/dports/biology/emboss/EMBOSS-6.6.0/emboss/ |
H A D | diffseq.c | 374 ajFmtPrintS(&tmp, "*length %d", diff->Len2); in diffseq_Diff() 379 ajFmtPrintS(&tmp, "*strand -"); in diffseq_Diff() 396 ajFmtPrintS(&tmp, "*end %d", diff->End2); in diffseq_Diff() 401 ajFmtPrintS(&tmp, "*sequence %S", tmpseq); in diffseq_Diff() 418 ajFmtPrintS(&tmp, "*end %d", diff->End2); in diffseq_Diff() 438 ajFmtPrintS(&tmp, "Overlap_end: %d in %S\n", in diffseq_Diff() 567 ajFmtPrintS(&conflictstr, "%S -> %S", in diffseq_WordMatchListConvDiffToFeat() 571 ajFmtPrintS(&conflictstr, "MISSING"); in diffseq_WordMatchListConvDiffToFeat() 613 ajFmtPrintS(&conflictstr, "%S -> %S", in diffseq_WordMatchListConvDiffToFeat() 617 ajFmtPrintS(&conflictstr, "MISSING"); in diffseq_WordMatchListConvDiffToFeat() [all …]
|
H A D | tfm.c | 92 ajFmtPrintS(&cmd,"%S %S",pager,path); in main() 173 ajFmtPrintS(&doctest,"%S%cprograms%ctext",roottmp,SLASH_CHAR, in tfm_FindAppDocRoot() 191 ajFmtPrintS(&tmpstr,"%Sdoc",docrootinst); in tfm_FindAppDocRoot() 208 ajFmtPrintS(docroot,"%Shtml%sembassy%s%S%s", in tfm_FindAppDocRoot() 214 ajFmtPrintS(docroot,"%Sprograms%shtml%s", in tfm_FindAppDocRoot() 217 ajFmtPrintS(docroot,"%Sprograms%shtml%s", in tfm_FindAppDocRoot() 222 ajFmtPrintS(docroot,"%Sprograms%stext%s",docrootinst,SLASH_STRING, in tfm_FindAppDocRoot() 240 ajFmtPrintS(docroot, "embassy/%S/emboss_doc/", embassy); in tfm_FindAppDocRoot() 346 ajFmtPrintS(&newpath,"%s",root); in tfm_FixImages() 360 ajFmtPrintS(line,"%Sfile:/%S%S%S",pre,newpath,name,post); in tfm_FixImages()
|
H A D | pepcoil.c | 271 ajFmtPrintS(&tmpstr, "*probability %.3f", in main() 274 ajFmtPrintS(&tmpstr, "*pos %d", in main() 329 ajFmtPrintS(&tmpstr, "*frames %d..%d", in main() 334 ajFmtPrintS(&tmpstr, "*predict coiled"); in main() 336 ajFmtPrintS(&tmpstr, "*probability %.3f", in main() 339 ajFmtPrintS(&tmpstr, "*pos %d", in main() 385 ajFmtPrintS(&tmpstr, "*predict coiled"); in main() 387 ajFmtPrintS(&tmpstr, "*probability %.3f", in main() 390 ajFmtPrintS(&tmpstr, "*pos %d", in main() 413 ajFmtPrintS(&tmpstr, "*probability %.3f", in main() [all …]
|
H A D | jaspscan.c | 365 ajFmtPrintS(&jdir,"%S%S",dir,jaspdir); in jaspscan_GetFileList() 369 ajFmtPrintS(&wstr,"%s%s",wild,J_EXT); in jaspscan_GetFileList() 1240 ajFmtPrintS(&str,"*pc %.3f",hit->scorepc); in jaspscan_ReportHits() 1243 ajFmtPrintS(&str,"*id %S",hit->matname); in jaspscan_ReportHits() 1252 ajFmtPrintS(&str,"*name %S",info->name); in jaspscan_ReportHits() 1264 ajFmtPrintS(&str,"*class %S",info->klass); in jaspscan_ReportHits() 1276 ajFmtPrintS(&str,"*pseq %S",info->protseq); in jaspscan_ReportHits() 1282 ajFmtPrintS(&str,"*exp %S",info->exp); in jaspscan_ReportHits() 1288 ajFmtPrintS(&str,"*pmid %S",info->pmid); in jaspscan_ReportHits() 1295 ajFmtPrintS(&str,"*info %.3f",fnum); in jaspscan_ReportHits() [all …]
|
H A D | density.c | 137 ajFmtPrintS(&hdr, "Window size = %d\n",window); in main() 329 ajFmtPrintS(&st,"Window = %d. A=Black C=Red G=Green T=Blue",window); in density_addquadgraph() 447 ajFmtPrintS(&st,"Window = %d. AT=Green GC=Blue",window); in density_adddualgraph() 523 ajFmtPrintS(&str,"*a %.3f",density->a[i]); in density_ReportHits() 526 ajFmtPrintS(&str,"*c %.3f",density->c[i]); in density_ReportHits() 529 ajFmtPrintS(&str,"*g %.3f",density->g[i]); in density_ReportHits() 532 ajFmtPrintS(&str,"*t %.3f",density->t[i]); in density_ReportHits() 535 ajFmtPrintS(&str,"*at %.3f",density->at[i]); in density_ReportHits() 538 ajFmtPrintS(&str,"*gc %.3f",density->gc[i]); in density_ReportHits()
|
H A D | pepdigest.c | 154 ajFmtPrintS(&tmpStr, in main() 173 ajFmtPrintS(&tmpStr, in main() 193 ajFmtPrintS(&tmpStr, in main() 321 ajFmtPrintS(&tmpStr, "*molwt %.3f", fr->molwt); in pepdigest_report_hits() 325 ajFmtPrintS(&tmpStr, "*cterm %c", *(s+(fr->start)-1)); in pepdigest_report_hits() 331 ajFmtPrintS(&tmpStr, "*nterm %c", *(s+(fr->end+1))); in pepdigest_report_hits()
|
H A D | embossupdate.c | 91 ajFmtPrintS(&updateurl, in main() 95 ajFmtPrintS(&updateurl, in main() 133 ajFmtPrintS(&fixversion, "%S.0", initversion); in main() 140 ajFmtPrintS(&fixversion, "%S.%u", initversion, lastfix); in main()
|
H A D | fuzztran.c | 269 ajFmtPrintS(&s, "*pat %S", v); in fuzztran_SourceFeature() 274 ajFmtPrintS(&s, "*mismatch %S", v); in fuzztran_SourceFeature() 277 ajFmtPrintS(&s, "*frame %d", framenum); in fuzztran_SourceFeature() 280 ajFmtPrintS(&s, "*start %d", ajFeatGetStart(protfeature)); in fuzztran_SourceFeature() 283 ajFmtPrintS(&s, "*end %d", ajFeatGetEnd(protfeature)); in fuzztran_SourceFeature() 289 ajFmtPrintS(&s, "*translation %S", t); in fuzztran_SourceFeature()
|
H A D | jaspextract.c | 160 ajFmtPrintS(&dir,"%S%s",datadir,Jprefix[i].Directory); in jaspextract_openoutdirs() 229 ajFmtPrintS(&matrixfile,"%S%s",directory,MATRIXFILE); in jaspextract_copyfiles() 268 ajFmtPrintS(&dest,"%S%s%c%S",datadir,Jprefix[i].Directory,SLASH_CHAR, in jaspextract_copyfiles() 333 ajFmtPrintS(&matrixfile,"%S%s",directory,MATRIXFILE); in jaspextract_readmatrixlist() 445 ajFmtPrintS(&dest,"%S%c%s",directory,SLASH_CHAR,MATRIXFILE); in jaspextract_writematrixfile()
|
H A D | eprimer32.c | 641 ajFmtPrintS(&str, "%s=", tag); in eprimer32_send_range() 655 ajFmtPrintS(&str, "\n"); in eprimer32_send_range() 690 ajFmtPrintS(&str, "%s=", tag); in eprimer32_send_range2() 697 ajFmtPrintS(&str, "%d-%d ", start, end); in eprimer32_send_range2() 702 ajFmtPrintS(&str, "\n"); in eprimer32_send_range2() 746 ajFmtPrintS(&str, "%s=", tag); in eprimer32_send_range_pair() 812 ajFmtPrintS(&str, "%s=%d\n", tag, value); in eprimer32_send_int() 840 ajFmtPrintS(&str, "%s=%f\n", tag, value); in eprimer32_send_float() 868 ajFmtPrintS(&str, "%s=%d\n", tag, value?1:0); in eprimer32_send_bool() 900 ajFmtPrintS(&str, "%s=%S\n", tag, value); in eprimer32_send_string() [all …]
|
H A D | pepinfo.c | 219 ajFmtPrintS(&tmpa, "%s residues in %s from position %d to %d", in main() 235 ajFmtPrintS(&tmpa, "Properties of residues in %s from position " in main() 244 ajFmtPrintS(&tmpa, "%s residues in %s from position %d to %d", in main() 247 ajFmtPrintS(&tmpb, "%s residues", propertyTitles[i]); in main() 339 ajFmtPrintS(&tmpa, "Results from %s", hydroTitles[i]); in main() 347 ajFmtPrintS(&tmpa, in main()
|
H A D | eprimer3.c | 618 ajFmtPrintS(&str, "%s=", tag); in eprimer3_send_range() 627 ajFmtPrintS(&str, "%d,%d ", start, end-start+1); in eprimer3_send_range() 632 ajFmtPrintS(&str, "\n"); in eprimer3_send_range() 667 ajFmtPrintS(&str, "%s=", tag); in eprimer3_send_range2() 674 ajFmtPrintS(&str, "%d-%d ", start, end); in eprimer3_send_range2() 679 ajFmtPrintS(&str, "\n"); in eprimer3_send_range2() 708 ajFmtPrintS(&str, "%s=%d\n", tag, value); in eprimer3_send_int() 736 ajFmtPrintS(&str, "%s=%f\n", tag, value); in eprimer3_send_float() 764 ajFmtPrintS(&str, "%s=%d\n", tag, value?1:0); in eprimer3_send_bool() 796 ajFmtPrintS(&str, "%s=%S\n", tag, value); in eprimer3_send_string() [all …]
|
H A D | primers.c | 619 (void) ajFmtPrintS(&str, "%s=", tag); in primers_send_range() 624 (void) ajFmtPrintS(&str, "%u,%u ", start, end-start+1); in primers_send_range() 628 (void) ajFmtPrintS(&str, "\n"); in primers_send_range() 691 (void) ajFmtPrintS(&str, "%s=%d\n", tag, value); in primers_send_int() 715 (void) ajFmtPrintS(&str, "%s=%f\n", tag, value); in primers_send_float() 739 (void) ajFmtPrintS(&str, "%s=%d\n", tag, value?1:0); in primers_send_bool() 766 (void) ajFmtPrintS(&str, "%s=%S\n", tag, value); in primers_send_string()
|
H A D | sirna.c | 474 ajFmtPrintS(&head2, "CDS region found in feature table " in sirna_begin() 491 ajFmtPrintS(&head2, "%s%s%s%s", in sirna_begin() 500 ajFmtPrintS(&head2, "%s%s%s%d", in sirna_begin() 645 ajFmtPrintS(&tmpStr, "*gc %4.1f", in sirna_output() 667 ajFmtPrintS(&tmpStr, "*forward %S", subseq); in sirna_output() 676 ajFmtPrintS(&tmpStr, "*reverse %S", subseq); in sirna_output() 699 ajFmtPrintS(&desc, "%%GC %4.1f Score %d ", in sirna_output()
|
H A D | dastest.c | 287 ajFmtPrintS(&idqry,"dasgff::%S:%S:%S", in main() 301 ajFmtPrintS(&qpath,"%S?segment=%S", in main() 324 ajFmtPrintS(&ffname, "%S.%S", source->uri, in main() 353 ajFmtPrintS(&idqry,"%S:%S:%S", in main() 477 ajFmtPrintS(&ffnamee, "%S.raw.dasgff", ffname); in dastestSaveRawFeatures() 529 ajFmtPrintS(&ffnamee, "%S.mapped.dasgff", ffname); in dastestSaveMappedFeatures()
|
H A D | restrict.c | 779 ajFmtPrintS(&tmpStr, "*enzyme %S", m->cod); in restrict_reportHits() 781 ajFmtPrintS(&tmpStr, "*site %S", m->pat); in restrict_reportHits() 783 ajFmtPrintS(&tmpStr, "*5prime %d", m->cut1); in restrict_reportHits() 785 ajFmtPrintS(&tmpStr, "*3prime %d", m->cut2); in restrict_reportHits() 789 ajFmtPrintS(&tmpStr, "*5frag %u", m->len1); in restrict_reportHits() 794 ajFmtPrintS(&tmpStr, "*3frag %u", m->len2); in restrict_reportHits() 802 ajFmtPrintS(&tmpStr, "*5primerev %d", m->cut3); in restrict_reportHits() 804 ajFmtPrintS(&tmpStr, "*3primerev %d", m->cut4); in restrict_reportHits() 808 ajFmtPrintS(&tmpStr, "*5fragrev %u", m->len3); in restrict_reportHits() 813 ajFmtPrintS(&tmpStr, "*3fragrev %u", m->len4); in restrict_reportHits()
|
H A D | dan.c | 448 ajFmtPrintS(&tmpStr, "*tm %4.1f", ta[*np]); in dan_reportgc() 450 ajFmtPrintS(&tmpStr, "*gc %4.1f", cga[*np]); in dan_reportgc() 454 ajFmtPrintS (&tmpStr, "*dg %.3f", DeltaG); in dan_reportgc() 456 ajFmtPrintS (&tmpStr, "*dh %.3f", DeltaH); in dan_reportgc() 458 ajFmtPrintS (&tmpStr, "*ds %.3f", DeltaS); in dan_reportgc() 472 ajFmtPrintS (&tmpStr, "*tmprod %4.1f", tpa[*np]); in dan_reportgc()
|
H A D | charge.c | 238 ajFmtPrintS(&st,"Window:%d",window); in charge_addgraph() 242 ajFmtPrintS(&st,"Charge"); in charge_addgraph() 245 ajFmtPrintS(&st,"Position"); in charge_addgraph()
|
/dports/biology/emboss/EMBOSS-6.6.0/ajax/core/ |
H A D | ajftp.c | 115 ajFmtPrintS(&portstr,"%d",iport); in ajFtpOpen() 155 ajFmtPrintS(&errstr, "socket connect failed for database '%S': %s", in ajFtpOpen() 258 ajFmtPrintS(&ftpcmd, "USER anonymous\r\n"); in ftpSend() 267 ajFmtPrintS(&ftpcmd, "PASS emboss-bug@emboss.open-bio.org\r\n"); in ftpSend() 277 ajFmtPrintS(&ftpcmd, "TYPE I\r\n"); in ftpSend() 286 ajFmtPrintS(&ftpcmd, "PASV\r\n"); in ftpSend() 295 ajFmtPrintS(&ftpcmd, "SIZE %S\r\n", get); in ftpSend() 312 ajFmtPrintS(&ftpcmd, "REST %Ld\r\n", fpos); in ftpSend() 322 ajFmtPrintS(&ftpcmd, "RETR %S\r\n", get); in ftpSend() 362 ajFmtPrintS(&hoststr, "%u.%u.%u.%u", ia, ib, ic, id); in ftpSend() [all …]
|
H A D | ajhttp.c | 294 ajFmtPrintS(&portstr,"%d",iport); in ajHttpOpen() 334 ajFmtPrintS(&errstr, "socket connect failed for database '%S': %s", in ajHttpOpen() 398 ajFmtPrintS(&portstr,"%d",proxyport); in ajHttpOpenProxy() 531 ajFmtPrintS(&gethead, "User-Agent: EMBOSS/%S (%S)\r\n", in httpSend() 540 ajFmtPrintS(&gethead, "Host: %S:%d\r\n", host, iport); in httpSend() 553 ajFmtPrintS(&gethead, "Connection: close\r\n"); in httpSend() 567 ajFmtPrintS(&gethead, "\r\n"); in httpSend() 958 ajFmtPrintS(urlget,"/%S",uo->Absolute); in ajHttpQueryUrl() 996 ajFmtPrintS(urlget,"/%S",uo->Absolute); in ajHttpUrlDeconstruct() 1200 ajFmtPrintS(&get, "GET http://%S:%d%S HTTP/%S\r\n", in ajHttpReadPos() [all …]
|
H A D | ajseqtype.c | 2031 ajFmtPrintS(&seqtypeCharsetAnyGap, "%s%s%s%s%s%s", in seqTypeStrAnyGap() 2060 ajFmtPrintS(&seqtypeCharsetDnaGap, "%s%s%s", in seqTypeStrDnaGap() 2086 ajFmtPrintS(&seqtypeCharsetNuc, "%s%s", in seqTypeStrNuc() 2111 ajFmtPrintS(&seqtypeCharsetNucGap, "%s%s%s", in seqTypeStrNucGap() 2137 ajFmtPrintS(&seqtypeCharsetNucGapPhylo, "%s%s%s%s", in seqTypeStrNucGapPhylo() 2164 ajFmtPrintS(&seqtypeCharsetNucPure, "%s", in seqTypeStrNucPure() 2188 ajFmtPrintS(&seqtypeCharsetProt, "%s%s", in seqTypeStrProt() 2213 ajFmtPrintS(&seqtypeCharsetProtAny, "%s%s%s%s%s", in seqTypeStrProtAny() 2241 ajFmtPrintS(&seqtypeCharsetProtGap, "%s%s%s", in seqTypeStrProtGap() 2295 ajFmtPrintS(&seqtypeCharsetProtPure, "%s", in seqTypeStrProtPure() [all …]
|
H A D | ajfeatwrite.c | 2256 ajFmtPrintS(&pos,"%d",gf->Start); in ajFeattableWritePir() 3371 ajFmtPrintS(&featoutStr, "/%S", tmptag); in featDumpEmbl() 3538 ajFmtPrintS(&featoutStr, "/%S", tmptag); in featDumpRefseq() 3701 ajFmtPrintS(&featoutStr, "/%S", tmptag); in featDumpRefseqp() 3946 ajFmtPrintS(&fromstr, "?"); in featDumpSwiss() 3949 ajFmtPrintS(&fromstr, "<%d", thys->Start); in featDumpSwiss() 3951 ajFmtPrintS(&fromstr, "%d", thys->Start); in featDumpSwiss() 3957 ajFmtPrintS(&tostr, "?%d", thys->End); in featDumpSwiss() 3959 ajFmtPrintS(&tostr, "?"); in featDumpSwiss() 3962 ajFmtPrintS(&tostr, ">%d", thys->End); in featDumpSwiss() [all …]
|
H A D | ajpat.c | 166 ajFmtPrintS(&pthis->Name, "pattern%Lu", in ajPatternSeqNewList() 209 ajFmtPrintS(&pthis->Name, "regex%Lu", in ajPatternRegexNewList() 804 ajFmtPrintS(&name, "%S%u", namestr, npat); in ajPatlistSeqRead() 949 ajFmtPrintS(&name, "%S%u", namestr, npat); in ajPatlistRegexRead() 977 ajFmtPrintS(&name, "%S%u", namestr, npat); in ajPatlistRegexRead() 1448 ajFmtPrintS(Pdoc, "%-12S %S\n", "Pattern_name", "Pattern"); in ajPatlistRegexDoc() 1477 ajFmtPrintS(Pdoc, "%-12s %8s %s\n", in ajPatlistSeqDoc()
|
/dports/biology/emboss/EMBOSS-6.6.0/nucleus/ |
H A D | embdbi.c | 506 ajFmtPrintS(&name, "%S%S", dbiDirFix, s2); in embDbiFileList() 602 ajFmtPrintS(&name, "%S%S", dbiDirFix, dbiInFname); in embDbiFileListExc() 688 ajFmtPrintS(&dbiCmdStr, "%S.%s", dbname, ext); in embDbiRmFile() 712 ajFmtPrintS (&filestr, "%S.%s", dbname, ext); in embDbiRmFile() 857 ajFmtPrintS(&dbiCmdStr, "%S -o %S %S %S", in embDbiSortFile() 860 ajFmtPrintS(&dbiCmdStr, "%S -o %S %S", in embDbiSortFile() 883 ajFmtPrintS(&dbiSortExt, "%s.srt", ext1); in embDbiSortFile() 929 ajFmtPrintS(&dbiInFname, "%S.%s", dbname, ext1); in embDbiSortFile() 930 ajFmtPrintS(&dbiOutFname, "%S.%s", dbname, ext2); in embDbiSortFile() 931 ajFmtPrintS(&dbiCmdStr, "%S -o %S %S %S", in embDbiSortFile() [all …]
|
/dports/biology/emboss/EMBOSS-6.6.0/ajax/ajaxdb/ |
H A D | ajmart.c | 1053 ajFmtPrintS(&get, "%S?type=registry\r\n", mq->Regpath); in ajMartGetRegistry() 1243 ajFmtPrintS(&get, "%S?type=datasets&mart=%S", path, spmart); in ajMartGetDatasets() 2646 ajFmtPrintS(&filterval,"%S",nameval); in ajMartFilterMatch() 2906 ajFmtPrintS(&get, "%S?query=%S", mq->Martpath, mq->Query); in ajMartSendQuery() 3770 ajFmtPrintS(&pushstr,"\"%s\" excluded = \"0\"",p); in ajMartParseParameters() 4259 ajFmtPrintS(&get, "%S?type=configuration&dataset=%S" in ajMartGetConfiguration() 4682 ajFmtPrintS(str,"%S+%S+%u",ho,pa,port); in martEncodeHname() 4788 ajFmtPrintS(&dir,"%S%c%S",mq->Cachedir,SLASH_CHAR, in martWriteCacheEntry() 4805 ajFmtPrintS(&fname,"%S%cRegistry",dir,SLASH_CHAR); in martWriteCacheEntry() 4835 ajFmtPrintS(&dir,"%S%c%S",mq->Cachedir,SLASH_CHAR, in martWriteCacheEntry() [all …]
|