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  • Committer: Bazaar Package Importer
  • Author(s): Aaron M. Ucko
  • Date: 2005-03-27 12:00:15 UTC
  • mfrom: (2.1.2 hoary)
  • Revision ID: james.westby@ubuntu.com-20050327120015-embhesp32nj73p9r
Tags: 6.1.20041020-3
http://bugs.debian.org/295110
* Fix FTBFS under GCC 4.0 caused by inconsistent use of "static" on
  functions.  (Closes: #295110.)
* Add a watch file, now that we can.  (Upstream's layout needs version=3.)

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api/wprint.c
29
29
*
30
30
* Version Creation Date:   7/15/95
31
31
*
32
 
* $Revision: 6.61 $
 
32
* $Revision: 6.71 $
33
33
*
34
34
* File Description: 
35
35
*
45
45
/*************************************
46
46
*
47
47
 * $Log: wprint.c,v $
 
48
 * Revision 6.71  2002/08/08 14:00:37  kans
 
49
 * added FANTOM_DB hyperlink
 
50
 *
 
51
 * Revision 6.70  2002/07/24 21:08:47  kans
 
52
 * reverted ncbi URL
 
53
 *
 
54
 * Revision 6.69  2002/07/23 16:44:35  kans
 
55
 * changed www.ncbi.nlm.nih.gov to www.ncbi.nih.gov
 
56
 *
 
57
 * Revision 6.68  2002/06/21 15:38:34  kans
 
58
 * added GABI db_xref
 
59
 *
 
60
 * Revision 6.67  2002/06/18 21:00:00  kans
 
61
 * added ISFinder as legal db_xref with hotlink
 
62
 *
 
63
 * Revision 6.66  2002/05/06 22:20:49  kans
 
64
 * added IFO and JCM db_xref hotlinks
 
65
 *
 
66
 * Revision 6.65  2002/04/18 22:24:16  kans
 
67
 * added dbEST and dbSTS links
 
68
 *
 
69
 * Revision 6.64  2002/02/20 21:59:44  tatiana
 
70
 * IMGT/LIGM dbxref added
 
71
 *
 
72
 * Revision 6.63  2002/02/01 19:40:01  kans
 
73
 * MGD uses id=MGI: URL prefix, strips MGI: if in db_xref text
 
74
 *
 
75
 * Revision 6.62  2002/01/02 13:21:16  kans
 
76
 * added WormBase links
 
77
 *
48
78
 * Revision 6.61  2001/12/06 17:00:41  kans
49
79
 * TextSave takes size_t, not Int2, otherwise titin protein tries to allocate negative number
50
80
 *
385
415
static Char link_pdb[MAX_WWWBUF];
386
416
static Char link_gdb_map[MAX_WWWBUF];
387
417
static Char link_UniSTS[MAX_WWWBUF];
 
418
static Char link_dbSTS[MAX_WWWBUF];
 
419
static Char link_dbEST[MAX_WWWBUF];
388
420
static Char link_omim[MAX_WWWBUF];
389
421
static Char link_locus[MAX_WWWBUF];
390
422
static Char link_snp[MAX_WWWBUF];
395
427
static Char link_fly_fbgn[MAX_WWWBUF];
396
428
static Char link_cdd[MAX_WWWBUF];
397
429
static Char link_niaest[MAX_WWWBUF];
 
430
static Char link_worm_sequence[MAX_WWWBUF];
 
431
static Char link_worm_locus[MAX_WWWBUF];
 
432
static Char link_imgt[MAX_WWWBUF];
 
433
static Char link_ifo[MAX_WWWBUF];
 
434
static Char link_jcm[MAX_WWWBUF];
 
435
static Char link_isfinder[MAX_WWWBUF];
 
436
static Char link_gabi[MAX_WWWBUF];
 
437
static Char link_fantom[MAX_WWWBUF];
398
438
 
399
439
#define DEF_LINK_FF  "/cgi-bin/Entrez/getfeat?"
400
440
 
406
446
#define DEF_LINK_CODE "/htbin-post/Taxonomy/wprintgc?"
407
447
 
408
448
#define DEF_LINK_COG "http://www.ncbi.nlm.nih.gov/cgi-bin/COG/palox?"
409
 
#define DEF_LINK_MGD "http://www.informatics.jax.org/searches/accession_report.cgi?id="
 
449
#define DEF_LINK_MGD "http://www.informatics.jax.org/searches/accession_report.cgi?id=MGI:"
410
450
#define DEF_LINK_FBGN "http://flybase.bio.indiana.edu/.bin/fbidq.html?"
411
451
#define DEF_LINK_FBAN "http://www.fruitfly.org/cgi-bin/annot/fban?"
412
452
 
433
473
#define DEF_LINK_GDB_SUFFIX "&match=Inclusive&order=Locus+Location"
434
474
 
435
475
#define DEF_LINK_UniSTS "http://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid="
 
476
#define DEF_LINK_dbSTS "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?"
 
477
#define DEF_LINK_dbEST "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?"
436
478
#define DEF_LINK_OMIM "http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id="
437
479
#define DEF_LINK_LOCUS "http://www.ncbi.nlm.nih.gov/LocusLink/LocRpt.cgi?l="
438
480
#define DEF_LINK_SNP "http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs="
441
483
 
442
484
#define DEF_LINK_CDD "http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid="
443
485
#define DEF_LINK_NIAEST "http://lgsun.grc.nia.nih.gov/cgi-bin/pro3?sname1="
 
486
#define DEF_LINK_WORM_SEQUENCE "http://www.wormbase.org/db/seq/sequence?name="
 
487
#define DEF_LINK_WORM_LOCUS "http://www.wormbase.org/db/gene/locus?name="
 
488
#define DEF_LINK_IMGT "http://imgt.cines.fr:8104/cgi-bin/IMGTlect.jv?query=202+"
 
489
#define DEF_LINK_IFO "http://www.ifo.or.jp/index_e.html"
 
490
#define DEF_LINK_JCM "http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM="
 
491
#define DEF_LINK_ISFINDER "http://www-is.biotoul.fr/scripts/is/is_spec.idc?name="
 
492
#define DEF_LINK_GABI "https://gabi.rzpd.de/cgi-bin-protected/GreenCards.pl.cgi?Mode=ShowBioObject&BioObjectName="
 
493
#define DEF_LINK_FANTOM "http://fantom.gsc.riken.go.jp/db/view/main.cgi?masterid="
444
494
 
445
495
/* now other data bases are linked to Entrez. may be changed later 
446
496
static char *link_epd = 
518
568
                link_omim, MAX_WWWBUF);
519
569
        GetAppParam("NCBI", "WWWENTREZ", "LINK_UniSTS", DEF_LINK_UniSTS, 
520
570
                link_UniSTS, MAX_WWWBUF);
 
571
        GetAppParam("NCBI", "WWWENTREZ", "LINK_dbSTS", DEF_LINK_dbSTS, 
 
572
                link_dbSTS, MAX_WWWBUF);
 
573
        GetAppParam("NCBI", "WWWENTREZ", "LINK_dbEST", DEF_LINK_dbEST, 
 
574
                link_dbEST, MAX_WWWBUF);
521
575
        GetAppParam("NCBI", "WWWENTREZ", "LINK_LOCUS", DEF_LINK_LOCUS, 
522
576
                link_locus, MAX_WWWBUF);
523
577
        GetAppParam("NCBI", "WWWENTREZ", "LINK_SNP", DEF_LINK_SNP, 
536
590
                link_cdd, MAX_WWWBUF);
537
591
        GetAppParam("NCBI", "WWWENTREZ", "LINK_NIAEST", DEF_LINK_NIAEST, 
538
592
                link_niaest, MAX_WWWBUF);
 
593
        GetAppParam("NCBI", "WWWENTREZ", "LINK_WORM_SEQUENCE", DEF_LINK_WORM_SEQUENCE, 
 
594
                link_worm_sequence, MAX_WWWBUF);
 
595
        GetAppParam("NCBI", "WWWENTREZ", "LINK_WORM_LOCUS", DEF_LINK_WORM_LOCUS, 
 
596
                link_worm_locus, MAX_WWWBUF);
 
597
        GetAppParam("NCBI", "WWWENTREZ", "LINK_IMGT", DEF_LINK_IMGT, 
 
598
                link_imgt, MAX_WWWBUF);
 
599
        GetAppParam("NCBI", "WWWENTREZ", "LINK_IFO", DEF_LINK_IFO, 
 
600
                link_ifo, MAX_WWWBUF);
 
601
        GetAppParam("NCBI", "WWWENTREZ", "LINK_JCM", DEF_LINK_JCM, 
 
602
                link_jcm, MAX_WWWBUF);
 
603
        GetAppParam("NCBI", "WWWENTREZ", "LINK_ISFINDER", DEF_LINK_ISFINDER,
 
604
                link_isfinder, MAX_WWWBUF);
 
605
        GetAppParam("NCBI", "WWWENTREZ", "LINK_GABI", DEF_LINK_GABI,
 
606
                link_gabi, MAX_WWWBUF);
 
607
        GetAppParam("NCBI", "WWWENTREZ", "LINK_FANTOM", DEF_LINK_FANTOM,
 
608
                link_fantom, MAX_WWWBUF);
539
609
 
540
610
}
541
611
 
1093
1163
                        ff_AddString(p);
1094
1164
                        AddLink("</a>");
1095
1165
                } 
 
1166
                if (( p = StringStr(str, "dbEST:")) != NULL) {
 
1167
                        nothing = FALSE;
 
1168
                        p += StringLen("dbEST:");
 
1169
                        l = StringLen(link_dbEST) + StringLen(p);
 
1170
                        prefix = "<a href=%sval=gnl|dbest|%s>"; 
 
1171
                        ll = StringLen(prefix); 
 
1172
                        s = (CharPtr)MemNew(l + ll);
 
1173
                        ss = (CharPtr)MemNew(p-str+1);
 
1174
                        StringNCpy(ss, str, p-str);
 
1175
                        ff_AddString(ss);
 
1176
                        MemFree(ss);
 
1177
                        while (*p == ' ')
 
1178
                                p++;
 
1179
                        sprintf(s, prefix, link_dbEST, p);
 
1180
                        AddLink(s);
 
1181
                        MemFree(s);
 
1182
                        ff_AddString(p);
 
1183
                        AddLink("</a>");
 
1184
                } 
 
1185
                if (( p = StringStr(str, "dbSTS:")) != NULL) {
 
1186
                        nothing = FALSE;
 
1187
                        p += StringLen("dbSTS:");
 
1188
                        l = StringLen(link_dbSTS) + StringLen(p);
 
1189
                        prefix = "<a href=%sval=gnl|dbsts|%s>"; 
 
1190
                        ll = StringLen(prefix); 
 
1191
                        s = (CharPtr)MemNew(l + ll);
 
1192
                        ss = (CharPtr)MemNew(p-str+1);
 
1193
                        StringNCpy(ss, str, p-str);
 
1194
                        ff_AddString(ss);
 
1195
                        MemFree(ss);
 
1196
                        while (*p == ' ')
 
1197
                                p++;
 
1198
                        sprintf(s, prefix, link_dbSTS, p);
 
1199
                        AddLink(s);
 
1200
                        MemFree(s);
 
1201
                        ff_AddString(p);
 
1202
                        AddLink("</a>");
 
1203
                } 
1096
1204
                if (( p = StringStr(str, "LocusID:")) != NULL) {
1097
1205
                        nothing = FALSE;
1098
1206
                        p += StringLen("LocusID:");
1169
1277
                        ff_AddString(p);
1170
1278
                        AddLink("</a>");
1171
1279
                } 
 
1280
                if (( p = StringStr(str, "IMGT/LIGM:")) != NULL) {
 
1281
                        nothing = FALSE;
 
1282
                        p += StringLen("IMGT/LIGM:");
 
1283
                        l = StringLen(link_imgt) + StringLen(p);
 
1284
                        prefix = "<a href=%s%s>"; 
 
1285
                        ll = StringLen(prefix); 
 
1286
                        s = (CharPtr)MemNew(l + ll);
 
1287
                        ss = (CharPtr)MemNew(p-str+1);
 
1288
                        StringNCpy(ss, str, p-str);
 
1289
                        ff_AddString(ss);
 
1290
                        MemFree(ss);
 
1291
                        while (*p == ' ')
 
1292
                                p++;
 
1293
                        sprintf(s, prefix, link_imgt, p);
 
1294
                        AddLink(s);
 
1295
                        MemFree(s);
 
1296
                        ff_AddString(p);
 
1297
                        AddLink("</a>");
 
1298
                } 
1172
1299
                if (( p = StringStr(str, "GDB:")) != NULL) {
1173
1300
                        p += StringLen("GDB:");
1174
1301
                        if (( pp = StringStr(p, "G00-")) != NULL) {
1304
1431
                        MemFree(ss);
1305
1432
                        while (*p == ' ')
1306
1433
                                p++;
 
1434
                        if (StringNICmp (p, "MGI:", 4) == 0) {
 
1435
                                p += 4;
 
1436
                        }
1307
1437
                        sprintf(s, prefix, link_mgd, p);
1308
1438
                        AddLink(s);
1309
1439
                        MemFree(s);
1348
1478
                        ff_AddString(p);
1349
1479
                        AddLink("</a>");
1350
1480
                } 
 
1481
                if (( p = StringStr(str, "WormBase:")) != NULL) {
 
1482
                        CharPtr worm_link = NULL;
 
1483
                        nothing = FALSE;
 
1484
                        p += StringLen("WormBase:");
 
1485
                        if (StringStr (str, "unc") != NULL) {
 
1486
                                worm_link = link_worm_locus;
 
1487
                                l = StringLen(worm_link) + StringLen(p);
 
1488
                                prefix = "<a href=%s%s;class=Locus>"; 
 
1489
                        } else {
 
1490
                                worm_link = link_worm_sequence;
 
1491
                                l = StringLen(worm_link) + StringLen(p);
 
1492
                                prefix = "<a href=%s%s;class=Sequence>"; 
 
1493
                        }
 
1494
                        ll = StringLen(prefix); 
 
1495
                        s = (CharPtr)MemNew(l + ll);
 
1496
                        ss = (CharPtr)MemNew(p-str+1);
 
1497
                        StringNCpy(ss, str, p-str);
 
1498
                        ff_AddString(ss);
 
1499
                        MemFree(ss);
 
1500
                        while (*p == ' ')
 
1501
                                p++;
 
1502
                        sprintf(s, prefix, worm_link, p);
 
1503
                        AddLink(s);
 
1504
                        MemFree(s);
 
1505
                        ff_AddString(p);
 
1506
                        AddLink("</a>");
 
1507
                } 
 
1508
                if (( p = StringStr(str, "IFO:")) != NULL) {
 
1509
                        nothing = FALSE;
 
1510
                        p += StringLen("IFO:");
 
1511
                        l = StringLen(link_ifo) + StringLen(p);
 
1512
                        prefix = "<a href=%s>"; 
 
1513
                        ll = StringLen(prefix); 
 
1514
                        s = (CharPtr)MemNew(l + ll);
 
1515
                        ss = (CharPtr)MemNew(p-str+1);
 
1516
                        StringNCpy(ss, str, p-str);
 
1517
                        ff_AddString(ss);
 
1518
                        MemFree(ss);
 
1519
                        while (*p == ' ')
 
1520
                                p++;
 
1521
                        sprintf(s, prefix, link_ifo);
 
1522
                        AddLink(s);
 
1523
                        MemFree(s);
 
1524
                        ff_AddString(p);
 
1525
                        AddLink("</a>");
 
1526
                } 
 
1527
                if (( p = StringStr(str, "JCM:")) != NULL) {
 
1528
                        nothing = FALSE;
 
1529
                        p += StringLen("JCM:");
 
1530
                        l = StringLen(link_jcm) + StringLen(p);
 
1531
                        prefix = "<a href=%s%s>"; 
 
1532
                        ll = StringLen(prefix); 
 
1533
                        s = (CharPtr)MemNew(l + ll);
 
1534
                        ss = (CharPtr)MemNew(p-str+1);
 
1535
                        StringNCpy(ss, str, p-str);
 
1536
                        ff_AddString(ss);
 
1537
                        MemFree(ss);
 
1538
                        while (*p == ' ')
 
1539
                                p++;
 
1540
                        sprintf(s, prefix, link_jcm, p);
 
1541
                        AddLink(s);
 
1542
                        MemFree(s);
 
1543
                        ff_AddString(p);
 
1544
                        AddLink("</a>");
 
1545
                }
 
1546
                if (( p = StringStr(str, "ISFinder:")) != NULL) {
 
1547
                        nothing = FALSE;
 
1548
                        p += StringLen("ISFinder:");
 
1549
                        l = StringLen(link_isfinder) + StringLen(p);
 
1550
                        prefix = "<a href=%s%s>"; 
 
1551
                        ll = StringLen(prefix); 
 
1552
                        s = (CharPtr)MemNew(l + ll);
 
1553
                        ss = (CharPtr)MemNew(p-str+1);
 
1554
                        StringNCpy(ss, str, p-str);
 
1555
                        ff_AddString(ss);
 
1556
                        MemFree(ss);
 
1557
                        while (*p == ' ')
 
1558
                                p++;
 
1559
                        sprintf(s, prefix, link_isfinder, p);
 
1560
                        AddLink(s);
 
1561
                        MemFree(s);
 
1562
                        ff_AddString(p);
 
1563
                        AddLink("</a>");
 
1564
                }
 
1565
                if (( p = StringStr(str, "GABI:")) != NULL) {
 
1566
                        nothing = FALSE;
 
1567
                        p += StringLen("GABI:");
 
1568
                        l = StringLen(link_gabi) + StringLen(p);
 
1569
                        prefix = "<a href=%s%s>"; 
 
1570
                        ll = StringLen(prefix); 
 
1571
                        s = (CharPtr)MemNew(l + ll);
 
1572
                        ss = (CharPtr)MemNew(p-str+1);
 
1573
                        StringNCpy(ss, str, p-str);
 
1574
                        ff_AddString(ss);
 
1575
                        MemFree(ss);
 
1576
                        while (*p == ' ')
 
1577
                                p++;
 
1578
                        sprintf(s, prefix, link_gabi, p);
 
1579
                        AddLink(s);
 
1580
                        MemFree(s);
 
1581
                        ff_AddString(p);
 
1582
                        AddLink("</a>");
 
1583
                }
 
1584
                if (( p = StringStr(str, "FANTOM_DB:")) != NULL) {
 
1585
                        nothing = FALSE;
 
1586
                        p += StringLen("FANTOM_DB:");
 
1587
                        l = StringLen(link_fantom) + StringLen(p);
 
1588
                        prefix = "<a href=%s%s>"; 
 
1589
                        ll = StringLen(prefix); 
 
1590
                        s = (CharPtr)MemNew(l + ll);
 
1591
                        ss = (CharPtr)MemNew(p-str+1);
 
1592
                        StringNCpy(ss, str, p-str);
 
1593
                        ff_AddString(ss);
 
1594
                        MemFree(ss);
 
1595
                        while (*p == ' ')
 
1596
                                p++;
 
1597
                        sprintf(s, prefix, link_fantom, p);
 
1598
                        AddLink(s);
 
1599
                        MemFree(s);
 
1600
                        ff_AddString(p);
 
1601
                        AddLink("</a>");
 
1602
                }
1351
1603
                if (nothing) {
1352
1604
                        ff_AddString(str);
1353
1605
                }