4 i, page_num;
35794
GrouP ed_grp, check_grp, action_grp, page_grp, box_grp;
35795
GrouP g1, g2, a;
35796
ButtoN b;
35797
35798
p = HiddenGroup (h, -1, 0, NULL);
35799
dlg = (BulkEditorDlgPtr) MemNew (sizeof (BulkEditorDlgData));
35800
35801
SetObjectExtra (p, dlg, CleanupBulkEditorDialog); /* need to cleanup values_list */
35802
dlg->dialog = (DialoG) p;
35803
dlg->todialog = ObjectListToBulkEditorDialog;
35804
dlg->fromdialog = GetSelectedObjectsFromBulkEditorDialog;
35805
dlg->testdialog = NULL;
35806
35807
dlg->collapse_by_default = collapse_by_default;
35808
dlg->single_click_func = single_click_func;
35809
dlg->double_click_func = double_click_func;
35810
dlg->field_list = field_list;
35811
dlg->metadata = metadata;
35812
35813
dlg->last_viewed_row = 0;
35814
dlg->last_viewed_col = 0;
35815
dlg->last_sorted_col = 0;
35816
dlg->row_list = MakeBulkEditorRowsFromObjectList(feat_list, dlg->field_list, dlg->last_sorted_col, dlg->metadata);
35817
if (dlg->collapse_by_default) {
35818
CollapseAllBulkEditRows (dlg->row_list);
35819
} else {
35820
ExpandAllBulkEditRows (dlg->row_list);
35821
}
35822
35823
/* count columns, look for editing functions */
35824
dlg->any_editing = FALSE;
35825
for (i = 0; field_list[i].name != NULL; i++) {
35826
if (field_list[i].create_dlg_func != NULL) {
35827
dlg->any_editing = TRUE;
35828
}
35829
num_columns++;
35830
}
35831
dlg->num_columns = num_columns;
35832
/* populate values list */
35833
35834
SelectFont (systemFont);
35835
dlg->col_list = AllocateDocColumnsForFieldList (field_list, &width, dlg->last_sorted_col);
35836
dlg->par_fmt.minLines = 1;
35837
dlg->par_fmt.minHeight = 1;
35838
35839
dlg->title_doc = DocumentPanel (p, width, stdLineHeight);
35840
InitBulkEdTitleDoc (dlg, dlg->title_doc);
35841
SetObjectExtra (dlg->title_doc, dlg, NULL);
35842
SetDocProcs (dlg->title_doc, ClickBulkTitle, NULL, NULL, NULL);
35843
35844
dlg->doc = DocumentPanel (p, width, 10 * stdLineHeight);
35845
SetObjectExtra (dlg->doc, dlg, NULL);
35846
SetDocProcs (dlg->doc, ClickBulkEdField, NULL, NULL, NULL);
35847
SetDocShade (dlg->doc, DrawBulkEdCell, NULL, HighlightBulkEdField, NULL);
35848
35849
ed_grp = HiddenGroup (p, 0, 0, NULL);
35850
dlg->editor_list = (DialoG PNTR) MemNew (sizeof(DialoG) * dlg->num_columns);
35851
for (i = 0; field_list[i].name != NULL; i++) {
35852
if (dlg->field_list[i].create_dlg_func == NULL) {
35853
dlg->editor_list[i] = NULL;
35854
} else {
35855
dlg->editor_list[i] = (dlg->field_list[i].create_dlg_func) (ed_grp, field_list[i].name, sep);
35856
Hide (dlg->editor_list[i]);
35857
}
35858
}
35859
35860
box_grp = HiddenGroup (p, 0, 2, NULL);
35861
35862
/* group that contains controls for checking and unchecking features */
35863
check_grp = NormalGroup (box_grp, -1, 0, "Check Features", programFont, NULL);
35864
SetGroupSpacing (check_grp, 10, 10);
35865
g1 = HiddenGroup (check_grp, 3, 0, NULL);
35866
SetGroupSpacing (g1, 10, 10);
35867
b = PushButton (g1, "Check All Features", BulkEditorCheckAll);
35868
SetObjectExtra (b, dlg, NULL);
35869
b = PushButton (g1, "Uncheck All Features", BulkEditorUncheckAll);
35870
SetObjectExtra (b, dlg, NULL);
35871
dlg->check_status = StaticPrompt (g1, "0 features are checked", 20 * stdCharWidth, dialogTextHeight, programFont, 'l');
35872
35873
g2 = HiddenGroup (check_grp, 4, 0, NULL);
35874
dlg->sel_unsel_grp = HiddenGroup (g2, 0, 2, NULL);
35875
RadioButton (dlg->sel_unsel_grp, "Check features where");
35876
RadioButton (dlg->sel_unsel_grp, "Uncheck features where");
35877
SetValue (dlg->sel_unsel_grp, 1);
35878
dlg->check_constraint_field = MakeBulkEditorFieldListPopup (g2, dlg->field_list, FALSE);
35879
dlg->check_constraint = StringConstraintDialogX (g2, NULL, FALSE);
35880
b = PushButton (g2, "Apply", BulkEditorStringConstraintCheck);
35881
SetObjectExtra (b, dlg, NULL);
35882
35883
if (dlg->any_editing) {
35884
/* group that contains controls for applying actions to check features */
35885
action_grp = NormalGroup (box_grp, -1, 0, "Action for Checked Features", programFont, NULL);
35886
a = HiddenGroup (action_grp, 2, 0, NULL);
35887
SetGroupSpacing (a, 10, 10);
35888
dlg->bulk_action = PopupList (a, TRUE, ChangeBulkEditorAction);
35889
SetObjectExtra (dlg->bulk_action, dlg, NULL);
35890
PopupItem (dlg->bulk_action, "Apply");
35891
PopupItem (dlg->bulk_action, "Edit");
35892
PopupItem (dlg->bulk_action, "Convert");
35893
PopupItem (dlg->bulk_action, "Parse");
35894
PopupItem (dlg->bulk_action, "Swap");
35895
PopupItem (dlg->bulk_action, "Remove");
35896
PopupItem (dlg->bulk_action, "Change Case");
35897
SetValue (dlg->bulk_action, 2);
35898
page_grp = HiddenGroup (a, 0, 0, NULL);
35899
page_num = 0;
35900
dlg->action_pages[page_num] = HiddenGroup (page_grp, 2, 0, NULL);
35901
dlg->bulk_apply = OneFieldBulkEditDialog (dlg->action_pages[page_num], eBulkApplyField, NULL, NULL, dlg->field_list);
35902
35903
page_num++;
35904
dlg->action_pages[page_num] = HiddenGroup (page_grp, 2, 0, NULL);
35905
dlg->bulk_edit = OneFieldBulkEditDialog (dlg->action_pages[page_num], eBulkEditField, NULL, NULL, dlg->field_list);
35906
35907
page_num++;
35908
dlg->action_pages[page_num] = HiddenGroup (page_grp, 2, 0, NULL);
35909
dlg->bulk_convert = TwoFieldBulkEditDialog (dlg->action_pages[page_num], eBulkConvertField, NULL, NULL, dlg->field_list, FALSE);
35910
35911
page_num++;
35912
dlg->action_pages[page_num] = HiddenGroup (page_grp, 2, 0, NULL);
35913
dlg->bulk_parse = TwoFieldBulkEditDialog (dlg->action_pages[page_num], eBulkParseField, NULL, NULL, dlg->field_list, FALSE);
35914
35915
page_num++;
35916
dlg->action_pages[page_num] = HiddenGroup (page_grp, 2, 0, NULL);
35917
dlg->bulk_swap = TwoFieldBulkEditDialog (dlg->action_pages[page_num], eBulkSwapField, NULL, NULL, dlg->field_list, FALSE);
35918
35919
page_num++;
35920
dlg->action_pages[page_num] = HiddenGroup (page_grp, 2, 0, NULL);
35921
dlg->bulk_remove = OneFieldBulkEditDialog (dlg->action_pages[page_num], eBulkRemoveField, NULL, NULL, dlg->field_list);
35922
35923
page_num++;
35924
dlg->action_pages[page_num] = HiddenGroup (page_grp, 2, 0, NULL);
35925
dlg->bulk_capitalize = OneFieldBulkEditDialog (dlg->action_pages[page_num], eBulkCapitalizeField, NULL, NULL, dlg->field_list);
35926
35927
AlignObjects (ALIGN_CENTER, (HANDLE) dlg->action_pages[0],
35928
(HANDLE) dlg->action_pages[1],
35929
(HANDLE) dlg->action_pages[2],
35930
(HANDLE) dlg->action_pages[3],
35931
(HANDLE) dlg->action_pages[4],
35932
(HANDLE) dlg->action_pages[5],
35933
(HANDLE) dlg->action_pages[6],
35934
NULL);
35935
35936
b = PushButton (action_grp, "Apply to Checked Features", ApplyBulkEdit);
35937
SetObjectExtra (b, dlg, NULL);
35938
AlignObjects (ALIGN_CENTER, (HANDLE) a, (HANDLE) b, NULL);
35939
}
35940
35941
35942
AlignObjects (ALIGN_CENTER, (HANDLE) dlg->title_doc, (HANDLE) dlg->doc, (HANDLE) ed_grp, (HANDLE) box_grp, NULL);
35943
35944
UpdateBulkEdDisplay (dlg);
35945
UpdateCheckStatus (dlg);
35946
ChangeBulkEditorAction (dlg->bulk_action);
35947
35948
return (DialoG) p;
35949
}
35950
35951
35952
NLM_EXTERN DialoG
35953
CreateBulkEditorDialog
35954
(GrouP h,
35955
BulkEdFieldPtr field_list,
35956
ValNodePtr feat_list,
35957
SeqEntryPtr sep,
35958
Boolean collapse_by_default,
35959
ClickableCallback single_click_func,
35960
ClickableCallback double_click_func)
35961
{
35962
return CreateBulkEditorDialogEx (h, field_list, feat_list, sep, collapse_by_default,
35963
single_click_func, double_click_func, NULL);
35964
}
35965
35966
35967
static Pointer BulkGetLocation (Uint1 data_choice, Pointer data, Pointer metadata)
35968
{
35969
SeqLocPtr slp;
35970
SeqFeatPtr sfp = (SeqFeatPtr) data;
35971
35972
if (sfp == NULL) return NULL;
35973
slp = (SeqLocPtr) AsnIoMemCopy (sfp->location, (AsnReadFunc) SeqLocAsnRead, (AsnWriteFunc) SeqLocAsnWrite);
35974
return slp;
35975
}
35976
35977
static void BulkSetLocation (Pointer target, Pointer data)
35978
{
35979
SeqFeatPtr sfp = (SeqFeatPtr) target;
35980
SeqLocPtr slp = (SeqLocPtr) data;
35981
if (sfp == NULL) return;
35982
sfp->location = SeqLocFree (sfp->location);
35983
sfp->location = (SeqLocPtr) AsnIoMemCopy (slp, (AsnReadFunc) SeqLocAsnRead, (AsnWriteFunc) SeqLocAsnWrite);
35984
}
35985
35986
static Int4 BulkFormatLocation (ColPtr col, CharPtr name)
35987
{
35988
if (col == NULL) return 0;
35989
35990
col->pixWidth = MAX (15, StringLen (name)) * stdCharWidth;
35991
col->pixInset = 1;
35992
col->charWidth = 0;
35993
col->charInset = 0;
35994
col->font = NULL;
35995
col->just = 'l';
35996
col->wrap = 1;
35997
col->bar = 0;
35998
col->underline = 0;
35999
col->left = 0;
36000
return col->pixWidth;
36001
}
36002
36003
static void BulkFreeLocation (Pointer data)
36004
{
36005
SeqLocPtr slp = (SeqLocPtr) data;
36006
36007
slp = SeqLocFree (slp);
36008
}
36009
36010
static CharPtr BulkDisplayLocation (Pointer data)
36011
{
36012
SeqLocPtr slp = (SeqLocPtr) data;
36013
36014
return SeqLocPrint (slp);
36015
}
36016
36017
static DialoG BulkNucLocationDialog (GrouP g, CharPtr name, SeqEntryPtr sep)
36018
{
36019
return CreateIntervalEditorDialog (g, NULL, 4, 2, sep, TRUE, FALSE);
36020
}
36021
36022
static Pointer BulkCopyLocation (Pointer data)
36023
{
36024
SeqLocPtr orig = (SeqLocPtr) data;
36025
SeqLocPtr new_loc;
36026
36027
if (orig == NULL) return NULL;
36028
new_loc = (SeqLocPtr) AsnIoMemCopy ((Pointer) orig,
36029
(AsnReadFunc) SeqLocAsnRead,
36030
(AsnWriteFunc) SeqLocAsnWrite);
36031
36032
return new_loc;
36033
}
36034
36035
NLM_EXTERN Int4 BulkFormatSimpleText (ColPtr col, CharPtr name)
36036
{
36037
if (col == NULL) return 0;
36038
36039
col->pixWidth = (MAX (15, StringLen (name)) + 3) * MaxCharWidth();
36040
col->pixInset = 0;
36041
col->charWidth = 0;
36042
col->charInset = 0;
36043
col->font = NULL;
36044
col->just = 'l';
36045
col->wrap = 1;
36046
col->bar = 0;
36047
col->underline = 0;
36048
col->left = 0;
36049
return col->pixWidth;
36050
}
36051
36052
NLM_EXTERN void BulkFreeSimpleText (Pointer data)
36053
{
36054
CharPtr str = (CharPtr) data;
36055
36056
str = MemFree (str);
36057
}
36058
36059
NLM_EXTERN CharPtr BulkDisplaySimpleText (Pointer data)
36060
{
36061
CharPtr str = (CharPtr) data;
36062
if (StringHasNoText (str)) {
36063
return NULL;
36064
} else {
36065
return StringSave ((CharPtr) data);
36066
}
36067
}
36068
36069
typedef struct bulksimpletext {
36070
DIALOG_MESSAGE_BLOCK
36071
TexT txt;
36072
} BulkSimpleTextData, PNTR BulkSimpleTextPtr;
36073
36074
static void StringToBulkSimpleTextDialog (DialoG d, Pointer data)
36075
{
36076
BulkSimpleTextPtr dlg;
36077
CharPtr str;
36078
36079
dlg = (BulkSimpleTextPtr) GetObjectExtra (d);
36080
if (dlg == NULL) return;
36081
36082
str = (CharPtr) data;
36083
if (str == NULL) {
36084
SetTitle (dlg->txt, "");
36085
} else {
36086
SetTitle (dlg->txt, str);
36087
}
36088
}
36089
36090
static Pointer BulkSimpleTextDialogToString (DialoG d)
36091
{
36092
BulkSimpleTextPtr dlg;
36093
36094
dlg = (BulkSimpleTextPtr) GetObjectExtra (d);
36095
if (dlg == NULL) return NULL;
36096
36097
return (Pointer) SaveStringFromText (dlg->txt);
36098
}
36099
36100
36101
36102
static DialoG BulkSimpleTextDialogEx (GrouP g, CharPtr name, SeqEntryPtr sep, Boolean use_scroll)
36103
{
36104
BulkSimpleTextPtr dlg;
36105
GrouP p;
36106
36107
p = HiddenGroup (g, 2, 0, NULL);
36108
SetGroupSpacing (p, 10, 10);
36109
dlg = (BulkSimpleTextPtr) MemNew (sizeof(BulkSimpleTextData));
36110
36111
SetObjectExtra (p, dlg, StdCleanupExtraProc);
36112
dlg->dialog = (DialoG) p;
36113
dlg->todialog = StringToBulkSimpleTextDialog;
36114
dlg->fromdialog = BulkSimpleTextDialogToString;
36115
dlg->testdialog = NULL;
36116
36117
StaticPrompt (p, name, 0, dialogTextHeight, programFont, 'l');
36118
if (use_scroll) {
36119
dlg->txt = ScrollText (p, 30, 4, programFont, TRUE, NULL);
36120
} else {
36121
dlg->txt = DialogText (p, "", 20, NULL);
36122
}
36123
36124
return (DialoG) p;
36125
}
36126
36127
NLM_EXTERN DialoG BulkSimpleTextDialog (GrouP g, CharPtr name, SeqEntryPtr sep)
36128
{
36129
return BulkSimpleTextDialogEx (g, name, sep, FALSE);
36130
}
36131
36132
static DialoG BulkSimpleTextScrollDialog (GrouP g, CharPtr name, SeqEntryPtr sep)
36133
{
36134
return BulkSimpleTextDialogEx (g, name, sep, TRUE);
36135
}
36136
36137
NLM_EXTERN Pointer BulkSimpleTextCopy (Pointer data)
36138
{
36139
CharPtr orig = (CharPtr) data;
36140
CharPtr new_str = StringSave (orig);
36141
return new_str;
36142
}
36143
36144
static Int4 BulkFormatTrueFalse (ColPtr col, CharPtr name)
36145
{
36146
size_t box_width = stdLineHeight - 3;
36147
if (col == NULL) return 0;
36148
36149
col->pixWidth = MAX (box_width, (StringLen (name) + 2) * MaxCharWidth());
36150
col->pixInset = 0;
36151
col->charWidth = 0;
36152
col->charInset = 0;
36153
col->font = NULL;
36154
col->just = 'l';
36155
col->wrap = 0;
36156
col->bar = 0;
36157
col->underline = 0;
36158
col->left = 0;
36159
return col->pixWidth;
36160
}
36161
36162
static void BulkDrawTrueFalse (Pointer p, RectPtr r)
36163
{
36164
RecT rct;
36165
36166
if (r == NULL) return;
36167
36168
rct = *r;
36169
rct.bottom = rct.top + stdLineHeight - 4;
36170
rct.right = rct.left + stdLineHeight - 4;
36171
InsetRect (&rct, 2, 2);
36172
FrameRect (&rct);
36173
36174
if (p != NULL) {
36175
MoveTo (rct.left, rct.top);
36176
LineTo (rct.right - 1, rct.bottom - 1);
36177
MoveTo (rct.left, rct.bottom - 1);
36178
LineTo (rct.right - 1, rct.top);
36179
}
36180
}
36181
36182
static Pointer BulkReleaseTrueFalse (Pointer p)
36183
{
36184
if (p == NULL) {
36185
p = (Pointer) StringSave ("TRUE");
36186
} else {
36187
p = MemFree (p);
36188
}
36189
return p;
36190
}
36191
36192
36193
static void BulkSetPseudo (Pointer target, Pointer val)
36194
{
36195
SeqFeatPtr sfp = (SeqFeatPtr) target;
36196
if (sfp == NULL) return;
36197
if (StringHasNoText ((CharPtr)val)) {
36198
sfp->pseudo = FALSE;
36199
} else {
36200
sfp->pseudo = TRUE;
36201
}
36202
}
36203
36204
static Pointer BulkGetPseudo (Pointer data)
36205
{
36206
SeqFeatPtr sfp = (SeqFeatPtr) data;
36207
if (sfp == NULL || ! sfp->pseudo) {
36208
return NULL;
36209
} else {
36210
return StringSave ("TRUE");
36211
}
36212
}
36213
36214
static void BulkSetComment (Pointer target, Pointer data)
36215
{
36216
CharPtr str = (CharPtr) data;
36217
SeqFeatPtr sfp = (SeqFeatPtr) target;
36218
if (sfp == NULL) return;
36219
36220
sfp->comment = MemFree (sfp->comment);
36221
if (str != NULL) {
36222
sfp->comment = StringSave (str);
36223
}
36224
}
36225
36226
static Pointer BulkGetComment (Uint1 data_choice, Pointer data, Pointer metadata)
36227
{
36228
SeqFeatPtr sfp = (SeqFeatPtr) data;
36229
if (sfp == NULL || StringHasNoText (sfp->comment)) {
36230
return NULL;
36231
} else {
36232
return (Pointer) StringSave (sfp->comment);
36233
}
36234
}
36235
36236
static void BulkCDSSetProtein (Pointer target, Pointer data)
36237
{
36238
SeqFeatXrefPtr xref;
36239
ProtRefPtr prp = NULL;
36240
BioseqPtr prot_bsp;
36241
SeqFeatPtr prot_feat;
36242
SeqMgrFeatContext fcontext;
36243
ValNodePtr prot_name_list = NULL, vnp;
36244
SeqFeatPtr sfp = (SeqFeatPtr) target;
36245
if (sfp == NULL) return;
36246
36247
prot_name_list = (ValNodePtr) data;
36248
36249
xref = sfp->xref;
36250
while (xref != NULL && xref->data.choice != SEQFEAT_PROT) {
36251
xref = xref->next;
36252
}
36253
if (xref != NULL) {
36254
prp = xref->data.value.ptrvalue;
36255
}
36256
36257
if (prp == NULL) {
36258
if (sfp->data.choice == SEQFEAT_PROT) {
36259
prp = (ProtRefPtr) sfp->data.value.ptrvalue;
36260
} else if (sfp->data.choice == SEQFEAT_CDREGION) {
36261
prot_bsp = BioseqFindFromSeqLoc (sfp->product);
36262
prot_feat = SeqMgrGetNextFeature (prot_bsp, NULL, SEQFEAT_PROT, FEATDEF_PROT, &fcontext);
36263
if (prot_feat == NULL && prot_name_list != NULL) {
36264
prot_feat = CreateNewFeatureOnBioseq (prot_bsp, SEQFEAT_PROT, NULL);
36265
prp = ProtRefNew ();
36266
prot_feat->data.value.ptrvalue = prp;
36267
SeqMgrIndexFeatures (prot_bsp->idx.entityID, NULL);
36268
}
36269
if (prot_feat != NULL) {
36270
prp = (ProtRefPtr) prot_feat->data.value.ptrvalue;
36271
}
36272
}
36273
}
36274
36275
if (prp == NULL && prot_name_list != NULL) {
36276
xref = SeqFeatXrefNew ();
36277
prp = ProtRefNew ();
36278
xref->data.choice = SEQFEAT_PROT;
36279
xref->data.value.ptrvalue = prp;
36280
xref->next = sfp->xref;
36281
sfp->xref = xref;
36282
}
36283
if (prp != NULL) {
36284
prp->name = ValNodeFreeData (prp->name);
36285
for (vnp = prot_name_list; vnp != NULL; vnp = vnp->next) {
36286
ValNodeAddPointer (&prp->name, vnp->choice, StringSave (vnp->data.ptrvalue));
36287
}
36288
}
36289
36290
}
36291
36292
static Pointer BulkCDSGetProtein (Uint1 data_choice, Pointer data, Pointer metadata)
36293
{
36294
SeqFeatXrefPtr xref;
36295
ProtRefPtr prp = NULL;
36296
BioseqPtr prot_bsp;
36297
SeqFeatPtr prot_feat;
36298
SeqMgrFeatContext fcontext;
36299
ValNodePtr prot_name_list = NULL, vnp;
36300
SeqFeatPtr sfp = (SeqFeatPtr) data;
36301
36302
if (sfp == NULL) return NULL;
36303
36304
xref = sfp->xref;
36305
while (xref != NULL && xref->data.choice != SEQFEAT_PROT) {
36306
xref = xref->next;
36307
}
36308
if (xref != NULL) {
36309
prp = xref->data.value.ptrvalue;
36310
}
36311
36312
if (prp == NULL) {
36313
if (sfp->data.choice == SEQFEAT_PROT) {
36314
prp = (ProtRefPtr) sfp->data.value.ptrvalue;
36315
} else if (sfp->data.choice == SEQFEAT_CDREGION) {
36316
prot_bsp = BioseqFindFromSeqLoc (sfp->product);
36317
prot_feat = SeqMgrGetNextFeature (prot_bsp, NULL, SEQFEAT_PROT, FEATDEF_PROT, &fcontext);
36318
if (prot_feat != NULL) {
36319
prp = (ProtRefPtr) prot_feat->data.value.ptrvalue;
36320
}
36321
}
36322
}
36323
36324
if (prp != NULL) {
36325
for (vnp = prp->name; vnp != NULL; vnp = vnp->next) {
36326
ValNodeAddPointer (&prot_name_list, vnp->choice, StringSave (vnp->data.ptrvalue));
36327
}
36328
}
36329
36330
return prot_name_list;
36331
}
36332
36333
static Pointer BulkCDSCopyProtein (Pointer data)
36334
{
36335
ValNodePtr new_prot_name_list = NULL, prot_name_list, vnp;
36336
36337
prot_name_list = (ValNodePtr) data;
36338
36339
for (vnp = prot_name_list; vnp != NULL; vnp = vnp->next) {
36340
ValNodeAddPointer (&new_prot_name_list, vnp->choice, StringSave (vnp->data.ptrvalue));
36341
}
36342
return new_prot_name_list;
36343
}
36344
36345
static Int4 BulkCDSFormatProtein (ColPtr col, CharPtr name)
36346
{
36347
if (col == NULL) return 0;
36348
36349
col->pixWidth = MAX (15, StringLen (name)) * MaxCharWidth();
36350
col->pixInset = 0;
36351
col->charWidth = 0;
36352
col->charInset = 0;
36353
col->font = NULL;
36354
col->just = 'l';
36355
col->wrap = 1;
36356
col->bar = 0;
36357
col->underline = 0;
36358
col->left = 0;
36359
return col->pixWidth;
36360
}
36361
36362
static CharPtr BulkCDSDisplayProtein (Pointer data)
36363
{
36364
ValNodePtr prot_name_list, vnp;
36365
CharPtr prot_text;
36366
Int4 text_len = 1;
36367
36368
if (data == NULL) return NULL;
36369
prot_name_list = (ValNodePtr) data;
36370
for (vnp = prot_name_list; vnp != NULL; vnp = vnp->next) {
36371
text_len += StringLen (vnp->data.ptrvalue) + 1;
36372
}
36373
prot_text = (CharPtr) MemNew (sizeof (Char) * text_len);
36374
prot_text[0] = 0;
36375
for (vnp = prot_name_list; vnp != NULL; vnp = vnp->next) {
36376
StringCat (prot_text, vnp->data.ptrvalue);
36377
if (vnp->next != NULL) {
36378
StringCat (prot_text, ";");
36379
}
36380
}
36381
return prot_text;
36382
}
36383
36384
36385
static Pointer BulkCDSSetProteinString (Pointer curr_val, ApplyValuePtr avp)
36386
{
36387
CharPtr curr_val_str;
36388
CharPtr new_str, name_str, cp;
36389
ValNodePtr name_list;
36390
36391
name_list = (ValNodePtr) curr_val;
36392
curr_val_str = BulkCDSDisplayProtein (name_list);
36393
name_list = ValNodeFreeData (name_list);
36394
36395
new_str = HandleApplyValue (curr_val_str, avp);
36396
36397
name_str = new_str;
36398
cp = StringChr (name_str, ';');
36399
while (cp != NULL) {
36400
*cp = 0;
36401
ValNodeAddPointer (&name_list, 0, StringSave (name_str));
36402
*cp = ';';
36403
name_str = cp + 1;
36404
cp = StringChr (name_str, ';');
36405
}
36406
ValNodeAddPointer (&name_list, 0, StringSave (name_str));
36407
new_str = MemFree (new_str);
36408
36409
return name_list;
36410
}
36411
36412
36413
static void BulkCDSFreeProtein (Pointer data)
36414
{
36415
ValNodePtr prot_name_list = (ValNodePtr) data;
36416
36417
ValNodeFreeData (prot_name_list);
36418
}
36419
36420
static DialoG BulkCDSProteinDialog (GrouP g, CharPtr name, SeqEntryPtr sep)
36421
{
36422
return CreateVisibleStringDialog (g, 3, -1, 25);
36423
}
36424
36425
static void BulkCDSSetProteinDesc (Pointer target, Pointer data)
36426
{
36427
SeqFeatXrefPtr xref;
36428
ProtRefPtr prp = NULL;
36429
BioseqPtr prot_bsp;
36430
SeqFeatPtr prot_feat;
36431
SeqMgrFeatContext fcontext;
36432
CharPtr prot_desc;
36433
SeqFeatPtr sfp = (SeqFeatPtr) target;
36434
if (sfp == NULL) return;
36435
36436
prot_desc = (CharPtr) data;
36437
36438
xref = sfp->xref;
36439
while (xref != NULL && xref->data.choice != SEQFEAT_PROT) {
36440
xref = xref->next;
36441
}
36442
if (xref != NULL) {
36443
prp = xref->data.value.ptrvalue;
36444
}
36445
36446
if (prp == NULL) {
36447
if (sfp->data.choice == SEQFEAT_PROT) {
36448
prp = (ProtRefPtr) sfp->data.value.ptrvalue;
36449
} else if (sfp->data.choice == SEQFEAT_CDREGION) {
36450
prot_bsp = BioseqFindFromSeqLoc (sfp->product);
36451
prot_feat = SeqMgrGetNextFeature (prot_bsp, NULL, SEQFEAT_PROT, FEATDEF_PROT, &fcontext);
36452
if (prot_feat == NULL && !StringHasNoText (prot_desc)) {
36453
prot_feat = CreateNewFeatureOnBioseq (prot_bsp, SEQFEAT_PROT, NULL);
36454
prp = ProtRefNew ();
36455
prot_feat->data.value.ptrvalue = prp;
36456
SeqMgrIndexFeatures (prot_bsp->idx.entityID, NULL);
36457
}
36458
if (prot_feat != NULL) {
36459
prp = (ProtRefPtr) prot_feat->data.value.ptrvalue;
36460
}
36461
}
36462
}
36463
36464
if (prp == NULL && !StringHasNoText (prot_desc)) {
36465
xref = SeqFeatXrefNew ();
36466
prp = ProtRefNew ();
36467
xref->data.choice = SEQFEAT_PROT;
36468
xref->data.value.ptrvalue = prp;
36469
xref->next = sfp->xref;
36470
sfp->xref = xref;
36471
}
36472
if (prp != NULL) {
36473
prp->desc = StringSave (prot_desc);
36474
}
36475
36476
}
36477
36478
36479
static Pointer BulkCDSGetProteinDesc (Uint1 data_choice, Pointer data, Pointer metadata)
36480
{
36481
SeqFeatXrefPtr xref;
36482
ProtRefPtr prp = NULL;
36483
BioseqPtr prot_bsp;
36484
SeqFeatPtr prot_feat;
36485
SeqMgrFeatContext fcontext;
36486
CharPtr prot_desc = NULL;
36487
SeqFeatPtr sfp = (SeqFeatPtr) data;
36488
36489
if (sfp == NULL) return NULL;
36490
36491
xref = sfp->xref;
36492
while (xref != NULL && xref->data.choice != SEQFEAT_PROT) {
36493
xref = xref->next;
36494
}
36495
if (xref != NULL) {
36496
prp = xref->data.value.ptrvalue;
36497
}
36498
36499
if (prp == NULL) {
36500
if (sfp->data.choice == SEQFEAT_PROT) {
36501
prp = (ProtRefPtr) sfp->data.value.ptrvalue;
36502
} else if (sfp->data.choice == SEQFEAT_CDREGION) {
36503
prot_bsp = BioseqFindFromSeqLoc (sfp->product);
36504
prot_feat = SeqMgrGetNextFeature (prot_bsp, NULL, SEQFEAT_PROT, FEATDEF_PROT, &fcontext);
36505
if (prot_feat != NULL) {
36506
prp = (ProtRefPtr) prot_feat->data.value.ptrvalue;
36507
}
36508
}
36509
}
36510
36511
if (prp != NULL) {
36512
prot_desc = StringSave (prp->desc);
36513
}
36514
36515
return prot_desc;
36516
}
36517
36518
36519
static void BulkGeneSetLocus (Pointer target, Pointer data)
36520
{
36521
CharPtr str = (CharPtr) data;
36522
GeneRefPtr grp;
36523
SeqFeatPtr sfp = (SeqFeatPtr) target;
36524
36525
if (sfp == NULL || sfp->idx.subtype != FEATDEF_GENE) return;
36526
36527
grp = (GeneRefPtr) sfp->data.value.ptrvalue;
36528
if (grp == NULL) {
36529
grp = GeneRefNew();
36530
sfp->data.value.ptrvalue = grp;
36531
}
36532
grp->locus = MemFree (grp->locus);
36533
if (str != NULL) {
36534
grp->locus = StringSave (str);
36535
}
36536
}
36537
36538
static Pointer BulkGeneGetLocus (Uint1 data_choice, Pointer data, Pointer metadata)
36539
{
36540
GeneRefPtr grp;
36541
SeqFeatPtr sfp = (SeqFeatPtr) data;
36542
36543
if (sfp == NULL || sfp->idx.subtype != FEATDEF_GENE || sfp->data.value.ptrvalue == NULL) {
36544
return NULL;
36545
}
36546
grp = (GeneRefPtr) sfp->data.value.ptrvalue;
36547
if (StringHasNoText (grp->locus)) {
36548
return NULL;
36549
} else {
36550
return (Pointer) StringSave (grp->locus);
36551
}
36552
}
36553
36554
static void BulkGeneSetLocusTag (Pointer target, Pointer data)
36555
{
36556
CharPtr str = (CharPtr) data;
36557
GeneRefPtr grp;
36558
SeqFeatPtr sfp = (SeqFeatPtr) target;
36559
36560
if (sfp == NULL || sfp->idx.subtype != FEATDEF_GENE) return;
36561
36562
grp = (GeneRefPtr) sfp->data.value.ptrvalue;
36563
if (grp == NULL) {
36564
grp = GeneRefNew();
36565
sfp->data.value.ptrvalue = grp;
36566
}
36567
grp->locus_tag = MemFree (grp->locus_tag);
36568
if (str != NULL) {
36569
grp->locus_tag = StringSave (str);
36570
}
36571
}
36572
36573
static Pointer BulkGeneGetLocusTag (Uint1 data_choice, Pointer data, Pointer metadata)
36574
{
36575
GeneRefPtr grp;
36576
SeqFeatPtr sfp = (SeqFeatPtr) data;
36577
36578
if (sfp == NULL || sfp->idx.subtype != FEATDEF_GENE || sfp->data.value.ptrvalue == NULL) {
36579
return NULL;
36580
}
36581
grp = (GeneRefPtr) sfp->data.value.ptrvalue;
36582
if (StringHasNoText (grp->locus_tag)) {
36583
return NULL;
36584
} else {
36585
return (Pointer) StringSave (grp->locus_tag);
36586
}
36587
}
36588
36589
static void BulkGeneSetDescription (Pointer target, Pointer data)
36590
{
36591
CharPtr str = (CharPtr) data;
36592
GeneRefPtr grp;
36593
SeqFeatPtr sfp = (SeqFeatPtr) target;
36594
36595
if (sfp == NULL || sfp->idx.subtype != FEATDEF_GENE) return;
36596
36597
grp = (GeneRefPtr) sfp->data.value.ptrvalue;
36598
if (grp == NULL) {
36599
grp = GeneRefNew();
36600
sfp->data.value.ptrvalue = grp;
36601
}
36602
grp->desc = MemFree (grp->desc);
36603
if (str != NULL) {
36604
grp->desc = StringSave (str);
36605
}
36606
}
36607
36608
static Pointer BulkGeneGetDescription (Uint1 data_choice, Pointer data, Pointer metadata)
36609
{
36610
GeneRefPtr grp;
36611
SeqFeatPtr sfp = (SeqFeatPtr) data;
36612
36613
if (sfp == NULL || sfp->idx.subtype != FEATDEF_GENE || sfp->data.value.ptrvalue == NULL) {
36614
return NULL;
36615
}
36616
grp = (GeneRefPtr) sfp->data.value.ptrvalue;
36617
if (StringHasNoText (grp->desc)) {
36618
return NULL;
36619
} else {
36620
return (Pointer) StringSave (grp->desc);
36621
}
36622
}
36623
36624
36625
static void BulkRNASetProduct (Pointer target, Pointer data)
36626
{
36627
RnaRefPtr rrp;
36628
CharPtr rna_product;
36629
SeqFeatPtr sfp = (SeqFeatPtr) target;
36630
36631
if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA) return;
36632
36633
rna_product = (CharPtr) data;
36634
36635
rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
36636
if (rrp == NULL && !StringHasNoText (rna_product)) {
36637
rrp = RnaRefNew ();
36638
rrp->ext.choice = 1;
36639
sfp->data.value.ptrvalue = rrp;
36640
}
36641
if (rrp->ext.choice == 0 && !StringHasNoText (rna_product)) {
36642
rrp->ext.choice = 1;
36643
} else if (rrp->ext.choice == 1 && StringHasNoText (rna_product)) {
36644
rrp->ext.choice = 0;
36645
rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
36646
}
36647
36648
if (rrp != NULL && rrp->ext.choice == 1) {
36649
rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
36650
rrp->ext.value.ptrvalue = StringSave (rna_product);
36651
}
36652
}
36653
36654
static Pointer BulkRNAGetProduct (Uint1 data_choice, Pointer data, Pointer metadata)
36655
{
36656
RnaRefPtr rrp;
36657
CharPtr rna_product = NULL;
36658
SeqFeatPtr sfp = (SeqFeatPtr) data;
36659
36660
if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA) return NULL;
36661
36662
rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
36663
if (rrp != NULL) {
36664
if (rrp->ext.choice == 1) {
36665
rna_product = StringSave( rrp->ext.value.ptrvalue);
36666
}
36667
}
36668
36669
36670
return rna_product;
36671
}
36672
36673
static Boolean IsBulkEditableRNA (SeqFeatPtr sfp)
36674
{
36675
RnaRefPtr rrp;
36676
36677
if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA) {
36678
return FALSE;
36679
}
36680
rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
36681
if (rrp != NULL && rrp->ext.choice != 1 && rrp->ext.choice != 0) {
36682
return FALSE;
36683
} else {
36684
return TRUE;
36685
}
36686
}
36687
36688
36689
/* template for setting simple text strings */
36690
NLM_EXTERN Pointer BulkSetSimpleTextString (Pointer curr_val, ApplyValuePtr avp)
36691
{
36692
CharPtr curr_val_str;
36693
36694
curr_val_str = (CharPtr)curr_val;
36695
return HandleApplyValue (curr_val_str, avp);
36696
}
36697
36698
/* for now, disallow pseudo editing and display. To add back, put in this line:
36699
{ "pseudo", BulkSetPseudo, BulkGetPseudo, NULL, NULL, NULL, BulkFormatTrueFalse, BulkDrawTrueFalse, BulkReleaseTrueFalse },
36700
*/
36701
/* for now, disallow location editing (but continue display). To add back, use BulkNucLocationDialog in dialog. */
36702
static BulkEdFieldData bulk_cds_fields[] = {
36703
{ "protein name", BulkCDSSetProtein, BulkCDSSetProteinString, BulkCDSGetProtein, BulkCDSDisplayProtein, BulkCDSFreeProtein, BulkCDSProteinDialog, BulkCDSFormatProtein, NULL, NULL, BulkCDSCopyProtein },
36704
{ "protein description", BulkCDSSetProteinDesc, BulkSetSimpleTextString, BulkCDSGetProteinDesc, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
36705
{ "location", BulkSetLocation, NULL, BulkGetLocation, BulkDisplayLocation, BulkFreeLocation, NULL, BulkFormatLocation, NULL, NULL, BulkCopyLocation },
36706
{ "comment", BulkSetComment, BulkSetSimpleTextString, BulkGetComment, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextScrollDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
36707
{ NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL}};
36708
36709
static BulkEdFieldData bulk_gene_fields[] = {
36710
{ "locus", BulkGeneSetLocus, BulkSetSimpleTextString, BulkGeneGetLocus, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
36711
{ "locus_tag", BulkGeneSetLocusTag, BulkSetSimpleTextString, BulkGeneGetLocusTag, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
36712
{ "description", BulkGeneSetDescription, BulkSetSimpleTextString, BulkGeneGetDescription, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
36713
{ "location", BulkSetLocation, NULL, BulkGetLocation, BulkDisplayLocation, BulkFreeLocation, NULL, BulkFormatLocation, NULL, NULL, BulkCopyLocation },
36714
{ "comment", BulkSetComment, BulkSetSimpleTextString, BulkGetComment, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextScrollDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
36715
{ NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL}};
36716
36717
static BulkEdFieldData bulk_rna_fields[] = {
36718
{ "product", BulkRNASetProduct, BulkSetSimpleTextString, BulkRNAGetProduct, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
36719
{ "location", BulkSetLocation, NULL, BulkGetLocation, BulkDisplayLocation, BulkFreeLocation, NULL, BulkFormatLocation, NULL, NULL, BulkCopyLocation },
36720
{ "comment", BulkSetComment, BulkSetSimpleTextString, BulkGetComment, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextScrollDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
36721
{ NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL}};
36722
36723
36724
static BulkEdFieldPtr GetBulkEditorFieldListForFeature (SeqFeatPtr sfp)
36725
{
36726
if (sfp == NULL) {
36727
return NULL;
36728
} else if (sfp->data.choice == SEQFEAT_CDREGION) {
36729
return bulk_cds_fields;
36730
} else if (sfp->data.choice == SEQFEAT_GENE) {
36731
return bulk_gene_fields;
36732
} else if (sfp->data.choice == SEQFEAT_RNA && IsBulkEditableRNA(sfp)) {
36733
/* Note - using FEATDEF_rRNA to represent all editable rRNA features */
36734
return bulk_rna_fields;
36735
} else {
36736
return NULL;
36737
}
36738
}
36739
36740
36741
static void BulkSrcSetTaxNameDesc (Pointer target, Pointer data)
36742
{
36743
CharPtr taxname;
36744
SeqDescrPtr sdp = (SeqDescrPtr) target;
36745
BioSourcePtr biop;
36746
36747
if (sdp == NULL || sdp->choice != Seq_descr_source || sdp->data.ptrvalue == NULL) return;
36748
36749
biop = (BioSourcePtr) sdp->data.ptrvalue;
36750
36751
taxname = (CharPtr) data;
36752
36753
if (biop->org == NULL) {
36754
biop->org = OrgRefNew();
36755
}
36756
SetTaxNameAndRemoveTaxRef (biop->org, StringSave (taxname));
36757
}
36758
36759
36760
NLM_EXTERN BioSourcePtr GetBioSourceFromObject (Uint1 choice, Pointer data);
36761
36762
static Pointer BulkSrcGetTaxNameDesc (Uint1 data_choice, Pointer data, Pointer metadata)
36763
{
36764
CharPtr taxname = NULL;
36765
BioSourcePtr biop = NULL;
36766
36767
biop = GetBioSourceFromObject (data_choice, data);
36768
if (biop == NULL) return NULL;
36769
36770
if (biop->org != NULL) {
36771
taxname = StringSave (biop->org->taxname);
36772
}
36773
36774
return taxname;
36775
}
36776
36777
36778
static void BulkSrcSetTaxNameFeat (Pointer target, Pointer data)
36779
{
36780
CharPtr taxname;
36781
SeqFeatPtr sfp = (SeqFeatPtr) target;
36782
BioSourcePtr biop;
36783
36784
if (sfp == NULL || sfp->data.choice != SEQFEAT_BIOSRC || sfp->data.value.ptrvalue == NULL) return;
36785
36786
biop = (BioSourcePtr) sfp->data.value.ptrvalue;
36787
36788
taxname = (CharPtr) data;
36789
36790
if (biop->org == NULL) {
36791
biop->org = OrgRefNew();
36792
}
36793
SetTaxNameAndRemoveTaxRef (biop->org, StringSave (taxname));
36794
}
36795
36796
36797
static Pointer BulkSrcGetTaxNameFeat (Uint1 data_choice, Pointer data, Pointer metadata)
36798
{
36799
CharPtr taxname = NULL;
36800
SeqFeatPtr sfp = (SeqFeatPtr) data;
36801
BioSourcePtr biop;
36802
36803
if (sfp == NULL || sfp->data.choice != SEQFEAT_BIOSRC || sfp->data.value.ptrvalue == NULL) return NULL;
36804
36805
biop = (BioSourcePtr) sfp->data.value.ptrvalue;
36806
36807
if (biop->org != NULL) {
36808
taxname = StringSave (biop->org->taxname);
36809
}
36810
36811
return taxname;
36812
}
36813
36814
36815
static BulkEdFieldData bulk_src_desc_fields[] = {
36816
{ "tax name", BulkSrcSetTaxNameDesc, BulkSetSimpleTextString, BulkSrcGetTaxNameDesc, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
36817
{ NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL}};
36818
36819
static BulkEdFieldData bulk_src_feat_fields[] = {
36820
{ "tax name", BulkSrcSetTaxNameFeat, BulkSetSimpleTextString, BulkSrcGetTaxNameFeat, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
36821
{ NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL}};
36822
36823
typedef struct bulkeditor {
36824
FORM_MESSAGE_BLOCK
36825
DialoG bulk_ed;
36826
BulkEdFieldPtr field_list;
36827
} BulkEditorData, PNTR BulkEditorPtr;
36828
36829
typedef struct collectfeat {
36830
Uint1 featdef;
36831
Uint1 featchoice;
36832
ValNodePtr feat_list;
36833
} CollectFeatData, PNTR CollectFeatPtr;
36834
36835
static void CollectFeaturesForBulkEditor (BioseqPtr bsp, Pointer data)
36836
{
36837
CollectFeatPtr cfp;
36838
SeqFeatPtr sfp;
36839
SeqMgrFeatContext fcontext;
36840
36841
if (bsp == NULL || data == NULL) return;
36842
cfp = (CollectFeatPtr) data;
36843
36844
for (sfp = SeqMgrGetNextFeature (bsp, NULL, cfp->featchoice, cfp->featdef, &fcontext);
36845
sfp != NULL;
36846
sfp = SeqMgrGetNextFeature (bsp, sfp, cfp->featchoice, cfp->featdef, &fcontext)) {
36847
ValNodeAddPointer (&(cfp->feat_list), OBJ_SEQFEAT, sfp);
36848
}
36849
}
36850
36851
static void AcceptBulkEditor (ButtoN b)
36852
{
36853
BulkEditorPtr bep;
36854
36855
bep = (BulkEditorPtr) GetObjectExtra (b);
36856
if (bep == NULL) return;
36857
36858
WatchCursor();
36859
Update();
36860
36861
ApplyBulkEditorToObjectList (bep->bulk_ed);
36862
36863
ObjMgrSetDirtyFlag (bep->input_entityID, TRUE);
36864
ObjMgrSendMsg (OM_MSG_UPDATE, bep->input_entityID, 0, 0);
36865
ArrowCursor ();
36866
Update ();
36867
Remove (bep->form);
36868
}
36869
36870
extern Uint1 GetSubtypeForBulkEdit (ValNodePtr feat_list)
36871
{
36872
ValNodePtr vnp_check;
36873
SeqFeatPtr sfp;
36874
Uint1 subtype = FEATDEF_BAD;
36875
36876
for (vnp_check = feat_list; vnp_check != NULL; vnp_check = vnp_check->next) {
36877
if (vnp_check->choice != OBJ_SEQFEAT) continue;
36878
sfp = vnp_check->data.ptrvalue;
36879
if (sfp->data.choice == SEQFEAT_RNA) {
36880
/* note - using FEATDEF_rRNA to represent all editable RNA features */
36881
if (!IsBulkEditableRNA(sfp)) {
36882
return FEATDEF_BAD;
36883
} else if (subtype == FEATDEF_BAD) {
36884
subtype = FEATDEF_rRNA;
36885
} else if (subtype != FEATDEF_rRNA) {
36886
return FEATDEF_BAD;
36887
}
36888
} else if (subtype == FEATDEF_BAD) {
36889
subtype = sfp->idx.subtype;
36890
} else if (subtype != sfp->idx.subtype) {
36891
return FEATDEF_BAD;
36892
}
36893
}
36894
return subtype;
36895
}
36896
36897
extern void BulkEditorFeatList (Uint2 entityID, ValNodePtr feat_list)
36898
{
36899
GrouP c;
36900
ButtoN b;
36901
BulkEditorPtr bep;
36902
GrouP h;
36903
WindoW w;
36904
SeqEntryPtr sep;
36905
BulkEdFieldPtr field_list = NULL;
36906
Uint1 subtype = 0;
36907
36908
if (feat_list == NULL) {
36909
Message (MSG_ERROR, "No features found!");
36910
return;
36911
}
36912
/* Create a new window, and a struct */
36913
/* to pass around the data in. */
36914
36915
sep = GetTopSeqEntryForEntityID (entityID);
36916
36917
subtype = GetSubtypeForBulkEdit (feat_list);
36918
if (subtype == FEATDEF_BAD) {
36919
Message (MSG_ERROR, "Can't bulk edit a list of mixed feature types!");
36920
return;
36921
}
36922
if (subtype == FEATDEF_CDS) {
36923
field_list = bulk_cds_fields;
36924
} else if (subtype == FEATDEF_GENE) {
36925
field_list = bulk_gene_fields;
36926
} else if (subtype == FEATDEF_rRNA) {
36927
/* Note - using FEATDEF_rRNA to represent all editable rRNA features */
36928
field_list = bulk_rna_fields;
36929
} else if (subtype == FEATDEF_BIOSRC) {
36930
field_list = bulk_src_feat_fields;
36931
} else {
36932
Message (MSG_ERROR, "No bulk editor for this feature type!");
36933
return;
36934
}
36935
36936
bep = (BulkEditorPtr) MemNew (sizeof (BulkEditorData));
36937
if (bep == NULL)
36938
return;
36939
36940
bep->field_list = field_list;
36941
36942
w = FixedWindow (-50, -33, -10, -10, "Bulk Editor",
36943
StdCloseWindowProc);
36944
SetObjectExtra (w, bep, StdCleanupFormProc);
36945
bep->form = (ForM) w;
36946
bep->input_entityID = entityID;
36947
36948
h = HiddenGroup (w, -1, 0, NULL);
36949
SetGroupSpacing (h, 10, 10);
36950
36951
/* want: Document with columns for pseudo (when appropriate), location, fields */
36952
/* when user clicks on field, should be able to edit contents */
36953
36954
bep->bulk_ed = CreateBulkEditorDialog (h, bep->field_list, feat_list, sep, TRUE, NULL, NULL);
36955
36956
/* Add Accept and Cancel buttons */
36957
36958
c = HiddenGroup (h, 3, 0, NULL);
36959
b = PushButton (c, "Accept", AcceptBulkEditor);
36960
SetObjectExtra (b, bep, NULL);
36961
PushButton (c, "Cancel", StdCancelButtonProc);
36962
36963
/* Line things up nicely */
36964
36965
AlignObjects (ALIGN_CENTER, (HANDLE) bep->bulk_ed,
36966
(HANDLE) c, NULL);
36967
36968
36969
/* Display the window now */
36970
36971
RealizeWindow (w);
36972
Show (w);
36973
Select (w);
36974
Update ();
36975
}
36976
36977
36978
extern Uint1 GetSubtypeForBulkDescrEdit (ValNodePtr descr_list)
36979
{
36980
ValNodePtr vnp_check;
36981
SeqDescrPtr sdp;
36982
Uint1 subtype = 0;
36983
36984
for (vnp_check = descr_list; vnp_check != NULL; vnp_check = vnp_check->next) {
36985
if (vnp_check->choice != OBJ_SEQDESC) continue;
36986
sdp = vnp_check->data.ptrvalue;
36987
if (subtype == 0) {
36988
subtype = sdp->choice;
36989
} else if (sdp->choice != subtype) {
36990
return 0;
36991
}
36992
}
36993
return subtype;
36994
}
36995
36996
36997
extern void BulkEditorDescrList (Uint2 entityID, ValNodePtr descr_list)
36998
{
36999
GrouP c;
37000
ButtoN b;
37001
BulkEditorPtr bep;
37002
GrouP h;
37003
WindoW w;
37004
SeqEntryPtr sep;
37005
BulkEdFieldPtr field_list = NULL;
37006
Uint1 subtype = 0;
37007
37008
if (descr_list == NULL) {
37009
Message (MSG_ERROR, "No descriptors found!");
37010
return;
37011
}
37012
/* Create a new window, and a struct */
37013
/* to pass around the data in. */
37014
37015
sep = GetTopSeqEntryForEntityID (entityID);
37016
37017
subtype = GetSubtypeForBulkDescrEdit (descr_list);
37018
if (subtype == 0) {
37019
Message (MSG_ERROR, "Can't bulk edit a list of mixed descriptor types!");
37020
return;
37021
}
37022
if (subtype == Seq_descr_source) {
37023
field_list = bulk_src_desc_fields;
37024
} else {
37025
Message (MSG_ERROR, "No bulk editor for this descriptor type!");
37026
return;
37027
}
37028
37029
bep = (BulkEditorPtr) MemNew (sizeof (BulkEditorData));
37030
if (bep == NULL)
37031
return;
37032
37033
bep->field_list = field_list;
37034
37035
w = FixedWindow (-50, -33, -10, -10, "Bulk Editor",
37036
StdCloseWindowProc);
37037
SetObjectExtra (w, bep, StdCleanupFormProc);
37038
bep->form = (ForM) w;
37039
bep->input_entityID = entityID;
37040
37041
h = HiddenGroup (w, -1, 0, NULL);
37042
SetGroupSpacing (h, 10, 10);
37043
37044
/* want: Document with columns for pseudo (when appropriate), location, fields */
37045
/* when user clicks on field, should be able to edit contents */
37046
37047
bep->bulk_ed = CreateBulkEditorDialog (h, bep->field_list, descr_list, sep, TRUE, NULL, NULL);
37048
37049
/* Add Accept and Cancel buttons */
37050
37051
c = HiddenGroup (h, 3, 0, NULL);
37052
b = PushButton (c, "Accept", AcceptBulkEditor);
37053
SetObjectExtra (b, bep, NULL);
37054
PushButton (c, "Cancel", StdCancelButtonProc);
37055
37056
/* Line things up nicely */
37057
37058
AlignObjects (ALIGN_CENTER, (HANDLE) bep->bulk_ed,
37059
(HANDLE) c, NULL);
37060
37061
37062
/* Display the window now */
37063
37064
RealizeWindow (w);
37065
Show (w);
37066
Select (w);
37067
Update ();
37068
}
37069
37070
37071
NLM_EXTERN void BulkEditorObjectList (Uint2 entityID, CharPtr title, ValNodePtr feat_list, BulkEdFieldPtr field_list)
37072
{
37073
GrouP c;
37074
ButtoN b;
37075
BulkEditorPtr bep;
37076
GrouP h;
37077
WindoW w;
37078
SeqEntryPtr sep;
37079
Uint1 subtype = 0;
37080
37081
if (feat_list == NULL) {
37082
Message (MSG_ERROR, "No features found!");
37083
return;
37084
}
37085
/* Create a new window, and a struct */
37086
/* to pass around the data in. */
37087
37088
sep = GetTopSeqEntryForEntityID (entityID);
37089
37090
bep = (BulkEditorPtr) MemNew (sizeof (BulkEditorData));
37091
if (bep == NULL)
37092
return;
37093
37094
bep->field_list = field_list;
37095
37096
w = FixedWindow (-50, -33, -10, -10, title,
37097
StdCloseWindowProc);
37098
SetObjectExtra (w, bep, StdCleanupFormProc);
37099
bep->form = (ForM) w;
37100
bep->input_entityID = entityID;
37101
37102
h = HiddenGroup (w, -1, 0, NULL);
37103
SetGroupSpacing (h, 10, 10);
37104
37105
/* want: Document with columns for pseudo (when appropriate), location, fields */
37106
/* when user clicks on field, should be able to edit contents */
37107
37108
bep->bulk_ed = CreateBulkEditorDialog (h, bep->field_list, feat_list, sep, TRUE, NULL, NULL);
37109
37110
/* Add Accept and Cancel buttons */
37111
37112
c = HiddenGroup (h, 3, 0, NULL);
37113
b = PushButton (c, "Accept", AcceptBulkEditor);
37114
SetObjectExtra (b, bep, NULL);
37115
PushButton (c, "Cancel", StdCancelButtonProc);
37116
37117
/* Line things up nicely */
37118
37119
AlignObjects (ALIGN_CENTER, (HANDLE) bep->bulk_ed,
37120
(HANDLE) c, NULL);
37121
37122
37123
/* Display the window now */
37124
37125
RealizeWindow (w);
37126
Show (w);
37127
Select (w);
37128
Update ();
37129
}
37130
37131
37132
static void BulkEditor (IteM i, Uint1 featchoice, Uint1 featdef)
37133
{
37134
BaseFormPtr bfp;
37135
SeqEntryPtr sep;
37136
CollectFeatData cfd;
37137
BulkEdFieldPtr field_list = NULL;
37138
37139
#ifdef WIN_MAC
37140
bfp = currentFormDataPtr;
37141
#else
37142
bfp = GetObjectExtra (i);
37143
#endif
37144
if (bfp == NULL) return;
37145
37146
/* Create a new window, and a struct */
37147
/* to pass around the data in. */
37148
37149
sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
37150
37151
if (featchoice == SEQFEAT_CDREGION || featdef == FEATDEF_CDS) {
37152
field_list = bulk_cds_fields;
37153
} else if (featchoice == SEQFEAT_GENE || featdef == FEATDEF_GENE) {
37154
field_list = bulk_gene_fields;
37155
} else if (featchoice == SEQFEAT_RNA) {
37156
field_list = bulk_rna_fields;
37157
} else {
37158
Message (MSG_ERROR, "No bulk editor for this feature type!");
37159
return;
37160
}
37161
37162
cfd.featchoice = featchoice;
37163
cfd.featdef = featdef;
37164
cfd.feat_list = NULL;
37165
VisitBioseqsInSep (sep, &cfd, CollectFeaturesForBulkEditor);
37166
37167
if (cfd.feat_list == NULL) {
37168
Message (MSG_ERROR, "No features found!");
37169
return;
37170
}
37171
37172
BulkEditorFeatList (bfp->input_entityID, cfd.feat_list);
37173
}
37174
37175
extern void BulkEditCDS (IteM i)
37176
{
37177
BulkEditor (i, SEQFEAT_CDREGION, FEATDEF_CDS);
37178
}
37179
37180
extern void BulkEditGene (IteM i)
37181
{
37182
BulkEditor (i, SEQFEAT_GENE, FEATDEF_GENE);
37183
}
37184
37185
extern void BulkEditRNA (IteM i)
37186
{
37187
BulkEditor (i, SEQFEAT_RNA, 0);
37188
}
37189
37190
37191
static Pointer GetBarcodeTestBarcodeID (Uint1 data_choice, Pointer data, Pointer metadata)
37192
{
37193
BarcodeTestResultsPtr res = (BarcodeTestResultsPtr) data;
37194
if (res == NULL || res->bsp == NULL) {
37195
return NULL;
37196
} else {
37197
return BarcodeTestBarcodeIdString (res->bsp);
37198
}
37199
}
37200
37201
37202
static Pointer GetBarcodeTestGenbankID (Uint1 data_choice, Pointer data, Pointer metadata)
37203
{
37204
BarcodeTestResultsPtr res = (BarcodeTestResultsPtr) data;
37205
if (res == NULL || res->bsp == NULL) {
37206
return NULL;
37207
} else {
37208
return BarcodeTestGenbankIdString (res->bsp);
37209
}
37210
}
37211
37212
37213
static Pointer GetBarcodeTestLengthResult (Uint1 data_choice, Pointer data, Pointer metadata)
37214
{
37215
BarcodeTestResultsPtr res = (BarcodeTestResultsPtr) data;
37216
if (res == NULL || !res->failed_tests[eBarcodeTest_Length]) {
37217
return NULL;
37218
} else {
37219
return StringSave ("TRUE");
37220
}
37221
}
37222
37223
37224
static Pointer GetBarcodeTestPrimersResult (Uint1 data_choice, Pointer data, Pointer metadata)
37225
{
37226
BarcodeTestResultsPtr res = (BarcodeTestResultsPtr) data;
37227
if (res == NULL || !res->failed_tests[eBarcodeTest_Primers]) {
37228
return NULL;
37229
} else {
37230
return StringSave ("TRUE");
37231
}
37232
}
37233
37234
37235
static Pointer GetBarcodeTestCountryResult (Uint1 data_choice, Pointer data, Pointer metadata)
37236
{
37237
BarcodeTestResultsPtr res = (BarcodeTestResultsPtr) data;
37238
if (res == NULL || !res->failed_tests[eBarcodeTest_Country]) {
37239
return NULL;
37240
} else {
37241
return StringSave ("TRUE");
37242
}
37243
}
37244
37245
37246
static Pointer GetBarcodeTestSpecimenVoucherResult (Uint1 data_choice, Pointer data, Pointer metadata)
37247
{
37248
BarcodeTestResultsPtr res = (BarcodeTestResultsPtr) data;
37249
if (res == NULL || !res->failed_tests[eBarcodeTest_SpecimenVoucher]) {
37250
return NULL;
37251
} else {
37252
return StringSave ("TRUE");
37253
}
37254
}
37255
37256
37257
static Pointer GetBarcodeTestPercentNsResult (Uint1 data_choice, Pointer data, Pointer metadata)
37258
{
37259
BarcodeTestResultsPtr res = (BarcodeTestResultsPtr) data;
37260
Char txt[5];
37261
if (res == NULL || !res->failed_tests[eBarcodeTest_PercentN]) {
37262
return NULL;
37263
} else {
37264
sprintf (txt, "%.1f", res->n_percent);
37265
return StringSave (txt);
37266
}
37267
}
37268
37269
37270
static Int4 BarcodeFormatBarcodeID (ColPtr col, CharPtr name)
37271
{
37272
if (col == NULL) return 0;
37273
37274
col->pixWidth = MAX (21, StringLen (name)) * MaxCharWidth();
37275
col->pixInset = 0;
37276
col->charWidth = 0;
37277
col->charInset = 0;
37278
col->font = NULL;
37279
col->just = 'l';
37280
col->wrap = 1;
37281
col->bar = 0;
37282
col->underline = 0;
37283
col->left = 0;
37284
return col->pixWidth;
37285
}
37286
37287
37288
static Int4 BarcodeFormatGenbankID (ColPtr col, CharPtr name)
37289
{
37290
if (col == NULL) return 0;
37291
37292
col->pixWidth = MAX (10, StringLen (name)) * MaxCharWidth();
37293
col->pixInset = 0;
37294
col->charWidth = 0;
37295
col->charInset = 0;
37296
col->font = NULL;
37297
col->just = 'l';
37298
col->wrap = 1;
37299
col->bar = 0;
37300
col->underline = 0;
37301
col->left = 0;
37302
return col->pixWidth;
37303
}
37304
37305
37306
static Int4 BarcodeFormatPercentN (ColPtr col, CharPtr name)
37307
{
37308
if (col == NULL) return 0;
37309
37310
col->pixWidth = MAX (5, StringLen (name)) * MaxCharWidth();
37311
col->pixInset = 0;
37312
col->charWidth = 0;
37313
col->charInset = 0;
37314
col->font = NULL;
37315
col->just = 'l';
37316
col->wrap = 1;
37317
col->bar = 0;
37318
col->underline = 0;
37319
col->left = 0;
37320
return col->pixWidth;
37321
}
37322
37323
37324
static BulkEdFieldData barcode_test_fields[] = {
37325
{ "Barcode ID", NULL, NULL, GetBarcodeTestBarcodeID, BulkDisplaySimpleText, BulkFreeSimpleText, NULL, BarcodeFormatBarcodeID, NULL, NULL, BulkSimpleTextCopy },
37326
{ "Genbank Accession", NULL, NULL, GetBarcodeTestGenbankID, BulkDisplaySimpleText, BulkFreeSimpleText, NULL, BarcodeFormatGenbankID, NULL, NULL, BulkSimpleTextCopy },
37327
{ "Length", NULL, NULL, GetBarcodeTestLengthResult, NULL, BulkFreeSimpleText, NULL, BulkFormatTrueFalse, BulkDrawTrueFalse, NULL, BulkSimpleTextCopy },
37328
{ "Primers", NULL, NULL, GetBarcodeTestPrimersResult, NULL, BulkFreeSimpleText, NULL, BulkFormatTrueFalse, BulkDrawTrueFalse, NULL, BulkSimpleTextCopy },
37329
{ "Country", NULL, NULL, GetBarcodeTestCountryResult, NULL, BulkFreeSimpleText, NULL, BulkFormatTrueFalse, BulkDrawTrueFalse, NULL, BulkSimpleTextCopy },
37330
{ "Specimen Voucher", NULL, NULL, GetBarcodeTestSpecimenVoucherResult, NULL, BulkFreeSimpleText, NULL, BulkFormatTrueFalse, BulkDrawTrueFalse, NULL, BulkSimpleTextCopy },
37331
{ "Percent Ns", NULL, NULL, GetBarcodeTestPercentNsResult, BulkDisplaySimpleText, BulkFreeSimpleText, NULL, BarcodeFormatPercentN, NULL, NULL, BulkSimpleTextCopy },
37332
{ NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL}};
37333
37334
static void NavigateToBarcodeTestResultBioseq (ValNodePtr object, Pointer userdata)
37335
{
37336
BaseFormPtr bfp;
37337
BarcodeTestResultsPtr res;
37338
37339
if (object == NULL) return;
37340
37341
res = (BarcodeTestResultsPtr) object->data.ptrvalue;
37342
37343
if (res == NULL || res->bsp == NULL) return;
37344
bfp = GetBaseFormForEntityID (res->bsp->idx.entityID);
37345
if (bfp != NULL) {
37346
Select (bfp->form);
37347
SetBioseqViewTargetByBioseq (bfp, res->bsp);
37348
}
37349
}
37350
37351
37352
extern DialoG BarcodeTestResultsDisplay (GrouP h, BarcodeTestConfigPtr cfg)
37353
{
37354
return CreateBulkEditorDialog (h, barcode_test_fields, NULL, NULL, FALSE, NavigateToBarcodeTestResultBioseq, NULL);
37355
}
37356
37357
extern SubSourcePtr FindBadLatLon (BioSourcePtr biop)
37358
{
37359
SubSourcePtr ssp, ssp_bad = NULL;
37360
Boolean format_ok, lat_in_range, lon_in_range;
37361
37362
if (biop == NULL)
37363
{
37364
return NULL;
37365
}
37366
37367
for (ssp = biop->subtype; ssp != NULL && ssp_bad == NULL; ssp = ssp->next)
37368
{
37369
if (ssp->subtype == SUBSRC_lat_lon)
37370
{
37371
IsCorrectLatLonFormat (ssp->name, &format_ok, &lat_in_range, &lon_in_range);
37372
if (!format_ok || !lat_in_range || !lon_in_range)
37373
{
37374
ssp_bad = ssp;
37375
}
37376
}
37377
}
37378
return ssp_bad;
37379
}
37380
37381
37382
static Pointer GetCurrentLatLon (Uint1 data_choice, Pointer data, Pointer metadata)
37383
{
37384
SubSourcePtr bad_ssp;
37385
BioSourcePtr biop;
37386
37387
biop = GetBioSourceFromObject (data_choice, data);
37388
if (biop == NULL) return NULL;
37389
37390
bad_ssp = FindBadLatLon (biop);
37391
if (bad_ssp == NULL)
37392
{
37393
return NULL;
37394
}
37395
else
37396
{
37397
return StringSave (bad_ssp->name);
37398
}
37399
}
37400
37401
37402
static Pointer GetCorrectedLatLon (Uint1 data_choice, Pointer data, Pointer metadata)
37403
{
37404
SubSourcePtr bad_ssp;
37405
CharPtr fix;
37406
BioSourcePtr biop;
37407
37408
biop = GetBioSourceFromObject (data_choice, data);
37409
if (biop == NULL) return NULL;
37410
37411
bad_ssp = FindBadLatLon (biop);
37412
if (bad_ssp == NULL)
37413
{
37414
return NULL;
37415
}
37416
else
37417
{
37418
fix = FixLatLonFormat (bad_ssp->name);
37419
if (fix == NULL)
37420
{
37421
return StringSave ("Unable to autocorrect");
37422
}
37423
else
37424
{
37425
return fix;
37426
}
37427
}
37428
}
37429
37430
37431
static BulkEdFieldData latlon_fields[] = {
37432
{ "Current Lat-lon", NULL, NULL, GetCurrentLatLon, BulkDisplaySimpleText, BulkFreeSimpleText, NULL, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
37433
{ "Suggested Correction", NULL, NULL, GetCorrectedLatLon, BulkDisplaySimpleText, BulkFreeSimpleText, NULL, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
37434
{ NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL}};
37435
37436
extern DialoG LatLonTestResultsDisplay (GrouP h)
37437
{
37438
return CreateBulkEditorDialog (h, latlon_fields, NULL, NULL, FALSE, ScrollToDiscrepancyItem, EditDiscrepancyItem);
37439
}
37440
37441
37442
static CharPtr GetSubSource (Uint1 data_choice, Pointer data, Uint1 subtype)
37443
{
37444
SubSourcePtr ssp;
37445
BioSourcePtr biop;
37446
37447
biop = GetBioSourceFromObject (data_choice, data);
37448
if (biop == NULL) return NULL;
37449
37450
for (ssp = biop->subtype; ssp != NULL && ssp->subtype != subtype; ssp = ssp->next)
37451
{}
37452
37453
if (ssp == NULL)
37454
{
37455
return NULL;
37456
}
37457
else
37458
{
37459
return StringSave (ssp->name);
37460
}
37461
}
37462
37463
37464
static Pointer GetCountry (Uint1 data_choice, Pointer data, Pointer metadata)
37465
{
37466
return GetSubSource (data_choice, data, SUBSRC_country);
37467
}
37468
37469
static Pointer GetLatLon (Uint1 data_choice, Pointer data, Pointer metadata)
37470
{
37471
return GetSubSource (data_choice, data, SUBSRC_lat_lon);
37472
}
37473
37474
37475
extern Pointer GetLatLonCountryCorrection (Uint1 data_choice, Pointer data, Pointer metadata)
37476
{
37477
SubSourcePtr ssp;
37478
BioSourcePtr biop;
37479
CharPtr country = NULL, cp;
37480
FloatHi lat, lon;
37481
Boolean found_lat_lon = FALSE;
37482
CharPtr msg = NULL;
37483
CharPtr guess_fmt = "Lat_lon does not map to '%s', but may be in '%s'";
37484
CharPtr guess;
37485
37486
biop = GetBioSourceFromObject (data_choice, data);
37487
if (biop == NULL) return NULL;
37488
37489
for (ssp = biop->subtype; ssp != NULL && (country == NULL || !found_lat_lon); ssp = ssp->next)
37490
{
37491
if (ssp->subtype == SUBSRC_country && !StringHasNoText (ssp->name))
37492
{
37493
country = StringSave (ssp->name);
37494
}
37495
else if (ssp->subtype == SUBSRC_lat_lon)
37496
{
37497
if (ParseLatLon (ssp->name, &lat, &lon))
37498
{
37499
found_lat_lon = TRUE;
37500
}
37501
}
37502
}
37503
37504
cp = StringChr (country, ':');
37505
if (cp != NULL)
37506
{
37507
*cp = 0;
37508
}
37509
37510
if (country == NULL && !found_lat_lon)
37511
{
37512
msg = StringSave ("Country and lat-lon not specified");
37513
}
37514
else if (country == NULL)
37515
{
37516
msg = StringSave ("Country not specified");
37517
}
37518
else if (!found_lat_lon)
37519
{
37520
msg = StringSave ("Lat-lon not specified.");
37521
}
37522
else if (!IsCountryInLatLonList (country))
37523
{
37524
msg = StringSave ("Country not in lat-lon list");
37525
}
37526
else if (TestLatLonForCountry (country, lat, lon))
37527
{
37528
msg = StringSave ("No conflict");
37529
}
37530
else if (TestLatLonForCountry (country, -lat, lon))
37531
{
37532
if (lat < 0.0) {
37533
msg = StringSave ("Latitude should be set to N (northern hemisphere)");
37534
} else {
37535
msg = StringSave ("Latitude should be set to S (southern hemisphere)");
37536
}
37537
} else if (TestLatLonForCountry (country, lat, -lon)) {
37538
if (lon < 0.0) {
37539
msg = StringSave ("Longitude should be set to E (eastern hemisphere)");
37540
} else {
37541
msg = StringSave ("Longitude should be set to W (western hemisphere)");
37542
}
37543
} else if (TestLatLonForCountry (country, lon, lat)) {
37544
msg = StringSave ("Latitude and longitude values appear to be exchanged");
37545
} else {
37546
guess = GuessCountryForLatLon (lat, lon);
37547
if (guess == NULL)
37548
{
37549
msg = StringSave ("Lat-lon does not map to country");
37550
}
37551
else
37552
{
37553
msg = (CharPtr) MemNew (sizeof (Char) * (StringLen (guess_fmt) + StringLen (country) + StringLen (guess)));
37554
sprintf (msg, guess_fmt, country, guess);
37555
}
37556
}
37557
return msg;
37558
}
37559
37560
static BulkEdFieldData latloncountry_fields[] = {
37561
{ "Lat-lon", NULL, NULL, GetLatLon, BulkDisplaySimpleText, BulkFreeSimpleText, NULL, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
37562
{ "Country", NULL, NULL, GetCountry, BulkDisplaySimpleText, BulkFreeSimpleText, NULL, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
37563
{ "Suggested Correction", NULL, NULL, GetLatLonCountryCorrection, BulkDisplaySimpleText, BulkFreeSimpleText, NULL, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
37564
{ NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL}};
37565
37566
extern DialoG LatLonCountryResultsDisplay (GrouP h)
37567
{
37568
return CreateBulkEditorDialog (h, latloncountry_fields, NULL, NULL, FALSE, ScrollToDiscrepancyItem, EditDiscrepancyItem);
37569
}
37570
37571
37572
static Pointer GetCurrentSpecificHost (Uint1 data_choice, Pointer data, Pointer metadata)
37573
{
37574
SpecificHostFixPtr s = (SpecificHostFixPtr) data;
37575
37576
if (s == NULL || StringHasNoText (s->bad_specific_host))
37577
{
37578
return NULL;
37579
}
37580
else
37581
{
37582
return StringSave (s->bad_specific_host);
37583
}
37584
}
37585
37586
37587
static Pointer GetCorrectedSpecificHost (Uint1 data_choice, Pointer data, Pointer metadata)
37588
{
37589
SpecificHostFixPtr s = (SpecificHostFixPtr) data;
37590
CharPtr new_spec_host;
37591
37592
if (s == NULL || StringHasNoText (s->bad_specific_host) || StringHasNoText (s->old_taxname))
37593
{
37594
return NULL;
37595
}
37596
else if (StringHasNoText (s->new_taxname))
37597
{
37598
return StringSave ("Unable to suggest correction");
37599
}
37600
else
37601
{
37602
new_spec_host = StringSave (s->bad_specific_host);
37603
FindReplaceString (&new_spec_host, s->old_taxname, s->new_taxname, TRUE, TRUE);
37604
return new_spec_host;
37605
}
37606
}
37607
37608
37609
static void ScrollToSpecificHostFix (ValNodePtr vnp, Pointer userdata)
37610
{
37611
SpecificHostFixPtr s;
37612
37613
if (vnp == NULL || vnp->data.ptrvalue == NULL) return;
37614
37615
s = (SpecificHostFixPtr) vnp->data.ptrvalue;
37616
ScrollToDiscrepancyItem (s->feat_or_desc, NULL);
37617
}
37618
37619
37620
static void EditSpecificHostFix (ValNodePtr vnp, Pointer userdata)
37621
{
37622
SpecificHostFixPtr s;
37623
37624
if (vnp == NULL || vnp->data.ptrvalue == NULL) return;
37625
37626
s = (SpecificHostFixPtr) vnp->data.ptrvalue;
37627
EditDiscrepancyItem (s->feat_or_desc, NULL);
37628
}
37629
37630
37631
static BulkEdFieldData specifichost_fields[] = {
37632
{ "Current Specific-host", NULL, NULL, GetCurrentSpecificHost, BulkDisplaySimpleText, BulkFreeSimpleText, NULL, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
37633
{ "Suggested Correction", NULL, NULL, GetCorrectedSpecificHost, BulkDisplaySimpleText, BulkFreeSimpleText, NULL, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
37634
{ NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL}};
37635
37636
extern DialoG SpecificHostResultsDisplay (GrouP h)
37637
{
37638
return CreateBulkEditorDialog (h, specifichost_fields, NULL, NULL, FALSE, ScrollToSpecificHostFix, EditSpecificHostFix);
37639
}
37640
37641
Loggerhead is a web-based interface for Breezy
Version: 2.0.1