/dports/biology/emboss/EMBOSS-6.6.0/emboss/ |
H A D | merger.c | 256 ajFmtPrintAppS(&tmpstr, "WARNING: *************************" in merger_Merge() 273 ajFmtPrintAppS(&tmpstr, "WARNING: **************************" in merger_Merge() 286 ajFmtPrintAppS(&tmpstr, in merger_Merge() 288 ajFmtPrintAppS(&tmpstr, "There is an equal amount of unaligned " in merger_Merge() 291 ajFmtPrintAppS(&tmpstr, "Sequence %s is being arbitrarily chosen " in merger_Merge() 302 ajFmtPrintAppS(&tmpstr, in merger_Merge() 397 ajFmtPrintAppS(&tmpstr, "WARNING: ***************************" in merger_Merge() 399 ajFmtPrintAppS(&tmpstr, "The region of alignment ends at " in merger_Merge() 417 ajFmtPrintAppS(&tmpstr, "The region of alignment ends at " in merger_Merge() 428 ajFmtPrintAppS(&tmpstr, "WARNING: ************************" in merger_Merge() [all …]
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H A D | patmatmotifs.c | 103 ajFmtPrintAppS(&tmpstr, "Full: %B\n", full); in main() 104 ajFmtPrintAppS(&tmpstr, "Prune: %B\n", prune); in main() 105 ajFmtPrintAppS(&tmpstr, "Data_file: %F\n", inf); in main() 184 ajFmtPrintAppS(&tailstr, "Motif: %S\n", name); in main() 185 ajFmtPrintAppS(&tailstr, "Count: %d\n\n", number); in main() 187 ajFmtPrintAppS(&tailstr, "%S\n", text); in main() 189 ajFmtPrintAppS(&tailstr, "\n***************\n\n"); in main()
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H A D | restrict.c | 329 ajFmtPrintAppS(&tmpStr,"DNA is circular\n"); in restrict_reportHits() 331 ajFmtPrintAppS(&tmpStr,"DNA is linear\n"); in restrict_reportHits() 505 ajFmtPrintAppS(&fragStr," %d\n",fx[i]); in restrict_reportHits() 568 ajFmtPrintAppS(&fragStr,"\n%S:\n[%S]", in restrict_reportHits() 646 ajFmtPrintAppS(&fragStr,"\n"); in restrict_reportHits() 647 ajFmtPrintAppS(&fragStr,"\t%d",fx[j]); in restrict_reportHits() 649 ajFmtPrintAppS(&fragStr,"\n"); in restrict_reportHits() 679 ajFmtPrintAppS(&fragStr,"\n%S:\n[%S]", in restrict_reportHits() 748 ajFmtPrintAppS(&fragStr,"\n"); in restrict_reportHits() 749 ajFmtPrintAppS(&fragStr,"\t%d",fx[j]); in restrict_reportHits() [all …]
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H A D | recoder.c | 724 ajFmtPrintAppS(tailstr,"%s:\n",title); in recoder_fmt_seq() 728 ajFmtPrintAppS(tailstr,"%-7d",start); in recoder_fmt_seq() 732 ajFmtPrintAppS(tailstr,"%c",p[i]); in recoder_fmt_seq() 735 ajFmtPrintAppS(tailstr," "); in recoder_fmt_seq() 737 ajFmtPrintAppS(tailstr,"\n%-7d",(start+m)); in recoder_fmt_seq() 746 ajFmtPrintAppS(tailstr,"%c",p[i]); in recoder_fmt_seq() 749 ajFmtPrintAppS(tailstr," "); in recoder_fmt_seq() 751 ajFmtPrintAppS(tailstr,"\n"); in recoder_fmt_seq() 755 ajFmtPrintAppS(tailstr,"\n\n"); in recoder_fmt_seq()
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H A D | silent.c | 630 ajFmtPrintAppS(tailstr,"%s:\n",title); in silent_fmt_sequence() 634 ajFmtPrintAppS(tailstr,"%-7d",start); in silent_fmt_sequence() 638 ajFmtPrintAppS(tailstr,"%c",p[i]); in silent_fmt_sequence() 641 ajFmtPrintAppS(tailstr," "); in silent_fmt_sequence() 643 ajFmtPrintAppS(tailstr,"\n%-7d",(start+m+1)); in silent_fmt_sequence() 652 ajFmtPrintAppS(tailstr,"%c",p[i]); in silent_fmt_sequence() 655 ajFmtPrintAppS(tailstr," "); in silent_fmt_sequence() 657 ajFmtPrintAppS(tailstr,"\n"); in silent_fmt_sequence() 661 ajFmtPrintAppS(tailstr,"\n\n"); in silent_fmt_sequence()
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H A D | water.c | 161 ajFmtPrintAppS(&tmpstr,"Longest_Similarity = %5.2f%%\n", in main() 163 ajFmtPrintAppS(&tmpstr,"Shortest_Identity = %5.2f%%\n", in main() 165 ajFmtPrintAppS(&tmpstr,"Shortest_Similarity = %5.2f%%", in main()
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H A D | needle.c | 169 ajFmtPrintAppS(&tmpstr,"Longest_Similarity = %5.2f%%\n", in main() 171 ajFmtPrintAppS(&tmpstr,"Shortest_Identity = %5.2f%%\n", in main() 173 ajFmtPrintAppS(&tmpstr,"Shortest_Similarity = %5.2f%%", in main()
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H A D | needleall.c | 190 ajFmtPrintAppS(&tmpstr,"Longest_Similarity = %5.2f%%\n", in main() 192 ajFmtPrintAppS(&tmpstr,"Shortest_Identity = %5.2f%%\n", in main() 194 ajFmtPrintAppS(&tmpstr,"Shortest_Similarity = %5.2f%%", in main()
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H A D | diffseq.c | 327 ajFmtPrintAppS(&tmpstr, "%S overlap starts at %d\n", in diffseq_Diff() 330 ajFmtPrintAppS(&tmpstr, "%S overlap starts at %d\n\n", in diffseq_Diff() 441 ajFmtPrintAppS(&tmp, "Overlap_end: %d in %S\n", in diffseq_Diff() 446 ajFmtPrintAppS(&tmp, "\n"); in diffseq_Diff() 447 ajFmtPrintAppS(&tmp, "SNP_count: %d\n", snps); in diffseq_Diff() 448 ajFmtPrintAppS(&tmp, "Transitions: %d\n", transitions); in diffseq_Diff() 449 ajFmtPrintAppS(&tmp, "Transversions: %d\n", transversions); in diffseq_Diff() 733 ajFmtPrintAppS(strval, " %S='%S'", tagnam, tagval); in diffseq_AddTags() 735 ajFmtPrintAppS(strval, " %S", tagnam); in diffseq_AddTags()
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H A D | etandem.c | 371 ajFmtPrintAppS(&tmpstr, "Threshold: %d\n", thresh); in main() 372 ajFmtPrintAppS(&tmpstr, "Minrepeat: %d\n", nmin); in main() 373 ajFmtPrintAppS(&tmpstr, "Maxrepeat: %d\n", nmax); in main() 374 ajFmtPrintAppS(&tmpstr, "Mismatch: %B\n", mismatch); in main() 375 ajFmtPrintAppS(&tmpstr, "Uniform: %B\n", uniform); in main()
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H A D | eprimer32.c | 751 ajFmtPrintAppS(&str,";"); in eprimer32_send_range_pair() 755 ajFmtPrintAppS(&str, "%u,%u", start, end-start+1); in eprimer32_send_range_pair() 761 ajFmtPrintAppS(&str, ",%u,%u", start, end-start+1); in eprimer32_send_range_pair() 765 ajFmtPrintAppS(&str, ",,"); in eprimer32_send_range_pair() 772 ajFmtPrintAppS(&str,";"); in eprimer32_send_range_pair() 773 ajFmtPrintAppS(&str, ",,"); in eprimer32_send_range_pair() 777 ajFmtPrintAppS(&str, ",%u,%u", start, end-start+1); in eprimer32_send_range_pair() 782 ajFmtPrintAppS(&str, "\n"); in eprimer32_send_range_pair()
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H A D | showfeat.c | 1008 ajFmtPrintAppS(tagstmp, " %S=\"%S\"", tagnam, tagval); in showfeat_MatchPatternTags() 1010 ajFmtPrintAppS(tagstmp, " %S", tagnam); in showfeat_MatchPatternTags() 1027 ajFmtPrintAppS(tagstmp, " %S=\"%S\"", tagnam, tagval); in showfeat_MatchPatternTags() 1029 ajFmtPrintAppS(tagstmp, " %S", tagnam); in showfeat_MatchPatternTags() 1068 ajFmtPrintAppS(posout, ","); in showfeat_AddPos() 1070 ajFmtPrintAppS(posout, "%d-%d", start, end); in showfeat_AddPos()
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H A D | cacheensembl.c | 195 ajFmtPrintAppS(&special, "SpeciesPrefix=%S;", in main() 199 ajFmtPrintAppS(&special, "SpeciesIdentifier=%u;", in main()
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H A D | equicktandem.c | 102 ajFmtPrintAppS(&tmpstr, "Threshold: %d\n", thresh); in main() 103 ajFmtPrintAppS(&tmpstr, "Maxrepeat: %d\n", maxrepeat); in main()
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/dports/biology/emboss/EMBOSS-6.6.0/ajax/core/ |
H A D | ajfeatwrite.c | 1407 ajFmtPrintAppS(&pos,"%S:",gf->Remote); in featWriteEmbl() 1413 ajFmtPrintAppS(&pos,"%S",gf->Label); in featWriteEmbl() 1418 ajFmtPrintAppS(&pos,"<%d",gf->Start); in featWriteEmbl() 1428 ajFmtPrintAppS(&pos,"%d",gf->Start); in featWriteEmbl() 1775 ajFmtPrintAppS(&pos,"%S:",gf->Remote); in feattableWriteRefseq() 1781 ajFmtPrintAppS(&pos,"%S",gf->Label); in feattableWriteRefseq() 1786 ajFmtPrintAppS(&pos,"<%d",gf->Start); in feattableWriteRefseq() 1796 ajFmtPrintAppS(&pos,"%d",gf->Start); in feattableWriteRefseq() 1941 ajFmtPrintAppS(&pos,"<%d",gf->Start); in featWriteRefseqp() 1946 ajFmtPrintAppS(&pos,"%d",gf->Start); in featWriteRefseqp() [all …]
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H A D | ajassemwrite.c | 274 ajFmtPrintAppS(&headertext, "@SQ\tSN:%S\tLN:%d", in assemoutWriteBam() 278 ajFmtPrintAppS(&headertext, "\tUR:%S", c->URI); in assemoutWriteBam() 281 ajFmtPrintAppS(&headertext, "\tM5:%S", c->MD5); in assemoutWriteBam() 286 ajFmtPrintAppS(&headertext, "\n"); in assemoutWriteBam() 293 ajFmtPrintAppS(&headertext, in assemoutWriteBam() 435 ajFmtPrintAppS(&headertext, "\n"); in assemoutWriteNextBam() 442 ajFmtPrintAppS(&headertext, in assemoutWriteNextBam() 1032 ajFmtPrintAppS(&cigar, "%d%c", count, mode); in assemoutMakeCigar() 1068 ajFmtPrintAppS(&cigar, "%d%c", count, mode); in assemoutMakeCigar() 1476 ajFmtPrintAppS(&CIGAR, "%dS", r->x2 - 1); in assemoutWriteSamAlignment() [all …]
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H A D | ajvarwrite.c | 600 ajFmtPrintAppS(&meta,"##%S=%S\n", in varoutWriteBcf() 610 ajFmtPrintAppS(&meta, in varoutWriteBcf() 653 ajFmtPrintAppS(&meta, ";"); in varoutWriteBcf() 657 ajFmtPrintAppS(&meta, ",Mixture="); in varoutWriteBcf() 672 ajFmtPrintAppS(&meta, ";"); in varoutWriteBcf() 676 ajFmtPrintAppS(&meta, "\">\n"); in varoutWriteBcf() 889 ajFmtPrintAppS(&meta, in varoutWriteNextBcf() 933 ajFmtPrintAppS(&meta, ";"); in varoutWriteNextBcf() 937 ajFmtPrintAppS(&meta, ",Mixture="); in varoutWriteNextBcf() 952 ajFmtPrintAppS(&meta, ";"); in varoutWriteNextBcf() [all …]
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H A D | ajvarbcf.c | 525 ajFmtPrintAppS(s, "%d", b->tid); in ajVarbcfFmtCore() 529 ajFmtPrintAppS(s,"%d\t", b->pos+1); in ajVarbcfFmtCore() 540 ajFmtPrintAppS(s, "%.3g", b->qual); in ajVarbcfFmtCore() 575 ajFmtPrintAppS(s, "%u", d[k]); in ajVarbcfFmtCore() 580 ajFmtPrintAppS(s, "%u",((ajushort*)b->gi[i].data)[j]); in ajVarbcfFmtCore() 584 ajFmtPrintAppS(s, "%u",((unsigned char*)b->gi[i].data)[j]); in ajVarbcfFmtCore() 588 ajFmtPrintAppS(s, "%u",((ajint*)b->gi[i].data)[j]); in ajVarbcfFmtCore() 612 ajFmtPrintAppS(s, "%.2f", f[k]); in ajVarbcfFmtCore()
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H A D | ajalign.c | 2882 ajFmtPrintAppS(&tmpstr, " (%S)", in alignWriteHeaderNum() 2885 ajFmtPrintAppS(&tmpstr, " %S", in alignWriteHeaderNum() 6190 ajFmtPrintAppS(cigar, "%uM",m); in alignCigar() 6196 ajFmtPrintAppS(cigar, "%uI",d); in alignCigar() 6206 ajFmtPrintAppS(cigar, "%uM",m); in alignCigar() 6212 ajFmtPrintAppS(cigar, "%uD",i); in alignCigar() 6229 ajFmtPrintAppS(cigar, "%uD",d); in alignCigar() 6236 ajFmtPrintAppS(cigar, "%uI",i); in alignCigar() 6243 ajFmtPrintAppS(cigar, "%uM",m); in alignCigar() 6245 ajFmtPrintAppS(cigar, "%uD",d); in alignCigar() [all …]
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H A D | ajassemread.c | 1538 ajFmtPrintAppS(&cigarstr, "%u%c", in asseminBamAlignmentRec2Emboss() 1601 ajFmtPrintAppS(&tagstr,"%s", &d[dpos]); in asseminBamAlignmentRec2Emboss() 1608 ajFmtPrintAppS(&tagstr,"%f", (float) *(&d[dpos])); in asseminBamAlignmentRec2Emboss() 1613 ajFmtPrintAppS(&tagstr,"%lf", (double) *(&d[dpos])); in asseminBamAlignmentRec2Emboss() 1622 ajFmtPrintAppS(&tagstr,"%d", in asseminBamAlignmentRec2Emboss() 1627 ajFmtPrintAppS(&tagstr,"%hd", in asseminBamAlignmentRec2Emboss() 1633 ajFmtPrintAppS(&tagstr,"%d", in asseminBamAlignmentRec2Emboss() 1639 ajFmtPrintAppS(&tagstr,"%u", in asseminBamAlignmentRec2Emboss() 1644 ajFmtPrintAppS(&tagstr,"%hu", in asseminBamAlignmentRec2Emboss() 1650 ajFmtPrintAppS(&tagstr,"%u", in asseminBamAlignmentRec2Emboss() [all …]
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/dports/biology/emboss/EMBOSS-6.6.0/ajax/ensembl/ |
H A D | ensbaseadaptor.c | 795 ajFmtPrintAppS(&columnnames, "%s, ", columnnamesrray[i]); in baseadaptorFetchAllStatement() 825 ajFmtPrintAppS(&joins, in baseadaptorFetchAllStatement() 838 ajFmtPrintAppS(&tablenames, "%s, ", ba->Tablenames[i]); in baseadaptorFetchAllStatement() 852 ajFmtPrintAppS(Pstatement, " %S FROM %S(%S)", in baseadaptorFetchAllStatement() 856 ajFmtPrintAppS(Pstatement, " %S", joins); in baseadaptorFetchAllStatement() 860 ajFmtPrintAppS(Pstatement, " WHERE %S", constraint); in baseadaptorFetchAllStatement() 866 ajFmtPrintAppS(Pstatement, " WHERE %s", ba->Defaultcondition); in baseadaptorFetchAllStatement() 869 ajFmtPrintAppS(Pstatement, " %s", ba->Finalcondition); in baseadaptorFetchAllStatement() 1249 ajFmtPrintAppS(&csv, "%u, ", *((ajuint *) keyarray[i])); in ensBaseadaptorFetchAllbyIdentifiers() 1459 ajFmtPrintAppS(Pstatement, in baseadaptorRetrieveAllStatement() [all …]
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H A D | ensqcalignment.c | 3020 ajFmtPrintAppS(Pstr, "%S:%d-%d:%d", anchor, start, end, strand); in ensQcalignmentReport() 3043 ajFmtPrintAppS(Pstr, in ensQcalignmentReport() 3061 ajFmtPrintAppS(Pstr, in ensQcalignmentReport() 3077 ajFmtPrintAppS(Pstr, in ensQcalignmentReport() 3085 ajFmtPrintAppS(Pstr, " (%d)", length); in ensQcalignmentReport() 3134 ajFmtPrintAppS(Pstr, in ensQcalignmentReport() 3152 ajFmtPrintAppS(Pstr, in ensQcalignmentReport() 3168 ajFmtPrintAppS(Pstr, in ensQcalignmentReport() 3176 ajFmtPrintAppS(Pstr, " (%d)", length); in ensQcalignmentReport() 3952 ajFmtPrintAppS(&constraint, in ensQcalignmentadaptorFetchAllbyQcdatabaseQuery() [all …]
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H A D | ensattribute.c | 880 ajFmtPrintAppS(&statement, " AND attrib_type.code = '%s'", txtcode); in ensAttributeadaptorFetchAllbyGene() 957 ajFmtPrintAppS(&statement, " AND attrib_type.code = '%s'", txtcode); in ensAttributeadaptorFetchAllbyOperon() 1034 ajFmtPrintAppS(&statement, " AND attrib_type.code = '%s'", txtcode); in ensAttributeadaptorFetchAllbyOperontranscript() 1111 ajFmtPrintAppS(&statement, " AND attrib_type.code = '%s'", txtcode); in ensAttributeadaptorFetchAllbySeqregion() 1246 ajFmtPrintAppS(&statement, " AND attrib_type.code = '%s'", txtcode); in ensAttributeadaptorFetchAllbyTranscript() 1323 ajFmtPrintAppS(&statement, " AND attrib_type.code = '%s'", txtcode); in ensAttributeadaptorFetchAllbyTranslation()
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/dports/biology/emboss/EMBOSS-6.6.0/ajax/ajaxdb/ |
H A D | ajtextdb.c | 7062 ajFmtPrintAppS(&get, in textAccessMrs5() 7081 ajFmtPrintAppS(&get, in textAccessMrs5() 7092 ajFmtPrintAppS(&get, in textAccessMrs5() 7094 ajFmtPrintAppS(&get, in textAccessMrs5() 7102 ajFmtPrintAppS(&get, in textAccessMrs5() 7234 ajFmtPrintAppS(&get, in textAccessMrs4() 7253 ajFmtPrintAppS(&get, in textAccessMrs4() 7266 ajFmtPrintAppS(&get, in textAccessMrs4() 7274 ajFmtPrintAppS(&get, in textAccessMrs4() 7406 ajFmtPrintAppS(&get, in textAccessMrs3() [all …]
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H A D | ajmart.c | 2649 ajFmtPrintAppS(&filterval,",%S",nameval); in ajMartFilterMatch() 2743 ajFmtPrintAppS(&mq->Query,"formatter = \"%S\" ", in ajMartMakeQueryXml() 2751 ajFmtPrintAppS(&mq->Query,"count = \"1\" "); in ajMartMakeQueryXml() 2754 ajFmtPrintAppS(&mq->Query,"header = \"1\" "); in ajMartMakeQueryXml() 2762 ajFmtPrintAppS(&mq->Query,">"); in ajMartMakeQueryXml() 2768 ajFmtPrintAppS(&mq->Query,"<Dataset "); in ajMartMakeQueryXml() 2770 ajFmtPrintAppS(&mq->Query,"interface = \"%S\" ", in ajMartMakeQueryXml() 2772 ajFmtPrintAppS(&mq->Query,">"); in ajMartMakeQueryXml() 2792 ajFmtPrintAppS(&mq->Query,"</Dataset>"); in ajMartMakeQueryXml() 2795 ajFmtPrintAppS(&mq->Query,"</Query>"); in ajMartMakeQueryXml() [all …]
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