/* wprint.c * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information (NCBI) * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government do not place any restriction on its use or reproduction. * We would, however, appreciate having the NCBI and the author cited in * any work or product based on this material * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * =========================================================================== * * File Name: wprint.c * * Author: Karl Sirotkin, Tom Madden, Tatiana Tatusov * * Version Creation Date: 7/15/95 * * $Revision: 6.61 $ * * File Description: * * Modifications: * -------------------------------------------------------------------------- * Date Name Description of modification * ------- ---------- ----------------------------------------------------- * * * ========================================================================== */ /************************************* * * $Log: wprint.c,v $ * Revision 6.61 2001/12/06 17:00:41 kans * TextSave takes size_t, not Int2, otherwise titin protein tries to allocate negative number * * Revision 6.60 2001/12/06 12:36:41 kans * switch from viewer.cgi to viewer.fcgi * * Revision 6.59 2001/11/27 18:45:16 kans * fixed FLYBASE capitalization, added niaEST * * Revision 6.58 2001/10/02 17:39:29 yaschenk * Removing memory leaks * * Revision 6.57 2001/08/06 23:59:45 kans * added third party annotation SeqID support * * Revision 6.56 2001/08/06 22:13:13 kans * using NUM_SEQID, added TPA ids to arrays * * Revision 6.55 2001/04/23 22:40:04 tatiana * estimated size increased in www_featkey() * * Revision 6.54 2001/04/12 22:31:37 yaschenk * fixing string size estimates in www_accession * * Revision 6.53 2001/02/01 16:23:09 tatiana * typo fixed in RGD link * * Revision 6.52 2001/01/03 17:01:44 tatiana * a bug fixed in LocGenomePrint, complement added * * Revision 6.51 2000/12/06 20:56:17 tatiana * AceView link added * * Revision 6.50 2000/12/05 23:04:37 tatiana * NT_ COMMENT formatted * * Revision 6.49 2000/12/05 01:22:18 tatiana * COG added * * Revision 6.47 2000/10/24 20:33:39 tatiana * added link to UniSTS and InterimID * * Revision 6.46 2000/10/18 21:19:59 kans * changed omim link * * Revision 6.45 2000/10/18 12:29:37 tatiana * rice link changed * * Revision 6.44 2000/09/05 18:22:48 kans * added CDD link * * Revision 6.43 2000/08/07 14:03:03 tatiana * printf format fix * * Revision 6.42 2000/07/25 14:40:37 tatiana * changed SGD link * * Revision 6.41 2000/07/20 21:22:36 tatiana * refseq hot link corrected * * Revision 6.40 2000/07/14 20:24:27 kans * added RGD as dbxref with web link * * Revision 6.39 2000/07/11 22:17:12 tatiana * fixed hot link for refseq * * Revision 6.38 2000/07/10 21:02:17 tatiana * added link to refseq * * Revision 6.37 2000/06/21 18:31:04 tatiana * fixed qmap.cgi syntax for dbsource link * * Revision 6.36 2000/03/23 14:45:53 tatiana * added links for MGD, FBgn, FBan * * Revision 6.35 2000/03/20 17:47:51 kans * changed rice link * * Revision 6.34 2000/03/09 22:16:56 kans * changed rice link * * Revision 6.33 2000/02/29 15:33:15 tatiana * RiceGenes URL changed * * Revision 6.32 2000/02/25 21:52:03 kans * changed flybase link to indiana university url * * Revision 6.31 2000/02/24 17:53:56 kans * added dbSNP and RATMAP to dbxref * * Revision 6.30 2000/01/11 17:14:13 tatiana * check for web symbols added in PrintComment * * Revision 6.29 1999/12/21 14:27:10 tatiana * version added to CONTIG line * * Revision 6.28 1999/11/02 19:57:04 tatiana * a typo fixed in PrintGenome * * Revision 6.27 1999/11/02 16:31:20 tatiana * fixed PrintGenome() * * Revision 6.26 1999/10/01 16:40:24 vakatov * Fixed a stack memory overrun bug in PrintDate() * * Revision 6.25 1999/09/29 17:20:38 tatiana * SeqIdFindBest changed to SeqIdSelect for CONTIG line * * Revision 6.24 1999/08/31 18:31:24 tatiana * OLDQUERY ifdef added * * Revision 6.23 1999/08/30 17:07:01 tatiana * minor changes for html version printing * * Revision 6.22 1999/05/13 23:00:44 tatiana * hot link added to REFSEQ in COMMENT * * Revision 6.21 1999/04/07 22:17:58 tatiana * added BR in web GARPHIK_FMT * * Revision 6.20 1999/04/07 20:49:18 tatiana * fix compiler warning www_protein_id() * * Revision 6.19 1999/04/06 22:37:14 tatiana * www_protein_id() added * * Revision 6.18 1999/04/06 14:56:57 tatiana * SWISS-PROT link disabled * * Revision 6.17 1999/04/06 14:41:44 tatiana * LocusLink corrections * * Revision 6.16 1999/03/30 21:02:18 tatiana * www_accession www_taxid added * * Revision 6.15 1999/03/29 18:15:33 tatiana * OMIM and LocusLink hyper-links added to dbxref * * Revision 6.14 1999/03/12 17:33:47 tatiana * www_featkey() added and type casting fixed * * Revision 6.13 1998/11/23 17:05:35 tatiana * a bug fixed in SP link in www_db_xref() * * Revision 6.12 1998/10/08 15:14:52 tatiana * link to SWISSPROT - expasy.hcuge.ch removed * * Revision 6.11 1998/08/19 18:42:08 tatiana * hot link to RiceGenes added * * Revision 6.10 1998/08/04 14:58:30 tatiana * ff_AddString changed to ff_AddStringWithTildes in www_PrintComment() * * Revision 6.9 1998/07/24 16:51:06 vakatov * added LIBCALL modifier to "www_PrintComment()" * * Revision 6.8 1998/07/23 22:41:52 tatiana * added www_PrintComment() * * Revision 6.7 1998/05/28 18:30:27 tatiana * typedef for HeadTailProc moved to ffprint.h * * Revision 6.6 1998/04/30 21:52:48 tatiana * *** empty log message *** * * Revision 6.5 1998/04/29 16:21:48 tatiana * www_dbsource(): db=n changed to db=s in query link * * Revision 6.4 1998/02/11 19:37:05 tatiana * check for NULL added in LocPrintGenome() * * Revision 6.3 1998/02/06 21:21:08 tatiana * db changed to s in query URL * * Revision 6.0 1997/08/25 18:08:38 madden * Revision changed to 6.0 * * Revision 5.21 1997/08/19 22:34:18 tatiana * bug fixed in PrintGenome() * * Revision 5.19 1997/08/07 22:18:13 tatiana * PrintGenome() fix for the WWW * * Revision 5.18 1997/08/06 22:38:03 tatiana * minor fixes in PrintGenome() * * Revision 5.17 1997/07/28 14:31:31 vakatov * Keep the head_tail_ff() proto in-sync with its header-located declaration * * Revision 5.16 1997/07/28 13:29:38 ostell * Moved GetUniGeneIDForSeqId() to seqmgr.c * * Revision 5.15 1997/07/25 15:51:37 tatiana * sition counts in PrintGenome * * Revision 5.14 1997/07/16 21:26:32 tatiana * PrintGenome() added * * Revision 5.13 1997/06/26 20:56:43 tatiana * a bug fixed in PrintSPBlock * * Revision 5.12 1997/06/23 19:18:53 tatiana * www_featloc() fixed * * Revision 5.11 1997/06/19 18:39:57 vakatov * [WIN32,MSVC++] Adopted for the "NCBIOBJ.LIB" DLL'ization * * Revision 5.10 1997/03/13 21:37:37 tatiana * query?-guid changed to query?uid in all Entrez limks * * Revision 5.9 1997/03/11 20:17:25 tatiana * OMIM hot links added to DBSOURCE * * Revision 5.8 1997/01/10 19:51:39 epstein * add missing LIBCALLs * * Revision 5.7 1997/01/06 21:38:52 vakatov * Removed local(static) NCBI_months[12] -- use that from the "ncbitime.[ch]" * * Revision 5.6 1996/12/03 15:50:43 tatiana * hot link to CK in db_xref added * * Revision 5.5 1996/08/16 20:35:44 tatiana * www_coded_by added * * Revision 5.4 1996/07/19 21:36:29 tatiana * protection for NULL acc added to PrintSPBlock() * * Revision 5.3 1996/07/19 18:13:16 tatiana * ddbj hot link bug fixed (gbj -> dbj) * * Revision 5.2 1996/07/12 19:49:52 tatiana * SP hot link added to db_xref * * Revision 5.1 1996/06/25 22:22:09 tatiana * new GDB hot list * * Revision 4.25 1996/04/29 19:54:11 tatiana * new SGD URL * * Revision 4.24 1996/04/15 16:08:36 tatiana * new line in DBSOURCE * * Revision 4.23 1996/04/15 14:37:43 tatiana * old_www_featloc removed * * Revision 4.21 1996/04/09 16:12:19 tatiana * *** empty log message *** * * Revision 4.20 1996/04/09 14:05:15 tatiana * DescrStructPtr changes * * Revision 4.18 1996/04/08 21:53:17 tatiana * change in www_featloc * * Revision 4.17 1996/03/27 15:40:55 epstein * re-retro previous 'referer' changes, and change swissprot output to point to protein DB * * Revision 4.16 1996/03/25 15:21:46 tatiana * www_featloc added * * Revision 4.15 1996/03/20 16:13:58 epstein * change print-logic to accomodate 'referer' script which logs references to external databases * * Revision 4.14 1996/02/28 04:53:06 ostell * minor fixes * * Revision 4.13 1996/02/26 03:45:24 ostell * fixed usage of GatherDescrListByChoice and changed function to allocate * first DescrStruct instead using static storage * * Revision 4.12 1996/02/26 00:46:18 ostell * removed unused local variables and integer size mismatch fusses * * Revision 4.11 1996/02/21 20:08:03 tatiana * a bug fixed n www_dbsource * * Revision 4.9 1995/12/20 22:43:19 tatiana * Int2 changed to Int4 in www_organism() * * Revision 4.8 1995/12/19 23:34:20 tatiana * hot link to SGD added * * Revision 4.7 1995/12/13 16:36:15 tatiana * hot link to db_xref added * * Revision 4.6 1995/11/24 15:38:44 tatiana * GetAppParam moved to init_www * * Revision 4.5 1995/11/22 18:58:01 tatiana * turn spaces to + in hotlink * * Revision 4.4 1995/11/17 21:48:28 tatiana * hot link to genetic code added * * Revision 4.3 1995/11/17 21:28:35 kans * asn2ff now uses gather (Tatiana) * * Revision 1.10 1995/07/17 19:33:20 kans * parameters combined into Asn2ffJobPtr structure * * **************************************/ #include #include #include #include #include #include #include #ifdef ENABLE_ENTREZ #include #endif #define MAX_WWWBUF 328 #define MAX_WWWLOC 2 static CharPtr lim_str [MAX_WWWLOC] = {">","<"}; static CharPtr www_lim_str [MAX_WWWLOC] = {">","<"}; static Char link_ff[MAX_WWWBUF]; static Char link_muid[MAX_WWWBUF]; static Char link_seq[MAX_WWWBUF]; static Char link_ace[MAX_WWWBUF]; static Char link_tax[MAX_WWWBUF]; static Char link_code[MAX_WWWBUF]; static Char link_fly[MAX_WWWBUF]; static Char link_cog[MAX_WWWBUF]; static Char link_sgd[MAX_WWWBUF]; static Char link_gdb[MAX_WWWBUF]; static Char link_ck[MAX_WWWBUF]; static Char link_rice[MAX_WWWBUF]; static Char link_sp[MAX_WWWBUF]; static Char link_pir[MAX_WWWBUF]; static Char link_pdb[MAX_WWWBUF]; static Char link_gdb_map[MAX_WWWBUF]; static Char link_UniSTS[MAX_WWWBUF]; static Char link_omim[MAX_WWWBUF]; static Char link_locus[MAX_WWWBUF]; static Char link_snp[MAX_WWWBUF]; static Char link_ratmap[MAX_WWWBUF]; static Char link_rgd[MAX_WWWBUF]; static Char link_mgd[MAX_WWWBUF]; static Char link_fly_fban[MAX_WWWBUF]; static Char link_fly_fbgn[MAX_WWWBUF]; static Char link_cdd[MAX_WWWBUF]; static Char link_niaest[MAX_WWWBUF]; #define DEF_LINK_FF "/cgi-bin/Entrez/getfeat?" #define DEF_LINK_ACE "http://www.ncbi.nlm.nih.gov/AceView/hs.cgi?" #define DEF_LINK_SEQ "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?" #define DEF_LINK_MUID "/entrez/utils/qmap.cgi?" #define DEF_LINK_TAX "/htbin-post/Taxonomy/wgetorg?" #define DEF_LINK_CODE "/htbin-post/Taxonomy/wprintgc?" #define DEF_LINK_COG "http://www.ncbi.nlm.nih.gov/cgi-bin/COG/palox?" #define DEF_LINK_MGD "http://www.informatics.jax.org/searches/accession_report.cgi?id=" #define DEF_LINK_FBGN "http://flybase.bio.indiana.edu/.bin/fbidq.html?" #define DEF_LINK_FBAN "http://www.fruitfly.org/cgi-bin/annot/fban?" /* #define DEF_LINK_FLY "/cgi-bin/Entrez/referer?http://morgan.harvard.edu/htbin-post/gene.script%3f" */ #define DEF_LINK_FLY "http://flybase.bio.indiana.edu/.bin/fbidq.html?" /* #define DEF_LINK_SGD "/cgi-bin/Entrez/referer?http://genome-www.stanford.edu/cgi-bin/dbrun/SacchDB%3ffind+SGDID+" */ #define DEF_LINK_SGD "/cgi-bin/Entrez/referer?http://genome-www4.stanford.edu/cgi-bin/SGD/locus.pl?locus=" #define DEF_LINK_GDB "http://gdbwww.gdb.org/gdb-bin/genera/genera/hgd/DBObject/GDB:" #define DEF_LINK_CK "http://flybane.berkeley.edu/cgi-bin/cDNA/CK_clone.pl?db=CK&dbid=" /* #define DEF_LINK_RICE "http://genome.cornell.edu:80/cgi-bin/webace?db=ricegenes&class=Probe&object=" */ #define DEF_LINK_RICE "http://ars-genome.cornell.edu/cgi-bin/WebAce/webace?db=ricegenes&class=Marker&object=" #define DEF_LINK_SP "/cgi-bin/Entrez/referer?http://expasy.hcuge.ch/cgi-bin/sprot-search-ac%3f" #define DEF_LINK_PDB "/cgi-bin/Entrez/referer?http://expasy.hcuge.ch/cgi-bin/get-pdb-entry%3f" #define DEF_LINK_GDB_PREFIX "http://gdbwww.gdb.org/gdb-bin/gdb/browser/bin/locq?ACTION=query&cyto=" #define DEF_LINK_GDB_SUFFIX "&match=Inclusive&order=Locus+Location" #define DEF_LINK_UniSTS "http://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=" #define DEF_LINK_OMIM "http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=" #define DEF_LINK_LOCUS "http://www.ncbi.nlm.nih.gov/LocusLink/LocRpt.cgi?l=" #define DEF_LINK_SNP "http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=" #define DEF_LINK_RATMAP "http://ratmap.gen.gu.se/action.lasso?-database=RATMAPfmPro&-layout=Detail&-response=/RM/Detail+Format.html&-search&-recid=" #define DEF_LINK_RGD "http://rgd.mcw.edu/query/query.cgi?id=" #define DEF_LINK_CDD "http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=" #define DEF_LINK_NIAEST "http://lgsun.grc.nia.nih.gov/cgi-bin/pro3?sname1=" /* now other data bases are linked to Entrez. may be changed later static char *link_epd = "/htbin-post/Entrez/query"; static char *link_tfd = "/htbin-post/Entrez/query"; */ static Boolean www = FALSE; static Pointer data = NULL; static HeadTailProc head = NULL; static HeadTailProc tail = NULL; NLM_EXTERN CharPtr PrintDate(NCBI_DatePtr date) { CharPtr retval = NULL; char month[4], year[5], day[3]; char result[15]; if ( date -> data[0] == 0){ /*---string---*/ if (StringICmp(date -> str,"Not given") != 0){ retval = StringSave(date -> str); } } else { /*---standard---*/ if (date->data[1] && date->data[2] && date->data[3]) { if ((int) (date -> data[1]) < 30) { sprintf(year, "%4d", (int) (date -> data[1] + 2000)); } else { sprintf(year, "%4d", (int) (date -> data[1] + 1900)); } sprintf(day, "%d", (int) (date -> data[3] )); StringCpy(month, NCBI_months[date->data[2] -1 ]); sprintf(result,"%s %s, %s.\n", month, day, year); retval = StringSave(result); } } return retval; } void PrintXrefButton PROTO((FILE *fp, SeqEntryPtr sep)); NLM_EXTERN void LIBCALL init_www(void) { www = TRUE; GetAppParam("NCBI", "WWWENTREZ", "LINK_FF", DEF_LINK_FF, link_ff, MAX_WWWBUF); GetAppParam("NCBI", "WWWENTREZ", "LINK_MUID", DEF_LINK_MUID, link_muid, MAX_WWWBUF); GetAppParam("NCBI", "WWWENTREZ", "LINK_ACE", DEF_LINK_ACE, link_ace, MAX_WWWBUF); GetAppParam("NCBI", "WWWENTREZ", "LINK_SEQ", DEF_LINK_SEQ, link_seq, MAX_WWWBUF); GetAppParam("NCBI", "WWWENTREZ", "LINK_TAX", DEF_LINK_TAX, link_tax, MAX_WWWBUF); GetAppParam("NCBI", "WWWENTREZ", "LINK_CODE", DEF_LINK_CODE, link_code, MAX_WWWBUF); GetAppParam("NCBI", "WWWENTREZ", "LINK_FLY", DEF_LINK_FLY, link_fly, MAX_WWWBUF); GetAppParam("NCBI", "WWWENTREZ", "LINK_COG", DEF_LINK_COG, link_cog, MAX_WWWBUF); GetAppParam("NCBI", "WWWENTREZ", "LINK_SGD", DEF_LINK_SGD, link_sgd, MAX_WWWBUF); GetAppParam("NCBI", "WWWENTREZ", "LINK_SGD", DEF_LINK_GDB, link_gdb, MAX_WWWBUF); GetAppParam("NCBI", "WWWENTREZ", "LINK_CK", DEF_LINK_CK, link_ck, MAX_WWWBUF); GetAppParam("NCBI", "WWWENTREZ", "LINK_RICE", DEF_LINK_RICE, link_rice, MAX_WWWBUF); GetAppParam("NCBI", "WWWENTREZ", "LINK_SP", DEF_LINK_SP, link_sp, MAX_WWWBUF); GetAppParam("NCBI", "WWWENTREZ", "LINK_PDB", DEF_LINK_PDB, link_pdb, MAX_WWWBUF); GetAppParam("NCBI", "WWWENTREZ", "LINK_OMIM", DEF_LINK_OMIM, link_omim, MAX_WWWBUF); GetAppParam("NCBI", "WWWENTREZ", "LINK_UniSTS", DEF_LINK_UniSTS, link_UniSTS, MAX_WWWBUF); GetAppParam("NCBI", "WWWENTREZ", "LINK_LOCUS", DEF_LINK_LOCUS, link_locus, MAX_WWWBUF); GetAppParam("NCBI", "WWWENTREZ", "LINK_SNP", DEF_LINK_SNP, link_snp, MAX_WWWBUF); GetAppParam("NCBI", "WWWENTREZ", "LINK_RATMAP", DEF_LINK_RATMAP, link_ratmap, MAX_WWWBUF); GetAppParam("NCBI", "WWWENTREZ", "LINK_RGD", DEF_LINK_RGD, link_rgd, MAX_WWWBUF); GetAppParam("NCBI", "WWWENTREZ", "LINK_MGD", DEF_LINK_MGD, link_mgd, MAX_WWWBUF); GetAppParam("NCBI", "WWWENTREZ", "LINK_FBGN", DEF_LINK_FBGN, link_fly_fbgn, MAX_WWWBUF); GetAppParam("NCBI", "WWWENTREZ", "LINK_FBAN", DEF_LINK_FBAN, link_fly_fban, MAX_WWWBUF); GetAppParam("NCBI", "WWWENTREZ", "LINK_CDD", DEF_LINK_CDD, link_cdd, MAX_WWWBUF); GetAppParam("NCBI", "WWWENTREZ", "LINK_NIAEST", DEF_LINK_NIAEST, link_niaest, MAX_WWWBUF); } NLM_EXTERN void LIBCALL fini_www(void) { www = FALSE; } NLM_EXTERN void LIBCALL head_tail_ff(Pointer mydata, HeadTailProc headfun, HeadTailProc tailfun) { data = mydata; head = headfun; tail = tailfun; } NLM_EXTERN void LIBCALL head_www(FILE *fp, SeqEntryPtr sep) { if (head != NULL) { head(data, fp); return; } if (!www) { return; } fprintf(fp, "Content-type: text/html\n\n"); fprintf(fp, "\n"); fprintf(fp, "%s", "GenBank entry"); fprintf(fp, "\n"); fprintf(fp, "\n"); fprintf(fp, "
\n"); fprintf(fp, "
");
} 

NLM_EXTERN void LIBCALL tail_www(FILE *fp)
{
	if (tail != NULL) {
		tail(data, fp);
		return;
	}
	if (!www) {
		return;
	}
	fprintf(fp, "
\n"); fprintf(fp, "
\n"); fprintf(fp, "\n"); fprintf(fp, "\n"); } NLM_EXTERN Boolean LIBCALL get_www(void) { return www; } /************************************************************************** * source is coming from GBBlock.source so we have to find real * organism name for the hot link ***************************************************************************/ NLM_EXTERN Boolean LIBCALL www_source(CharPtr orgname, OrgRefPtr orp) { Int2 l, ll, lll; CharPtr s; if (www && orp) { l = StringLen(link_tax); lll = StringLen(orgname); ll = StringLen(""); s = (CharPtr)MemNew(l+ ll + lll); sprintf(s, "", link_tax, orp->taxname?orp->taxname:orp->common); AddLink(s); MemFree(s); ff_AddString(orgname); AddLink(""); } else { ff_AddString(orgname); } return TRUE; } NLM_EXTERN Boolean LIBCALL www_organism(CharPtr orgname, Int4 id) { Int2 l, ll, lll; CharPtr s, linkname, ss; if (www) { l = StringLen(link_tax); lll = StringLen(orgname); linkname = StringSave(orgname); for (ss = linkname; *ss != '\0'; ss++) { if (*ss == ' ') { *ss = '+'; } } if (id != -1) { ll = StringLen(""); } else { ll = StringLen(""); } s = (CharPtr)MemNew(l+ ll + lll); if (id != -1) { sprintf(s, "", link_tax, id); } else { sprintf(s, "", link_tax, linkname); } AddLink(s); MemFree(s); ff_AddString(orgname); AddLink(""); MemFree(linkname); } else { ff_AddString(orgname); } return TRUE; } NLM_EXTERN Boolean LIBCALL www_taxid(CharPtr orgname, Int4 id) { Int2 l, ll, lll; CharPtr s, linkname, ss; if (www) { l = StringLen(link_tax); lll = StringLen(orgname); linkname = StringSave(orgname); for (ss = linkname; *ss != '\0'; ss++) { if (*ss == ' ') { *ss = '+'; } } if (id != -1) { ll = StringLen(""); } else { ll = StringLen(""); } s = (CharPtr)MemNew(l+ ll + lll); if (id != -1) { sprintf(s, "", link_tax, id); } else { sprintf(s, "", link_tax, linkname); } AddLink(s); MemFree(s); ff_AddString(orgname); /* ff_AddInteger(" (%d)", id);*/ AddLink(""); MemFree(linkname); } else { ff_AddString(orgname); } return TRUE; } NLM_EXTERN Boolean LIBCALL www_featkey(CharPtr key, Int4 gi, Int2 entityID, Int2 itemID) { Int2 l, ll; CharPtr s; if (www) { l = StringLen(link_ff); ll = StringLen(""); s = (CharPtr)MemNew(l+ ll + 3*7); sprintf(s, "", link_ff, (Int4) gi, itemID, entityID); AddLink(s); MemFree(s); ff_AddString(key); AddLink(""); } else { ff_AddString(key); } return TRUE; } NLM_EXTERN Boolean LIBCALL www_gcode(CharPtr gcode) { Int2 l, ll, gc, lll = 1; CharPtr s; if (www) { gc = atoi(gcode); if (gc >= 10) lll = 2; l = StringLen(link_code); ll = StringLen(""); s = (CharPtr)MemNew(l+ ll + lll); sprintf(s, "", link_code, gc); AddLink(s); MemFree(s); ff_AddInteger("%d", gc); AddLink(""); } else { ff_AddString(gcode); } return TRUE; } NLM_EXTERN Boolean LIBCALL www_muid(Int4 muid) { Int2 l, ll; CharPtr s; if (www) { l = StringLen(link_muid); ll = StringLen(""); s = (CharPtr)MemNew(l+ ll + 10); sprintf(s, "", link_muid, (Int4) muid); AddLink(s); MemFree(s); ff_AddInteger("%ld", (long) muid); AddLink(""); } else { ff_AddInteger("%ld", (long) muid); } return TRUE; } NLM_EXTERN Boolean LIBCALL www_extra_acc(CharPtr acc, Boolean ncbi) { Int2 l, ll; CharPtr s, prefix; if (www && !ncbi) { l = StringLen(link_seq); prefix = ""; ll = StringLen(prefix); s = (CharPtr)MemNew(l+ ll + 10); sprintf(s, prefix, link_seq, acc); AddLink(s); MemFree(s); ff_AddString( acc); AddLink(""); } else { ff_AddString( acc); } return TRUE; } NLM_EXTERN Boolean LIBCALL www_genpept_gi(CharPtr str) { Int2 l, ll; Int4 gi; CharPtr s, prefix; if(www) { l = StringLen(link_seq); prefix = ""; ll = StringLen(prefix); s = (CharPtr)MemNew(l+ ll + 10); if (StringNCmp(str, "gi|", 3) == 0) { str += 3; gi = atoi(str); ff_AddString("gi|"); sprintf(s, prefix, link_seq, gi); AddLink(s); MemFree(s); ff_AddInteger("%ld", (long) gi); AddLink(""); for(; IS_DIGIT(*str); str++); ff_AddString(str); } } else { ff_AddString(str); } return TRUE; } NLM_EXTERN Boolean LIBCALL www_dbsource(CharPtr str, Boolean first, Uint1 choice) { Int2 l, ll; CharPtr s, prefix=NULL, p, text, link=NULL; if(www) { if (choice == SEQID_PIR /*|| choice == SEQID_SWISSPROT*/) { link = link_seq; prefix = ""; } else if (choice == SEQID_PDB || choice == SEQID_PRF) { link = link_seq; prefix = ""; } else if (choice == SEQID_EMBL || choice == SEQID_GENBANK || choice == SEQID_DDBJ || choice == SEQID_GIBBSQ || choice == SEQID_GIBBMT || choice == SEQID_GI || choice == SEQID_GIIM || choice == SEQID_OTHER || choice == SEQID_TPG || choice == SEQID_TPE || choice == SEQID_TPD) { link = link_seq; prefix = ""; } else { ff_AddStringWithTildes(str); return TRUE; } l = StringLen(link); ll = StringLen(prefix); if ((p = StringStr(str, "accession")) != NULL) { p += 9; while (*p == ' ') { p++; } text = TextSave(str, p-str); if (first == FALSE) { ff_AddString(", "); } ff_AddString(text); MemFree(text); text = StringSave(p); if (text[StringLen(text)-1] == ';') { text[StringLen(text)-1] = '\0'; } s = (CharPtr)MemNew(l+ ll + StringLen(text) + 1); sprintf(s, prefix, link, text); AddLink(s); MemFree(s); MemFree(text); ff_AddString(p); AddLink(""); } else { if (first == FALSE) { ff_AddString(", "); } ff_AddString(str); } } else { ff_AddStringWithTildes(str); } return TRUE; } NLM_EXTERN Boolean www_coded_by(CharPtr str) { Int2 l, ll; CharPtr s, ss, prefix, p, text, link; if(www) { link = link_seq; prefix = ""; p = StringChr(str, ':'); while (p != NULL) { for (ss = p-1; ss > str && IS_ALPHANUM(*ss); ss--); if (ss > str) { ss++; text = TextSave(str, ss-str); ff_AddString(text); MemFree(text); } text = TextSave(ss, p-ss); l = StringLen(link); ll = StringLen(prefix); s = (CharPtr)MemNew(l+ ll + StringLen(text)); sprintf(s, prefix, link, text); AddLink(s); MemFree(s); ff_AddString(text); AddLink(""); str = p; p = StringChr(str+1, ':'); } ff_AddString(str); } else { ff_AddString(str); } return TRUE; } NLM_EXTERN Boolean LIBCALL www_map(CharPtr str) { Int2 l, ll, lll, llll; CharPtr s, prefix; if (www) { l = StringLen(DEF_LINK_GDB_PREFIX); prefix = ""; ll = StringLen(prefix); lll = StringLen(str); llll = StringLen(DEF_LINK_GDB_SUFFIX); s = (CharPtr)MemNew(l+ ll + lll + llll); sprintf(s, prefix, DEF_LINK_GDB_PREFIX, str, DEF_LINK_GDB_SUFFIX); AddLink(s); MemFree(s); ff_AddString(str); AddLink(""); } else { ff_AddString(str); } return TRUE; } NLM_EXTERN Boolean LIBCALL www_protein_id(CharPtr str) { Int2 l, ll; CharPtr s, prefix; if (www) { l = StringLen(link_seq); prefix = ""; ll = StringLen(prefix) + StringLen(str); s = (CharPtr)MemNew(l + ll); sprintf(s, prefix, link_seq, str); AddLink(s); MemFree(s); ff_AddString(str); AddLink(""); } else { ff_AddString(str); } return TRUE; } NLM_EXTERN Boolean LIBCALL www_db_xref(CharPtr str) { Int2 l, ll; Int4 gi; CharPtr s, prefix, ss, p, pp; Boolean nothing = TRUE; Char id[10]; Int2 id1, id2; if (www) { while ((p= StringStr(str, "FLYBASE:")) != NULL) { nothing = FALSE; p += StringLen("FlyBase:"); l = StringLen(link_fly); prefix = ""; ll = StringLen(prefix); s = (CharPtr)MemNew(l+ ll + 20); ss = (CharPtr)MemNew(p-str+1); StringNCpy(ss, str, p-str); ff_AddString(ss); MemFree(ss); while (*p == ' ') p++; for (pp = p; *pp != '\0' && *pp != ';'; pp++); ss = (CharPtr)MemNew(pp-p+1); StringNCpy(ss, p, pp-p); sprintf(s, prefix, link_fly, ss); AddLink(s); MemFree(s); ff_AddString(ss); AddLink(""); ff_AddChar(';'); str = pp+1; } if (( p = StringStr(str, "COG:")) != NULL) { nothing = FALSE; p += StringLen("COG:"); l = StringLen(link_cog) + StringLen(p); prefix = ""; ll = StringLen(prefix); s = (CharPtr)MemNew(l + ll); ss = (CharPtr)MemNew(p-str+1); StringNCpy(ss, str, p-str); ff_AddString(ss); MemFree(ss); while (*p == ' ') p++; sprintf(s, prefix, link_cog, p); AddLink(s); MemFree(s); ff_AddString(p); AddLink(""); } if (( p = StringStr(str, "FLYBASE:FBa")) != NULL) { nothing = FALSE; p += StringLen("FLYBASE:"); l = StringLen(link_fly_fban) + StringLen(p); prefix = ""; ll = StringLen(prefix); s = (CharPtr)MemNew(l + ll); ss = (CharPtr)MemNew(p-str+1); StringNCpy(ss, str, p-str); ff_AddString(ss); MemFree(ss); while (*p == ' ') p++; sprintf(s, prefix, link_fly_fban, p); AddLink(s); MemFree(s); ff_AddString(p); AddLink(""); } if (( p = StringStr(str, "FLYBASE:FBgn")) != NULL) { nothing = FALSE; p += StringLen("FLYBASE:"); l = StringLen(link_fly_fbgn) + StringLen(p); prefix = ""; ll = StringLen(prefix); s = (CharPtr)MemNew(l + ll); ss = (CharPtr)MemNew(p-str+1); StringNCpy(ss, str, p-str); ff_AddString(ss); MemFree(ss); while (*p == ' ') p++; sprintf(s, prefix, link_fly_fbgn, p); AddLink(s); MemFree(s); ff_AddString(p); AddLink(""); } if (( p = StringStr(str, "PID:g")) != NULL) { nothing = FALSE; p += StringLen("PID:g"); l = StringLen(link_seq); prefix = ""; ll = StringLen(prefix); s = (CharPtr)MemNew(l+ ll + 10); gi = atoi(p); ss = (CharPtr)MemNew(p-str+1); StringNCpy(ss, str, p-str); ff_AddString(ss); MemFree(ss); sprintf(s, prefix, link_seq, gi); AddLink(s); MemFree(s); ff_AddInteger("%ld", (long) gi); AddLink(""); } /* if (( p = StringStr(str, "SWISS-PROT:")) != NULL) { nothing = FALSE; p += StringLen("SWISS-PROT:"); l = StringLen(link_seq) + StringLen(p); prefix = ""; ll = StringLen(prefix); s = (CharPtr)MemNew(l + ll); ss = (CharPtr)MemNew(p-str+1); StringNCpy(ss, str, p-str); ff_AddString(ss); MemFree(ss); while (*p == ' ') p++; sprintf(s, prefix, link_seq, p); AddLink(s); MemFree(s); ff_AddString(p); AddLink(""); } */ if (( p = StringStr(str, "UniSTS:")) != NULL) { nothing = FALSE; p += StringLen("UniSTS:"); l = StringLen(link_UniSTS) + StringLen(p); prefix = ""; ll = StringLen(prefix); s = (CharPtr)MemNew(l + ll); ss = (CharPtr)MemNew(p-str+1); StringNCpy(ss, str, p-str); ff_AddString(ss); MemFree(ss); while (*p == ' ') p++; sprintf(s, prefix, link_UniSTS, p); AddLink(s); MemFree(s); ff_AddString(p); AddLink(""); } if (( p = StringStr(str, "LocusID:")) != NULL) { nothing = FALSE; p += StringLen("LocusID:"); l = StringLen(link_locus) + StringLen(p); prefix = ""; ll = StringLen(prefix); s = (CharPtr)MemNew(l + ll); ss = (CharPtr)MemNew(p-str+1); StringNCpy(ss, str, p-str); ff_AddString(ss); MemFree(ss); while (*p == ' ') p++; sprintf(s, prefix, link_locus, p); AddLink(s); MemFree(s); ff_AddString(p); AddLink(""); } if (( p = StringStr(str, "InterimID:")) != NULL) { nothing = FALSE; p += StringLen("InterimID:"); l = StringLen(link_locus) + StringLen(p); prefix = ""; ll = StringLen(prefix); s = (CharPtr)MemNew(l + ll); ss = (CharPtr)MemNew(p-str+1); StringNCpy(ss, str, p-str); ff_AddString(ss); MemFree(ss); while (*p == ' ') p++; sprintf(s, prefix, link_locus, p); AddLink(s); MemFree(s); ff_AddString(p); AddLink(""); } if (( p = StringStr(str, "MIM:")) != NULL) { nothing = FALSE; p += StringLen("MIM:"); l = StringLen(link_omim) + StringLen(p); prefix = ""; ll = StringLen(prefix); s = (CharPtr)MemNew(l + ll); ss = (CharPtr)MemNew(p-str+1); StringNCpy(ss, str, p-str); ff_AddString(ss); MemFree(ss); while (*p == ' ') p++; sprintf(s, prefix, link_omim, p); AddLink(s); MemFree(s); ff_AddString(p); AddLink(""); } if (( p = StringStr(str, "SGD:")) != NULL) { nothing = FALSE; p += StringLen("SGD:"); l = StringLen(link_sgd) + StringLen(p); prefix = ""; ll = StringLen(prefix); s = (CharPtr)MemNew(l + ll); ss = (CharPtr)MemNew(p-str+1); StringNCpy(ss, str, p-str); ff_AddString(ss); MemFree(ss); while (*p == ' ') p++; sprintf(s, prefix, link_sgd, p); AddLink(s); MemFree(s); ff_AddString(p); AddLink(""); } if (( p = StringStr(str, "GDB:")) != NULL) { p += StringLen("GDB:"); if (( pp = StringStr(p, "G00-")) != NULL) { pp += StringLen("G00-"); id1 = atoi(pp); for (; *pp != '\0' && *pp != '-'; pp++); id2 = atoi(pp+1); sprintf(id, "%d%d", id1, id2); l = StringLen(link_gdb) + StringLen(p); prefix = ""; ll = StringLen(prefix); s = (CharPtr)MemNew(l + ll); ss = (CharPtr)MemNew(p-str+1); StringNCpy(ss, str, p-str); ff_AddString(ss); MemFree(ss); sprintf(s, prefix, link_gdb, id); AddLink(s); MemFree(s); ff_AddString(p); AddLink(""); nothing = FALSE; } else if (IS_DIGIT(*p)) { l = StringLen(link_gdb) + StringLen(p); prefix = ""; ll = StringLen(prefix); s = (CharPtr)MemNew(l + ll); ss = (CharPtr)MemNew(p-str+1); StringNCpy(ss, str, p-str); ff_AddString(ss); MemFree(ss); sprintf(s, prefix, link_gdb, p); AddLink(s); MemFree(s); ff_AddString(p); AddLink(""); nothing = FALSE; } } if (( p = StringStr(str, "CK:")) != NULL) { nothing = FALSE; p += StringLen("CK:"); l = StringLen(link_ck) + StringLen(p); prefix = ""; ll = StringLen(prefix); s = (CharPtr)MemNew(l + ll); sprintf(s, prefix, link_ck, p); AddLink(s); MemFree(s); ff_AddString(p); AddLink(""); } if (( p = StringStr(str, "RiceGenes:")) != NULL) { nothing = FALSE; p += StringLen("RiceGenes:"); l = StringLen(link_rice) + StringLen(p); prefix = ""; ll = StringLen(prefix); s = (CharPtr)MemNew(l + ll); sprintf(s, prefix, link_rice, p); AddLink(s); MemFree(s); ff_AddString(p); AddLink(""); } if (( p = StringStr(str, "dbSNP:")) != NULL) { nothing = FALSE; p += StringLen("dbSNP:"); l = StringLen(link_snp) + StringLen(p); prefix = ""; ll = StringLen(prefix); s = (CharPtr)MemNew(l + ll); ss = (CharPtr)MemNew(p-str+1); StringNCpy(ss, str, p-str); ff_AddString(ss); MemFree(ss); while (*p == ' ') p++; sprintf(s, prefix, link_snp, p); AddLink(s); MemFree(s); ff_AddString(p); AddLink(""); } if (( p = StringStr(str, "RATMAP:")) != NULL) { nothing = FALSE; p += StringLen("RATMAP:"); l = StringLen(link_ratmap) + StringLen(p); prefix = ""; ll = StringLen(prefix); s = (CharPtr)MemNew(l + ll); ss = (CharPtr)MemNew(p-str+1); StringNCpy(ss, str, p-str); ff_AddString(ss); MemFree(ss); while (*p == ' ') p++; sprintf(s, prefix, link_ratmap, p); AddLink(s); MemFree(s); ff_AddString(p); AddLink(""); } if (( p = StringStr(str, "RGD:")) != NULL) { nothing = FALSE; p += StringLen("RGD:"); l = StringLen(link_rgd) + StringLen(p); prefix = ""; ll = StringLen(prefix); s = (CharPtr)MemNew(l + ll); ss = (CharPtr)MemNew(p-str+1); StringNCpy(ss, str, p-str); ff_AddString(ss); MemFree(ss); while (*p == ' ') p++; sprintf(s, prefix, link_rgd, p); AddLink(s); MemFree(s); ff_AddString(p); AddLink(""); } if (( p = StringStr(str, "MGD:")) != NULL) { nothing = FALSE; p += StringLen("MGD:"); l = StringLen(link_mgd) + StringLen(p); prefix = ""; ll = StringLen(prefix); s = (CharPtr)MemNew(l + ll); ss = (CharPtr)MemNew(p-str+1); StringNCpy(ss, str, p-str); ff_AddString(ss); MemFree(ss); while (*p == ' ') p++; sprintf(s, prefix, link_mgd, p); AddLink(s); MemFree(s); ff_AddString(p); AddLink(""); } if (( p = StringStr(str, "CDD:")) != NULL) { nothing = FALSE; p += StringLen("CDD:"); l = StringLen(link_cdd) + StringLen(p); prefix = ""; ll = StringLen(prefix); s = (CharPtr)MemNew(l + ll); ss = (CharPtr)MemNew(p-str+1); StringNCpy(ss, str, p-str); ff_AddString(ss); MemFree(ss); while (*p == ' ') p++; sprintf(s, prefix, link_cdd, p); AddLink(s); MemFree(s); ff_AddString(p); AddLink(""); } if (( p = StringStr(str, "niaEST:")) != NULL) { nothing = FALSE; p += StringLen("niaEST:"); l = StringLen(link_niaest) + StringLen(p); prefix = ""; ll = StringLen(prefix); s = (CharPtr)MemNew(l + ll); ss = (CharPtr)MemNew(p-str+1); StringNCpy(ss, str, p-str); ff_AddString(ss); MemFree(ss); while (*p == ' ') p++; sprintf(s, prefix, link_niaest, p); AddLink(s); MemFree(s); ff_AddString(p); AddLink(""); } if (nothing) { ff_AddString(str); } } else { ff_AddString(str); } return TRUE; } NLM_EXTERN Boolean LIBCALL www_note_gi(CharPtr str) { Int2 l, ll; Int4 gi; CharPtr s, prefix, ss, p, pp; Boolean nothing = TRUE; if (www) { while ((p= StringStr(str, "FlyBase: ")) != NULL) { nothing = FALSE; p += StringLen("FlyBase: "); l = StringLen(link_fly); prefix = ""; ll = StringLen(prefix); s = (CharPtr)MemNew(l+ ll + 20); ss = (CharPtr)MemNew(p-str+1); StringNCpy(ss, str, p-str); ff_AddString(ss); MemFree(ss); while (*p == ' ') p++; for (pp = p; *pp != '\0' && *pp != ';'; pp++); ss = (CharPtr)MemNew(pp-p+1); StringNCpy(ss, p, pp-p); sprintf(s, prefix, link_fly, ss); AddLink(s); MemFree(s); ff_AddString(ss); AddLink(""); ff_AddChar(';'); str = pp+1; } if (( p = StringStr(str, "NCBI gi: ")) != NULL) { nothing = FALSE; p += StringLen("NCBI gi: "); l = StringLen(link_seq); prefix = ""; ll = StringLen(prefix); s = (CharPtr)MemNew(l+ ll + 10); gi = atoi(p); ss = (CharPtr)MemNew(p-str+1); StringNCpy(ss, str, p-str); ff_AddString(ss); MemFree(ss); sprintf(s, prefix, link_seq, gi); AddLink(s); MemFree(s); ff_AddInteger("%ld", (long) gi); AddLink(""); } if (( p = StringStr(str, "AceView:")) != NULL) { nothing = FALSE; /* p += StringLen("AceView:");*/ gi = atoi(p + StringLen("AceView:")); l = StringLen(link_ace) + StringLen(p); prefix = ""; ll = StringLen(prefix); s = (CharPtr)MemNew(l + ll); ss = (CharPtr)MemNew(p-str+1); StringNCpy(ss, str, p-str); ff_AddString(ss); MemFree(ss); sprintf(s, prefix, link_ace, gi); AddLink(s); MemFree(s); ff_AddString("AceView"); /* ff_AddInteger("%ld", (long) gi);*/ AddLink(""); } if (nothing) { ff_AddString(str); } } else { ff_AddString(str); } return TRUE; } NLM_EXTERN Boolean LIBCALL www_xref(CharPtr str, Uint1 xref_class) { Int2 l, ll; CharPtr s, link, prefix, ss; if (www) { ss = (CharPtr)MemNew(StringLen(str) + 1); StringCpy(ss, str); if (xref_class == 5) { link = link_seq; /*link_sp*/ prefix = ""; } else if (xref_class == 8) { link = link_seq; /*link_epd*/ prefix = ""; } else if (xref_class == 10) { link = link_seq; /* link_tfd */ prefix = ""; } else if (xref_class == 11) { link = link_fly; prefix = ""; } if (link && prefix) { l = StringLen(link); ll = StringLen(prefix); s = (CharPtr)MemNew(l+ ll + 10); if (*(ss + StringLen(ss) - 1) == '.') *(ss + StringLen(ss) - 1) = '\0'; sprintf(s, prefix, link, ss); AddLink(s); MemFree(s); } ff_AddString( str); AddLink(""); MemFree(ss); } else { ff_AddString( str); } return TRUE; } NLM_EXTERN Boolean LIBCALL www_xref_button(FILE *fp, CharPtr str, Uint1 xref_class, Uint1 db) { Int2 l, ll; CharPtr s, link, prefix, ss; if (www) { ss = (CharPtr)MemNew(StringLen(str) + 1); StringCpy(ss, str); if (xref_class == 5) { link = link_seq; /* link_sp */ prefix = ""; } else if (xref_class == 8) { link = link_seq; /* link_epd */ prefix = ""; } else if (xref_class == 10) { link = link_seq; /*link_tfd*/ prefix = ""; } else if (xref_class == 11) { link = link_fly; prefix = ""; } if (xref_class == 255) { /*for PIR and S-P use db */ link = link_seq; prefix = ""; } if (link && prefix) { l = StringLen(link); ll = StringLen(prefix); if (db == SEQID_PIR) { s = (CharPtr)MemNew(l+ ll + 20); sprintf(s, prefix, link, str, str); } else { s = (CharPtr)MemNew(l+ ll + 10); if (*(ss + StringLen(ss) - 1) == '.') { *(ss + StringLen(ss) - 1) = '\0'; } sprintf(s, prefix, link, ss); } fprintf(fp, "%s", s, str); MemFree(s); } MemFree(ss); } return TRUE; } NLM_EXTERN Boolean LIBCALL PrintSPBlock (Asn2ffJobPtr ajp, GBEntryPtr gbp) { Int2 l, ll; CharPtr link, prefix, s; ValNodePtr vnp=NULL, v; CharPtr string, acc = NULL; ValNodePtr ds_vnp, tvnp; DescrStructPtr dsp; SPBlockPtr spb; SeqIdPtr sid; TextSeqIdPtr tid; Boolean has_link = FALSE, first; DbtagPtr db; tvnp = GatherDescrListByChoice(ajp, gbp, Seq_descr_sp); for (ds_vnp= tvnp; ds_vnp; ds_vnp=ds_vnp->next) { dsp = (DescrStructPtr) ds_vnp->data.ptrvalue; vnp = dsp->vnp; gbp->descr = dsp; spb = (SPBlockPtr)vnp->data.ptrvalue; MemFree(vnp); if (spb->_class == 1) { ff_AddString("class: standard."); NewContLine(); } else if (spb->_class == 2) { ff_AddString("class: preliminary."); NewContLine(); } if (spb->extra_acc) { ff_AddString("extra accessions:"); for (v = spb->extra_acc; v; v= v->next) { ff_AddString((CharPtr)v->data.ptrvalue); ff_AddString(","); } } if (spb->imeth) { ff_AddString("seq starts with Met"); } if (spb->plasnm) { ff_AddString("plasmid:"); for (v = spb->plasnm; v; v= v->next) { ff_AddString((CharPtr)v->data.ptrvalue); ff_AddString(","); } } if (spb->created) { string = PrintDate(spb->created); ff_AddString("created: "); ff_AddString(string); } if (spb->sequpd) { string = PrintDate(spb->sequpd); ff_AddString("sequence updated: "); ff_AddString(string); } if (spb->annotupd) { string = PrintDate(spb->annotupd); ff_AddString("annotation updated: "); ff_AddString(string); } if (spb->seqref) { ff_AddString("xrefs: "); first = TRUE; for (sid = spb->seqref; sid; sid= sid->next) { link = link_seq; if (first == FALSE) { ff_AddString(", "); } has_link = TRUE; first = FALSE; if(sid->choice == SEQID_GI) { prefix = ""; ff_AddString("gi: "); acc = (CharPtr)MemNew(10); sprintf(acc, "%ld", (long) sid->data.intvalue); } else { prefix = ""; tid = (TextSeqIdPtr)sid->data.ptrvalue; acc = tid->accession; } switch(sid->choice) { case SEQID_GENBANK: ff_AddString("genbank accession "); break; case SEQID_EMBL: ff_AddString("embl accession "); break; case SEQID_PIR: ff_AddString("pir locus "); break; case SEQID_SWISSPROT: ff_AddString("swissprot accession "); break; case SEQID_DDBJ: ff_AddString("ddbj accession "); break; case SEQID_PRF: ff_AddString("prf accession "); break; case SEQID_GI: ff_AddString("gi: "); break; case SEQID_TPG: ff_AddString("genbank third party accession "); break; case SEQID_TPE: ff_AddString("embl third party accession "); break; case SEQID_TPD: ff_AddString("ddbj third party accession "); break; default: acc = NULL; break; } if (www && has_link) { if (acc && link && prefix) { l = StringLen(link); ll = StringLen(prefix); if (sid->choice == SEQID_PIR) { s = (CharPtr)MemNew(l+ ll + 40); sprintf(s, prefix, link, acc, acc); } else if (sid->choice == SEQID_GI) { s = (CharPtr)MemNew(l+ ll + 10); sprintf(s, prefix, link, sid->data.intvalue); } else { s = (CharPtr)MemNew(l+ ll + 10); sprintf(s, prefix, link, acc); } } AddLink(s); /* MemFree(s); */ ff_AddString( acc); AddLink(""); } else if (acc) { ff_AddString( acc); } } } first = TRUE; for (vnp = spb->dbref; vnp; vnp=vnp->next) { db = (DbtagPtr)vnp->data.ptrvalue; has_link = FALSE; if (first) { NewContLine(); ff_AddString("xrefs (non-sequence databases): "); first = FALSE; } else { ff_AddString(", "); } ff_AddString(db->db); if (StringCmp(db->db, "MIM") == 0) { prefix = ""; l = StringLen(link_omim); ll = StringLen(prefix); s = (CharPtr)MemNew(l+ ll + 10); has_link = TRUE; } if (db->tag && db->tag->str) { ff_AddString(" "); if (www && has_link) { sprintf(s, prefix, link_omim, db->tag->str); AddLink(s); MemFree(s); ff_AddString(db->tag->str); AddLink(""); } else { ff_AddString(db->tag->str); } } else if (db->tag && db->tag->id) { ff_AddString(" "); if (www && has_link) { sprintf(s, "", link_omim, db->tag->id); AddLink(s); MemFree(s); ff_AddInteger("%d", db->tag->id); AddLink(""); } else { ff_AddInteger("%d", db->tag->id); } } } } return TRUE; } NLM_EXTERN CharPtr LIBCALL www_featloc(CharPtr loc) { Int2 i, n, k, l1, l2; CharPtr buf, tmp, ptr, s, eptr; if (loc == NULL) { return NULL; } n = StringLen(loc); eptr = loc + n - 1; for (i = 0, k = 0; i < MAX_WWWLOC; i++) { s = loc; while (s < eptr) { if ((ptr = StringStr(s, lim_str[i])) != NULL) { n += StringLen(www_lim_str[i]) - StringLen(lim_str[i]); k++; s = ptr + StringLen(lim_str[i]); } else { break; } } } if (k == 0) { return StringSave(loc); } buf = (CharPtr)MemNew(n + 1); StringCpy(buf, loc); for (i = 0; i < MAX_WWWLOC; i++) { s = buf; while ((ptr = StringStr(s, lim_str[i])) != NULL) { l1 = StringLen(www_lim_str[i]); l2 = StringLen(lim_str[i]); if (l1 != l2) { MemMove(ptr+l1, ptr+l2, StringLen(ptr+l2)); } MemCpy(ptr, www_lim_str[i], l1); s = ptr + l1; } } return buf; } static void LitPrintGenome(SeqLitPtr slp) { static Char val[166]; if (slp->seq_data != NULL) /* not a gap */ { if (slp->length == 0) /* unknown length */ { sprintf(val, "gap(%d)", slp->length); ff_AddString(val); } else { /* don't know what to do here */ } } else { /* gap length was set */ sprintf(val, ",gap(%d)", slp->length); ff_AddString(val); } } static void LocPrintGenome(Asn2ffJobPtr ajp, GBEntryPtr gbp, SeqLocPtr slp_head) { SeqLocPtr slp, sslp; Boolean first = TRUE; static Char buf[14], val[166], temp[166]; SeqIdPtr sid, newid; Int4 from, to, start, stop, beg, end, lcur, lprev; SeqIntPtr sint; BioseqPtr bsp = NULL, b = NULL; SeqEntryPtr sep = NULL; Int4 uid; Boolean is_network, is_link = FALSE; Int2 p1=0, p2=0; DeltaSeqPtr dsp; static Uint1 fasta_order[NUM_SEQID] = { 33, /* 0 = not set */ 20, /* 1 = local Object-id */ 15, /* 2 = gibbsq */ 16, /* 3 = gibbmt */ 30, /* 4 = giim Giimport-id */ 10, /* 5 = genbank */ 10, /* 6 = embl */ 10, /* 7 = pir */ 10, /* 8 = swissprot */ 15, /* 9 = patent */ 20, /* 10 = other TextSeqId */ 20, /* 11 = general Dbtag */ 255, /* 12 = gi */ 10, /* 13 = ddbj */ 10, /* 14 = prf */ 12, /* 15 = pdb */ 10, /* 16 = tpg */ 10, /* 17 = tpe */ 10 /* 18 = tpd */ }; Int2 l, ll; CharPtr s, prefix; #ifdef ENABLE_ENTREZ if ( !EntrezInit("asn2ff", FALSE, &is_network) ) { return; } #endif for (slp = slp_head; slp; slp = slp->next) { is_link = FALSE; from = to = 0; sid = SeqLocId(slp); if (slp->choice == SEQLOC_INT || slp->choice == SEQLOC_WHOLE) { start = from = SeqLocStart(slp); stop = to = SeqLocStop(slp); } else if (slp->choice == SEQLOC_NULL){ sprintf(val, ",%s", "gap()"); ff_AddString(val); continue; } else { continue; } if (sid == NULL) { continue; } if (sid->choice == SEQID_GI) { newid = GetSeqIdForGI(sid->data.intvalue); } else if (sid->choice == SEQID_GENERAL) { #ifdef ENABLE_ENTREZ if ((uid = GetUniGeneIDForSeqId(sid)) != 0) sep = EntrezSeqEntryGet(uid, -1); if (sep && IS_Bioseq(sep)){ bsp = (BioseqPtr) sep -> data.ptrvalue; } if (bsp && (bsp->seq_ext_type == 1 || bsp->seq_ext_type == 4)) { lcur = lprev = 0; for (sslp = slp_head; sslp; sslp = sslp->next) { is_link = FALSE; lprev = lcur; lcur += SeqLocLen(sslp); beg = SeqLocStart(sslp); end = SeqLocStop(sslp); sid = SeqLocId(sslp); if (from > lcur || to < lprev) { continue; } if (from > lprev) { /* first */ start = beg + from - lprev; } else { start = beg; /* middle */ } if (to > lcur) { /* middle */ stop = end; } else { stop = beg + to - lprev; } if (first) { first = FALSE; } else { ff_AddChar(','); } if (sid->choice == SEQID_GI) { newid = GetSeqIdForGI(sid->data.intvalue); if (newid == NULL) { newid = sid; } } else { newid = sid; } if (ajp->show_version) { SeqIdWrite(SeqIdSelect(newid, fasta_order, NUM_SEQID), buf, PRINTID_TEXTID_ACC_VER, 13); } else { SeqIdWrite(SeqIdSelect(newid, fasta_order, NUM_SEQID), buf, PRINTID_TEXTID_ACCESSION, 10); } if (www && newid) { l = StringLen(link_seq); if (newid->choice == SEQID_GENERAL) { uid = GetUniGeneIDForSeqId(newid); if (uid != 0) { prefix = ""; ll = StringLen(prefix); s = (CharPtr)MemNew(l+ ll + 10); sprintf(s, prefix, link_seq, uid); if (SeqLocStrand(slp) == Seq_strand_minus) { ff_AddString("complement("); } ff_AddString(buf); p1 = StringLen(buf); p2 = 0; is_link = TRUE; } else { if (SeqLocStrand(slp) == Seq_strand_minus) { ff_AddString("complement("); } ff_AddString(buf); } } else { prefix = ""; ll = StringLen(prefix); s = (CharPtr)MemNew(l+ ll + 10); sprintf(s, prefix, link_seq, buf); if (SeqLocStrand(slp) == Seq_strand_minus) { ff_AddString("complement("); } ff_AddString(buf); p1 = StringLen(buf); p2 = 0; is_link = TRUE; } } else { if (SeqLocStrand(slp) == Seq_strand_minus) { ff_AddString("complement("); } ff_AddString(buf); } if (SeqLocStrand(slp) == Seq_strand_minus) { sprintf(val,":%ld..%ld)",(long) start+1, (long) stop+1 ); } else { sprintf(val,":%ld..%ld",(long) start+1, (long) stop+1 ); } ff_AddString(val); p1 += StringLen(val); p2 += StringLen(val); if (is_link) { AddLinkLater(s, p1); MemFree(s); AddLinkLater("", p2); } } continue; } newid = sid; #else newid = sid; #endif } else { newid = sid; } if (first) { first = FALSE; } else { ff_AddChar(','); } if (ajp->show_version) { SeqIdWrite(SeqIdSelect(newid, fasta_order, NUM_SEQID), buf, PRINTID_TEXTID_ACC_VER, 13); } else { SeqIdWrite(SeqIdSelect(newid, fasta_order, NUM_SEQID), buf, PRINTID_TEXTID_ACCESSION, 10); } if (www && newid) { l = StringLen(link_seq); if (newid->choice == SEQID_GENERAL) { uid = GetUniGeneIDForSeqId(newid); if (uid != 0) { prefix = ""; ll = StringLen(prefix); s = (CharPtr)MemNew(l+ ll + 10); sprintf(s, prefix, link_seq, uid); if (SeqLocStrand(slp) == Seq_strand_minus) { ff_AddString("complement("); } ff_AddString( buf); p1 = StringLen(buf); p2 = 0; is_link = TRUE; } else { ff_AddString( buf); } } else { prefix = ""; ll = StringLen(prefix); s = (CharPtr)MemNew(l+ ll + 10); sprintf(s, prefix, link_seq, buf); if (SeqLocStrand(slp) == Seq_strand_minus) { ff_AddString("complement("); } ff_AddString( buf); p1 = StringLen(buf); p2 = 0; is_link = TRUE; } } else { if (SeqLocStrand(slp) == Seq_strand_minus) { ff_AddString("complement("); } ff_AddString( buf); } if (SeqLocStrand(slp) == Seq_strand_minus) { sprintf(val,":%ld..%ld)",(long) start+1, (long) stop+1 ); } else { sprintf(val,":%ld..%ld",(long) start+1, (long) stop+1 ); } ff_AddString(val); p1 += StringLen(val); p2 += StringLen(val); if (is_link) { AddLinkLater(s, p1); MemFree(s); AddLinkLater("", p2); } } } void PrintGenome(Asn2ffJobPtr ajp, GBEntryPtr gbp) { SeqLocPtr slp_head=NULL; Boolean first = TRUE; Boolean is_network; DeltaSeqPtr dsp; SeqLitPtr litp; Int2 l, ll; CharPtr s, prefix; #ifdef ENABLE_ENTREZ if ( !EntrezInit("asn2ff", FALSE, &is_network) ) { return; } #endif ff_StartPrint(0, 12, ASN2FF_GB_MAX, NULL); if (www && ajp->format == GRAPHIK_FMT) { if (gbp->bsp && gbp->bsp->seq_ext == NULL) { return; } ff_AddString("CONTIG   "); } else { ff_AddString("CONTIG"); } TabToColumn(13); ff_AddString("join("); if (gbp->bsp->seq_ext_type == 1) { slp_head = (SeqLocPtr) gbp->bsp->seq_ext; LocPrintGenome(ajp, gbp, slp_head); } else if (gbp->bsp->seq_ext_type == 4) { for (dsp = (DeltaSeqPtr) gbp->bsp->seq_ext; dsp; dsp=dsp->next) { if (dsp->choice == 1) { /* SeqLoc */ slp_head = (SeqLocPtr)(dsp->data.ptrvalue); if (first == FALSE) { ff_AddString(","); } LocPrintGenome(ajp, gbp, slp_head); } else { litp = (SeqLitPtr)(dsp->data.ptrvalue); if (litp == NULL) continue; LitPrintGenome(litp); } if (first) first = FALSE; } } ff_AddChar(')'); ff_EndPrint(); /*PrintTerminator();*/ } NLM_EXTERN void LIBCALL www_accession (CharPtr string) { Int2 l, ll; CharPtr s, prefix=NULL, p, link=NULL; if (string == NULL) { return; } if (!www) { ff_AddString(string); } else { link = link_seq; prefix = ""; s = (CharPtr)MemNew(StringLen(link_seq)+ StringLen(prefix) + StringLen(string) + 10); sprintf(s, prefix, link, string); AddLink(s); MemFree(s); ff_AddString(string); AddLink(""); } return; } static Boolean iscospa(Char c) { return (isspace(c) || c == ',' || c == ' ') ; } NLM_EXTERN void LIBCALL www_PrintComment (CharPtr string, Boolean identifier, Uint1 format) { Int2 lpref, l, ll; Int4 gi; CharPtr s, prefix=NULL, p, pp, link=NULL, www_str, acc, ss; Boolean isfirst = TRUE; if (string == NULL) { return; } if (format == EMBL_FMT || format == PSEUDOEMBL_FMT || format == EMBLPEPT_FMT) { if (identifier == TRUE) PrintXX(); ff_StartPrint(5, 5, ASN2FF_EMBL_MAX, "CC"); } else { ff_StartPrint(0, 12, ASN2FF_GB_MAX, NULL); if (identifier == TRUE) { if (format == GRAPHIK_FMT && www) { ff_AddString("
COMMENT   "); } else { ff_AddString("COMMENT"); } } TabToColumn(13); } if (!www) { ff_AddStringWithTildes(string); ff_EndPrint(); return; } if ((p = StringStr(string, "REFSEQ")) != NULL) { acc = TextSave(string, p-string); ff_AddString(acc); MemFree(acc); p += 7; AddLink(""); ff_AddString("REFSEQ:"); AddLink(""); string = p; if ((p = StringStr(string, "was derived from ")) != NULL) { p += StringLen("was derived from "); s = TextSave(string, p-string); ff_AddString(s); MemFree(s); prefix = ""; lpref = StringLen(link_seq)+ StringLen(prefix); for (; isspace(*p); p++) ; isfirst = TRUE; do { if (isfirst) { isfirst = FALSE; } else { ff_AddString(", "); } for (pp=p; *pp != '\0' && !iscospa(*pp); pp++) ; acc = TextSave(p, pp-p); if (acc[StringLen(acc)-1] == '.') { acc[StringLen(acc)-1] = '\0'; } s = (CharPtr)MemNew(lpref + StringLen(acc)+1); sprintf(s, prefix, link_seq, acc); AddLink(s); MemFree(s); ff_AddString(acc); MemFree(acc); AddLink(""); for (p = pp; iscospa(*p); p++) ; } while (*p != '\0'); ff_AddString("."); } else { ff_AddString(string); } ff_EndPrint(); return; } if (( p = StringStr(string, "AceView:")) != NULL) { /* p += StringLen("AceView:");*/ gi = atoi(p + StringLen("AceView:")); l = StringLen(link_ace) + StringLen(p); prefix = ""; ll = StringLen(prefix); s = (CharPtr)MemNew(l + ll); ss = (CharPtr)MemNew(p-string+1); StringNCpy(ss, string, p-string); ff_AddString(ss); MemFree(ss); sprintf(s, prefix, link_ace, gi); AddLink(s); MemFree(s); ff_AddString("AceView"); /* ff_AddInteger("%ld", (long) gi);*/ AddLink(""); ff_EndPrint(); return; } while ((p = StringStr(string, "gi:")) != NULL) { p += 3; s = TextSave(string, p-string); ff_AddString(s); gi = atoi(p); link = link_seq; prefix = ""; s = (CharPtr)MemNew(StringLen(link_seq)+ StringLen(prefix) + 12); sprintf(s, prefix, link, gi); AddLink(s); MemFree(s); ff_AddInteger("%d", gi); AddLink(""); while (IS_DIGIT(*p)) p++; string = p; } www_str = www_featloc(string); ff_AddStringWithTildes(www_str); MemFree(www_str); ff_EndPrint(); return; } /* PrintComment */