~ubuntu-branches/ubuntu/edgy/ncbi-tools6/edgy

#define DEF_LINK_GENEDB "http://www.genedb.org/genedb/Dispatcher?formType=navBar&submit=Search+for&organism=All%3Apombe%3Acerevisiae%3Adicty%3Aasp%3Atryp%3Aleish%3Amalaria%3Astyphi%3Aglossina&desc=yes&ohmr=%2F&name="

214

217

215

218

static Char link_geneid [MAX_WWWBUF];

216

#define DEF_LINK_GENEID "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=retrieve&dopt=graphics&list_uids="

219

#define DEF_LINK_GENEID "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=full_report&list_uids="

217

220

218

221

static Char link_zfin [MAX_WWWBUF];

219

222

#define DEF_LINK_ZFIN "http://zfin.org/cgi-bin/webdriver?MIval=aa-markerview.apg&OID="

278

281

static Char link_uspto [MAX_WWWBUF];

279

282

#define DEF_LINK_USPTO "http://patft.uspto.gov/netacgi/nph-Parser?patentnumber="

280

283

284

static Char link_vector [MAX_WWWBUF];

285

#define DEF_LINK_VECTOR "http://www.vectorbase.org/Genome/BRCGene/?"

286

287

static Char link_mirbase [MAX_WWWBUF];

288

#define DEF_LINK_MIRBASE "http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?acc="

289

281

290

282

291

/* www utility functions */

283

292

296

305

GetAppParam ("NCBI", "WWWENTREZ", "LINK_FEAT", DEF_LINK_FEAT, link_feat, MAX_WWWBUF);

297

306

GetAppParam ("NCBI", "WWWENTREZ", "LINK_FEATC", DEF_LINK_FEATC, link_featc, MAX_WWWBUF);

298

307

GetAppParam ("NCBI", "WWWENTREZ", "LINK_SEQ", DEF_LINK_SEQ, link_seq, MAX_WWWBUF);

308

GetAppParam ("NCBI", "WWWENTREZ", "LINK_PROJID", DEF_LINK_PROJID, link_projid, MAX_WWWBUF);

299

309

GetAppParam ("NCBI", "WWWENTREZ", "LINK_WGS", DEF_LINK_WGS, link_wgs, MAX_WWWBUF);

300

310

GetAppParam ("NCBI", "WWWENTREZ", "LINK_OMIM", DEF_LINK_OMIM, link_omim, MAX_WWWBUF);

301

311

GetAppParam ("NCBI", "WWWENTREZ", "LINK_REF", DEF_LINK_REF, ref_link, MAX_WWWBUF);

306

316

GetAppParam ("NCBI", "WWWENTREZ", "LINK_ECAMBIG", DEF_LINK_ECAMBIG, ec_ambig, MAX_WWWBUF);

307

317

GetAppParam ("NCBI", "WWWENTREZ", "LINK_FF", DEF_LINK_FF, link_ff, MAX_WWWBUF);

308

318

GetAppParam ("NCBI", "WWWENTREZ", "LINK_MUID", DEF_LINK_MUID, link_muid, MAX_WWWBUF);

309

GetAppParam ("NCBI", "WWWENTREZ", "LINK_FF", DEF_LINK_FF, link_ff, MAX_WWWBUF);

310

GetAppParam ("NCBI", "WWWENTREZ", "LINK_MUID", DEF_LINK_MUID, link_muid, MAX_WWWBUF);

311

319

GetAppParam ("NCBI", "WWWENTREZ", "LINK_ACE", DEF_LINK_ACE, link_ace, MAX_WWWBUF);

312

320

GetAppParam ("NCBI", "WWWENTREZ", "LINK_TAX", DEF_LINK_TAX, link_tax, MAX_WWWBUF);

313

321

GetAppParam ("NCBI", "WWWENTREZ", "LINK_CODE", DEF_LINK_CODE, link_code, MAX_WWWBUF);

367

375

GetAppParam ("NCBI", "WWWENTREZ", "LINK_BOLD", DEF_LINK_BOLD, link_bold, MAX_WWWBUF);

368

376

GetAppParam ("NCBI", "WWWENTREZ", "LINK_HPRD", DEF_LINK_HPRD, link_hprd, MAX_WWWBUF);

369

377

GetAppParam ("NCBI", "WWWENTREZ", "LINK_USPTO", DEF_LINK_USPTO, link_uspto, MAX_WWWBUF);

378

GetAppParam ("NCBI", "WWWENTREZ", "LINK_VECTOR", DEF_LINK_VECTOR, link_vector, MAX_WWWBUF);

379

GetAppParam ("NCBI", "WWWENTREZ", "LINK_MIRBASE", DEF_LINK_MIRBASE, link_mirbase, MAX_WWWBUF);

370

380

}

371

381

372

382

666

676

FF_www_db_xref_std (ffstring, db, identifier, link);

667

677

}

668

678

679

static void FF_www_db_xref_vector (

680

StringItemPtr ffstring,

681

CharPtr db,

682

CharPtr identifier,

683

BioseqPtr bsp,

684

CharPtr link

685

)

686

{

687

Char ch;

688

Char buf [512], tax [256];

689

CharPtr ptr;

690

691

StringCpy (buf, link);

692

if (bsp != NULL) {

693

if (BioseqToGeneticCode (bsp, NULL, NULL, NULL, tax, sizeof (tax), NULL)) {

694

ptr = tax;

695

ch = *ptr;

696

while (ch != '\0') {

697

if (IS_WHITESP (ch)) {

698

*ptr = '_';

699

}

700

ptr++;

701

ch = *ptr;

702

}

703

StringCat (buf, "org=");

704

StringCat (buf, tax);

705

StringCat (buf, "&");

706

}

707

}

708

StringCat (buf, "gene=");

709

FF_www_db_xref_std (ffstring, db, identifier, buf);

710

}

711

669

712

static void FF_www_db_xref_null (

670

713

StringItemPtr ffstring,

671

714

CharPtr db,

684

727

static void Do_www_db_xref(

685

728

IntAsn2gbJobPtr ajp,

686

729

StringItemPtr ffstring,

687

CharPtr db, CharPtr identifier

730

CharPtr db,

731

CharPtr identifier,

732

BioseqPtr bsp

688

733

)

689

734

{

690

735

if ( ffstring == NULL || db == NULL || identifier == NULL ) return;

809

854

FF_www_db_xref_null(ffstring, db, identifier, link_bold);

810

855

} else if ( StringCmp(db , "HPRD") == 0) {

811

856

FF_www_db_xref_hprd(ffstring, db, identifier, link_hprd);

857

} else if ( StringCmp(db , "VectorBase") == 0) {

858

FF_www_db_xref_vector(ffstring, db, identifier, bsp, link_vector);

859

} else if ( StringCmp(db , "miRBase") == 0) {

860

FF_www_db_xref_std(ffstring, db, identifier, link_mirbase);

812

861

813

862

} else {

814

863

/* default: no link just the text */

819

868

NLM_EXTERN void FF_www_db_xref(

820

869

IntAsn2gbJobPtr ajp,

821

870

StringItemPtr ffstring,

822

CharPtr db, CharPtr identifier

871

CharPtr db,

872

CharPtr identifier,

873

BioseqPtr bsp

823

874

)

824

875

{

825

876

if ( ffstring == NULL || db == NULL || identifier == NULL ) return;

826

877

827

878

if ( GetWWW(ajp) ) {

828

Do_www_db_xref (ajp, ffstring, db, identifier);

879

Do_www_db_xref (ajp, ffstring, db, identifier, bsp);

829

880

} else { /* not in www mode */

830

881

if (StringCmp(db , "MGD") == 0 || StringCmp(db , "MGI") == 0) {

831

882

if (StringNICmp (identifier, "MGI:", 4) == 0) {

881

932

}

882

933

ajp->www = TRUE;

883

934

884

Do_www_db_xref (ajp, ffstring, dbt->db, buf);

935

Do_www_db_xref (ajp, ffstring, dbt->db, buf, NULL);

885

936

886

937

ajp->www = FALSE;

887

938

1078

1129

1079

1130

{

1080

1131

AuthorPtr ap;

1132

ValNodePtr clist;

1081

1133

ValNodePtr conslist;

1082

1134

Int2 count;

1083

1135

ValNodePtr head = NULL;

1147

1199

prefix = ", ";

1148

1200

}

1149

1201

1202

prefix = NULL;

1203

clist = NULL;

1150

1204

for (vnp = conslist; vnp != NULL; vnp = vnp->next) {

1151

1205

str = NULL;

1152

1206

pid = (PersonIdPtr) vnp->data.ptrvalue;

1153

1207

if (pid->choice == 5) {

1154

str = MakeSingleAuthorString (format, NULL, (CharPtr) pid->data, NULL, NULL, index, NULL);

1155

if ((! StringHasNoText (str)) && consortP != NULL && *consortP == NULL) {

1156

*consortP = StringSave (str);

1157

}

1158

1159

/* optionally populate gbseq for XML-ized GenBank format */

1160

1161

if (gbref != NULL) {

1162

gbref->consortium = StringSave (str);

1163

}

1164

1165

str = MemFree (str);

1166

}

1208

str = MakeSingleAuthorString (format, prefix, (CharPtr) pid->data, NULL, NULL, index, NULL);

1209

if (str != NULL) {

1210

ValNodeAddStr (&clist, 0, str);

1211

}

1212

prefix = "; ";

1213

}

1214

}

1215

if (clist != NULL) {

1216

str = MergeFFValNodeStrs (clist);

1217

if ((! StringHasNoText (str)) && consortP != NULL && *consortP == NULL) {

1218

*consortP = StringSave (str);

1219

}

1220

1221

/* optionally populate gbseq for XML-ized GenBank format */

1222

1223

if (gbref != NULL) {

1224

gbref->consortium = StringSave (str);

1225

}

1226

1227

str = MemFree (str);

1228

ValNodeFreeData (clist);

1167

1229

}

1168

1230

1169

1231

ValNodeFree (pidlist);

2504

2566

}

2505

2567

2506

2568

static CharPtr FormatCitPat (

2507

FmtType format,

2569

FmtType format,

2570

ModType mode,

2508

2571

CitPatPtr cpp,

2509

SeqIdPtr seqidp,

2572

SeqIdPtr seqidp,

2510

2573

IntAsn2gbJobPtr ajp

2511

2574

)

2512

2575

2513

2576

{

2514

2577

AffilPtr afp;

2515

2578

AuthListPtr alp;

2579

IdPatPtr cit;

2516

2580

CharPtr consortium = NULL;

2517

2581

Char date [40];

2518

2582

ValNodePtr head = NULL;

2583

Boolean is_us_pre_grant = FALSE;

2519

2584

CharPtr prefix = NULL;

2520

2585

CharPtr rsult = NULL;

2521

2586

SeqIdPtr sip;

2527

2592

2528

2593

if (cpp == NULL) return NULL;

2529

2594

2595

if (StringHasNoText (cpp->number) &&

2596

StringDoesHaveText (cpp->app_number) &&

2597

StringCmp (cpp->country, "US") == 0 &&

2598

mode != RELEASE_MODE) {

2599

for (sip = seqidp; sip != NULL; sip = sip->next) {

2600

if (sip->choice != SEQID_PATENT) continue;

2601

psip = (PatentSeqIdPtr) sip->data.ptrvalue;

2602

if (psip == NULL) continue;

2603

cit = psip->cit;

2604

if (cit == NULL) continue;

2605

if (StringDoesHaveText (cit->app_number)) {

2606

is_us_pre_grant = TRUE;

2607

}

2608

}

2609

}

2610

2530

2611

if (format == GENBANK_FMT || format == GENPEPT_FMT) {

2531

ValNodeCopyStr (&head, 0, "Patent: ");

2532

suffix = " ";

2612

if (is_us_pre_grant) {

2613

ValNodeCopyStr (&head, 0, "Pre-Grant Patent: ");

2614

suffix = " ";

2615

} else {

2616

ValNodeCopyStr (&head, 0, "Patent: ");

2617

suffix = " ";

2618

}

2533

2619

} else if (format == EMBL_FMT || format == EMBLPEPT_FMT) {

2534

2620

ValNodeCopyStr (&head, 0, "Patent number ");

2535

2621

}

2550

2636

ValNodeCopyStr (&head, 0, cpp->number);

2551

2637

}

2552

2638

} else if (! StringHasNoText (cpp->app_number)) {

2553

AddValNodeString (&head, "(", cpp->app_number, ")");

2639

if (is_us_pre_grant) {

2640

AddValNodeString (&head, NULL, cpp->app_number, NULL);

2641

} else {

2642

AddValNodeString (&head, "(", cpp->app_number, ")");

2643

}

2554

2644

}

2555

2645

2556

2646

if (! StringHasNoText (cpp->doc_type)) {

2922

3012

2923

3013

static CharPtr GetPubJournal (

2924

3014

FmtType format,

3015

ModType mode,

2925

3016

Boolean dropBadCitGens,

2926

3017

Boolean noAffilOnUnpub,

2927

3018

Boolean citArtIsoJta,

2928

3019

PubdescPtr pdp,

2929

3020

CitSubPtr csp,

2930

SeqIdPtr seqidp,

3021

SeqIdPtr seqidp,

2931

3022

IndxPtr index,

2932

3023

IntAsn2gbJobPtr ajp

2933

3024

)

2996

3087

case PUB_Patent :

2997

3088

cpp = (CitPatPtr) vnp->data.ptrvalue;

2998

3089

if (cpp != NULL) {

2999

journal = FormatCitPat (format, cpp, seqidp, ajp);

3090

journal = FormatCitPat (format, mode, cpp, seqidp, ajp);

3000

3091

}

3001

3092

break;

3002

3093

default :

3221

3312

static void AddReferenceToGbseq (

3222

3313

GBSeqPtr gbseq,

3223

3314

GBReferencePtr gbref,

3224

CharPtr str

3315

CharPtr str,

3316

RefBlockPtr rbp,

3317

BioseqPtr bsp

3225

3318

)

3226

3319

3227

3320

{

3228

CharPtr copy;

3229

CharPtr ptr;

3230

CharPtr ref;

3321

Char buf [32];

3322

CharPtr copy;

3323

ValNodePtr head = NULL;

3324

IntRefBlockPtr irp;

3325

SeqLocPtr loc;

3326

CharPtr ptr;

3327

CharPtr ref;

3328

SeqLocPtr slp;

3329

Int4 start;

3330

Int4 stop;

3331

CharPtr tmp;

3231

3332

3232

if (gbseq == NULL || gbref == NULL || StringHasNoText (str)) return;

3333

if (gbseq == NULL || gbref == NULL || StringHasNoText (str) || rbp == NULL || bsp == NULL) return;

3233

3334

3234

3335

copy = StringSave (str);

3235

3336

3244

3345

ref = copy + 12;

3245

3346

ptr = StringStr (ref, "\n AUTHORS");

3246

3347

if (ptr == NULL) {

3348

ptr = StringStr (ref, "\n CONSRTM");

3349

}

3350

if (ptr == NULL) {

3247

3351

ptr = StringStr (ref, ")\n");

3352

if (ptr != NULL) {

3353

ptr++;

3354

}

3248

3355

}

3249

3356

if (ptr != NULL) {

3250

3357

*ptr = '\0';

3267

3374

Asn2gnbkCompressSpaces (gbref->journal);

3268

3375

3269

3376

MemFree (copy);

3377

3378

if (rbp->sites == 1 || rbp->sites == 2) {

3379

gbref->position = StringSave ("sites");

3380

} else if (rbp->sites == 3) {

3381

} else {

3382

irp = (IntRefBlockPtr) rbp;

3383

loc = irp->loc;

3384

if (loc != NULL) {

3385

slp = SeqLocFindNext (loc, NULL);

3386

while (slp != NULL) {

3387

start = SeqLocStart (slp) + 1;

3388

stop = SeqLocStop (slp) + 1;

3389

if (head == NULL) {

3390

sprintf (buf, "%ld..%ld", (long) start, (long) stop);

3391

} else {

3392

sprintf (buf, "; %ld..%ld", (long) start, (long) stop);

3393

}

3394

ValNodeCopyStr (&head, 0, buf);

3395

slp = SeqLocFindNext (loc, slp);

3396

}

3397

tmp = MergeFFValNodeStrs (head);

3398

ValNodeFreeData (head);

3399

gbref->position = tmp;

3400

} else {

3401

start = 1;

3402

stop = bsp->length;

3403

sprintf (buf, "%ld..%ld", (long) start, (long) stop);

3404

gbref->position = StringSave (buf);

3405

}

3406

}

3270

3407

}

3271

3408

3272

3409

static Boolean IsCitSub (

3348

3485

Int4 pmid = 0;

3349

3486

CharPtr prefix = NULL;

3350

3487

RefBlockPtr rbp;

3488

ValNodePtr remarks = NULL;

3489

CharPtr remprefix = NULL;

3351

3490

SubmitBlockPtr sbp;

3352

3491

SeqDescrPtr sdp;

3353

3492

SeqFeatPtr sfp = NULL;

3598

3737

3599

3738

/* print author list */

3600

3739

3601

FFRecycleString(ajp, temp);

3602

temp = FFGetString(ajp);

3603

FFStartPrint(temp, afp->format, 2, 12, "AUTHORS", 12, 5, 5, "RA", FALSE);

3604

3605

3740

str = NULL;

3606

3741

consortium = NULL;

3607

3742

3611

3746

TrimSpacesAroundString (str);

3612

3747

}

3613

3748

3614

if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {

3615

suffix = NULL;

3616

trailingPeriod = TRUE;

3617

} else if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) {

3618

trailingPeriod = FALSE;

3619

len = StringLen (str);

3620

if (len > 0 && str [len - 1] != '.') {

3621

suffix = ".;";

3622

} else {

3623

suffix = ";";

3624

}

3625

}

3749

if (str != NULL || StringHasNoText (consortium)) {

3750

FFRecycleString(ajp, temp);

3751

temp = FFGetString(ajp);

3752

FFStartPrint(temp, afp->format, 2, 12, "AUTHORS", 12, 5, 5, "RA", FALSE);

3626

3753

3627

/* if no authors were found, period will still be added by this call */

3628

if (str != NULL) {

3629

FFAddTextToString(temp, NULL, str, suffix, trailingPeriod, FALSE, TILDE_TO_SPACES);

3630

} else {

3631

3754

if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {

3632

FFAddOneChar(temp, '.', FALSE);

3755

suffix = NULL;

3756

trailingPeriod = TRUE;

3633

3757

} else if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) {

3634

FFAddOneChar(temp, ';', FALSE);

3635

}

3636

}

3637

3638

MemFree (str);

3639

if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {

3758

trailingPeriod = FALSE;

3759

len = StringLen (str);

3760

if (len > 0 && str [len - 1] != '.') {

3761

suffix = ".;";

3762

} else {

3763

suffix = ";";

3764

}

3765

}

3766

3767

/* if no authors were found, period will still be added by this call */

3768

if (str != NULL) {

3769

FFAddTextToString(temp, NULL, str, suffix, trailingPeriod, FALSE, TILDE_TO_SPACES);

3770

} else if (StringHasNoText (consortium)) {

3771

if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {

3772

FFAddOneChar(temp, '.', FALSE);

3773

} else if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) {

3774

FFAddOneChar(temp, ';', FALSE);

3775

}

3776

}

3777

3778

if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {

3640

3779

FFLineWrap(ffstring, temp, 12, 12, ASN2FF_GB_MAX, NULL);

3641

} else {

3780

} else {

3642

3781

FFLineWrap(ffstring, temp, 5, 5, ASN2FF_EMBL_MAX, "RA");

3782

}

3643

3783

}

3784

MemFree (str);

3644

3785

3645

3786

/* print consortium */

3646

3787

3730

3871

citArtIsoJta = FALSE;

3731

3872

}

3732

3873

3733

str = GetPubJournal (afp->format, ajp->flags.dropBadCitGens,

3734

ajp->flags.noAffilOnUnpub, citArtIsoJta,

3735

pdp, csp, bsp->id, index, ajp);

3874

str = GetPubJournal (afp->format, ajp->mode, ajp->flags.dropBadCitGens,

3875

ajp->flags.noAffilOnUnpub, citArtIsoJta, pdp, csp,

3876

bsp->id, index, ajp);

3736

3877

if (str == NULL) {

3737

3878

str = StringSave ("Unpublished");

3738

3879

}

3815

3956

3816

3957

if (gbseq != NULL) {

3817

3958

if (gbref != NULL) {

3818

gbref->medline = muid;

3819

3959

gbref->pubmed = pmid;

3820

3960

}

3821

3961

}

3825

3965

3826

3966

if (gbseq != NULL) {

3827

3967

if (gbref != NULL) {

3828

AddReferenceToGbseq (gbseq, gbref, str);

3968

AddReferenceToGbseq (gbseq, gbref, str, rbp, bsp);

3829

3969

}

3830

3970

}

3831

3971

3858

3998

FFRecycleString(ajp, temp);

3859

3999

temp = FFGetString(ajp);

3860

4000

4001

if (remprefix != NULL) {

4002

ValNodeCopyStr (&remarks, 0, remprefix);

4003

}

4004

ValNodeCopyStr (&remarks, 0, pdp->comment);

4005

remprefix = "; ";

3861

4006

FFStartPrint (temp, afp->format, 2, 12, prefix, 12, 5, 5, NULL, FALSE);

3862

4007

FFAddOneString (temp, pdp->comment, FALSE, TRUE, TILDE_EXPAND);

3863

4008

/* AddCommentWithURLlinks(ajp, temp, NULL, pdp->comment, NULL); */

3866

4011

3867

4012

if (gbseq != NULL) {

3868

4013

if (gbref != NULL) {

4014

3869

4015

gbref->remark = StringSave (pdp->comment);

4016

3870

4017

}

3871

4018

}

3872

4019

3890

4037

temp = FFGetString(ajp);

3891

4038

3892

4039

sprintf (buf, "GenBank staff at the National Library of Medicine created this entry [NCBI gibbsq %ld] from the original journal article.", (long) gibbsq);

4040

if (remprefix != NULL) {

4041

ValNodeCopyStr (&remarks, 0, remprefix);

4042

}

4043

ValNodeCopyStr (&remarks, 0, buf);

4044

remprefix = "; ";

3893

4045

FFStartPrint (temp, afp->format, 2, 12, prefix, 12, 5, 5, NULL, FALSE);

3894

4046

FFAddOneString (temp, buf, FALSE, FALSE, TILDE_EXPAND);

3895

4047

FFLineWrap(ffstring, temp, 12, 12, ASN2FF_GB_MAX, NULL);

3906

4058

temp = FFGetString(ajp);

3907

4059

3908

4060

sprintf (buf, "This sequence comes from %s", str);

4061

if (remprefix != NULL) {

4062

ValNodeCopyStr (&remarks, 0, remprefix);

4063

}

4064

ValNodeCopyStr (&remarks, 0, buf);

4065

remprefix = "; ";

3909

4066

FFStartPrint (temp, afp->format, 2, 12, prefix, 12, 5, 5, NULL, FALSE);

3910

4067

FFAddOneString (temp, buf, TRUE, TRUE, TILDE_EXPAND);

3911

4068

FFLineWrap(ffstring, temp, 12, 12, ASN2FF_GB_MAX, NULL);

3916

4073

FFRecycleString(ajp, temp);

3917

4074

temp = FFGetString(ajp);

3918

4075

3919

FFStartPrint (temp ,afp->format, 2, 12, prefix, 12, 5, 5, NULL, FALSE);

4076

if (remprefix != NULL) {

4077

ValNodeCopyStr (&remarks, 0, remprefix);

4078

}

4079

ValNodeCopyStr (&remarks, 0, "Polyadenylate residues occurring in the figure were omitted from the sequence.");

4080

remprefix = "; ";

4081

FFStartPrint (temp, afp->format, 2, 12, prefix, 12, 5, 5, NULL, FALSE);

3920

4082

FFAddOneString (temp, "Polyadenylate residues occurring in the figure were omitted from the sequence.", TRUE, TRUE, TILDE_EXPAND);

3921

4083

FFLineWrap(ffstring, temp, 12, 12, ASN2FF_GB_MAX, NULL);

3922

4084

prefix = NULL;

3931

4093

temp = FFGetString(ajp);

3932

4094

3933

4095

sprintf (buf, "Map location: %s", str);

4096

if (remprefix != NULL) {

4097

ValNodeCopyStr (&remarks, 0, remprefix);

4098

}

4099

ValNodeCopyStr (&remarks, 0, buf);

4100

remprefix = "; ";

3934

4101

FFStartPrint (temp, afp->format, 2, 12, prefix, 12, 5, 5, NULL, FALSE);

3935

4102

FFAddOneString (temp, buf, TRUE, TRUE, TILDE_EXPAND);

3936

4103

FFLineWrap(ffstring, temp, 12, 12, ASN2FF_GB_MAX, NULL);

3952

4119

FFRecycleString(ajp, temp);

3953

4120

temp = FFGetString(ajp);

3954

4121

4122

len = StringLen (crp->exp) + 20;

4123

str = MemNew (sizeof (Char) * len);

4124

if (str != NULL) {

4125

sprintf (str, "Erratum:[%s]", crp->exp);

4126

if (remprefix != NULL) {

4127

ValNodeCopyStr (&remarks, 0, remprefix);

4128

}

4129

ValNodeCopyStr (&remarks, 0, str);

4130

remprefix = "; ";

4131

str = MemFree (str);

4132

}

3955

4133

FFStartPrint (temp, afp->format, 2, 12, prefix, 12, 5, 5, NULL, FALSE);

3956

4134

FFAddOneString (temp, "Erratum:", FALSE, FALSE, TILDE_TO_SPACES);

3957

4135

FFAddTextToString (temp, "[", crp->exp, "]", FALSE, TRUE, TILDE_EXPAND);

3968

4146

FFRecycleString(ajp, temp);

3969

4147

temp = FFGetString(ajp);

3970

4148

4149

if (remprefix != NULL) {

4150

ValNodeCopyStr (&remarks, 0, remprefix);

4151

}

4152

ValNodeCopyStr (&remarks, 0, csp->descr);

4153

remprefix = "; ";

3971

4154

FFStartPrint (temp, afp->format, 2, 12, prefix, 12, 5, 5, NULL, FALSE);

3972

4155

/* FFAddOneString (temp, csp->descr, FALSE, TRUE, TILDE_EXPAND); */

3973

4156

AddCommentWithURLlinks(ajp, temp, NULL, csp->descr, NULL);

3984

4167

3985

4168

if (gbseq != NULL) {

3986

4169

if (gbref != NULL) {

3987

AddReferenceToGbseq (gbseq, gbref, str);

4170

if (remarks != NULL) {

4171

gbref->remark = MergeFFValNodeStrs (remarks);

4172

}

4173

4174

AddReferenceToGbseq (gbseq, gbref, str, rbp, bsp);

3988

4175

}

3989

4176

}

4177

ValNodeFreeData (remarks);

3990

4178

3991

4179

FFRecycleString(ajp, ffstring);

3992

4180

FFRecycleString(ajp, temp);

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