| /dports/biology/emboss/EMBOSS-6.6.0/emboss/ |
| H A D | megamerger.c | 172 ajStrAssignSubS(&seqstr, s2, 0, p->seq2start-1); in megamerger_Merge()
181 ajStrAssignSubS(&seqstr, s1, 0, p->seq1start-1); in megamerger_Merge()
194 ajStrAssignSubS(&tmp, s1, 0, p->seq1start-1); in megamerger_Merge()
204 ajStrAssignSubS(&tmp, s2, 0, p->seq2start-1); in megamerger_Merge()
236 ajStrAssignSubS(&tmp, s1, prev1end, p->seq1start-1); in megamerger_Merge()
259 ajStrAssignSubS(&tmp, s2, prev2end, p->seq2start-1); in megamerger_Merge()
273 ajStrAssignSubS(&tmp, s1, prev1end, p->seq1start-1); in megamerger_Merge()
333 ajStrAssignSubS(&tmp, s1, prev1end, ajSeqGetLen(seq1)-1); in megamerger_Merge()
342 ajStrAssignSubS(&tmp, s2, prev2end, ajSeqGetLen(seq2)-1); in megamerger_Merge()
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| H A D | epestfind.c | 137 ajStrAssignSubS(&substr, str, 0, (iter->Ptr - iter->Start))
154 ajStrAssignSubS(&substr,str,(iter->Ptr - iter->Start), \
418 ajStrAssignSubS(&substr, str, in main()
422 ajStrAssignSubS(&substr, str, in main()
427 ajStrAssignSubS(&substr, str, in main()
431 ajStrAssignSubS(&substr, str, in main()
607 ajStrAssignSubS(&substr, str, (pstdat->Begin), (pstdat->End)); in main()
677 ajStrAssignSubS(&substr, str, ((i - 1) * 60), (i * 60 - 1)); in main()
680 ajStrAssignSubS(&substr, map, ((i - 1) * 60), (i * 60 - 1)); in main()
687 ajStrAssignSubS(&substr, str, ((i - 1) * 60), (seqlen - 1)); in main()
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| H A D | prima.c | 463 ajStrAssignSubS(&p1,substr,v1,v2); in main()
470 ajStrAssignSubS(&p2,substr,v1,v2); in main()
506 ajStrAssignSubS(&p1,substr,v1,v2); in main()
521 ajStrAssignSubS(&p2,substr,v1,v2); in main()
523 ajStrAssignSubS(&p1,substr,v1,v2); in main()
842 ajStrAssignSubS(&str1,tmp->substr,0,cut); in prima_reject_self()
843 ajStrAssignSubS(&str2,tmp->substr,cut+1,len-1); in prima_reject_self()
876 ajStrAssignSubS(&str1,tmp->substr,0,cut); in prima_reject_self()
877 ajStrAssignSubS(&str2,tmp->substr,cut+1,len-1); in prima_reject_self()
1233 ajStrAssignSubS(&str1, fstr, 0, cut); in prima_testtarget()
[all …]
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| H A D | pepinfo.c | 185 ajStrAssignSubS(&key, ajSeqGetSeqS(inseq), j, j); in main()
307 ajStrAssignSubS(&key, ajSeqGetSeqS(inseq), (j+k), (j+k)); in main()
422 ajStrAssignSubS(&aa, ajSeqGetSeqS(seq), i, i); in pepinfo_printIntResults()
461 ajStrAssignSubS(&aa, ajSeqGetSeqS(seq), i, i); in pepinfo_printFloatResults()
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| H A D | restover.c | 353 ajStrAssignSubS(&overhang, ajSeqGetSeqS( seq), m->cut1, m->cut2-1); in restover_printHits()
356 ajStrAssignSubS(&overhang, ajSeqGetSeqS( seq), m->cut2, m->cut1-1); in restover_printHits()
385 ajStrAssignSubS(&overhang, ajSeqGetSeqS( seq), in restover_printHits()
389 ajStrAssignSubS(&overhang, ajSeqGetSeqS( seq), in restover_printHits()
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| H A D | diffseq.c | 356 ajStrAssignSubS(&tmp, s1, diff->Start1-1, diff->End1-1); in diffseq_Diff()
400 ajStrAssignSubS(&tmpseq, s2, diff->Start2-1, diff->End2-1); in diffseq_Diff()
556 ajStrAssignSubS(&replacestr, ajSeqGetSeqS(seq2), in diffseq_WordMatchListConvDiffToFeat()
565 ajStrAssignSubS(&sourcestr, ajSeqGetSeqS(seq1), in diffseq_WordMatchListConvDiffToFeat()
602 ajStrAssignSubS(&replacestr, ajSeqGetSeqS(seq1), in diffseq_WordMatchListConvDiffToFeat()
611 ajStrAssignSubS(&sourcestr, ajSeqGetSeqS(seq2), in diffseq_WordMatchListConvDiffToFeat()
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| H A D | cai.c | 60 ajStrAssignSubS(&substr,ajSeqGetSeqS(seq),beg-1,end-1); in main()
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| H A D | cutseq.c | 57 ajStrAssignSubS(&str, ajSeqGetSeqS(seq), beg, end); in main()
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| H A D | cusp.c | 60 ajStrAssignSubS(&substr,ajSeqGetSeqS(seq),beg-1,end-1); in main()
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| H A D | backtranseq.c | 56 ajStrAssignSubS(&substr,ajSeqGetSeqS(a),beg-1,end-1); in main()
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| H A D | maskseq.c | 58 ajStrAssignSubS(&str, ajSeqGetSeqS(seq), beg, end); in main()
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| H A D | chips.c | 66 ajStrAssignSubS(&substr,ajSeqGetSeqS(seq),beg-1,end-1); in main()
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| H A D | coderet.c | 326 ajStrAssignSubS(&subseq, strseq, i, j-1); in coderet_put_rest()
356 ajStrAssignSubS(&subseq, strseq, i, j); in coderet_put_rest()
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| H A D | vectorstrip.c | 879 ajStrAssignSubS(&outs, ajSeqGetSeqS(seqcp), start-1, end-1); in vectorstrip_print_sequence()
883 ajStrAssignSubS(&fivetrim, ajSeqGetSeqS(seqcp), 0, start-2); in vectorstrip_print_sequence()
890 ajStrAssignSubS(&threetrim, ajSeqGetSeqS(seqcp), in vectorstrip_print_sequence()
1027 ajStrAssignSubS(&tmp, seqstr, x, x+linelen-1); in vectorstrip_reportseq()
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| H A D | showorf.c | 542 ajStrAssignSubS(&s,substr,start,end); in showorf_showTransb()
609 ajStrAssignSubS(&s,pseqs[i],start,end); in showorf_showTransb()
678 ajStrAssignSubS(&s,pseqs[i],start,end); in showorf_showTransb()
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| H A D | getorf.c | 579 ajStrAssignSubS(&aroundstr, ajSeqGetSeqS(seq), s-1, e-1); in getorf_WriteORF()
592 ajStrAssignSubS(&aroundstr, ajSeqGetSeqS(seq), s-1, e-1); in getorf_WriteORF()
605 ajStrAssignSubS(&aroundstr, ajSeqGetSeqS(seq), s-1, e-1); in getorf_WriteORF()
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| H A D | patmattest.c | 98 ajStrAssignSubS(&new,ajSeqGetSeqS(seq),embPatMatchGetStart(results,j), in main()
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| H A D | patmatdb.c | 123 ajStrAssignSubS(&temp, str, zstart, zend); in main()
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| H A D | chaos.c | 66 ajStrAssignSubS(&str,ajSeqGetSeqS(sequence),begin,end); in main()
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| /dports/biology/emboss/EMBOSS-6.6.0/nucleus/ |
| H A D | embindex.c | 700 ajStrAssignSubS(&embindexLine, kwline, 5, -1); in embBtreeEmblKW()
714 ajStrAssignSubS(&str,token,0,maxlen-1); in embBtreeEmblKW()
754 ajStrAssignSubS(&embindexLine, txline, 5, -1); in embBtreeEmblTX()
769 ajStrAssignSubS(&str,token,0,maxlen-1); in embBtreeEmblTX()
813 ajStrAssignSubS(&embindexLine, acline, 5, -1); in embBtreeEmblAC()
884 ajStrAssignSubS(&embindexLine, idline, 5, -1); in embBtreeEmblSV()
951 ajStrAssignSubS(&str,token,0,maxlen-1); in embBtreeEmblDE()
1636 ajStrAssignSubS(&str,token,0,maxlen-1); in embBtreeGenBankKW()
1690 ajStrAssignSubS(&str,token,0,maxlen-1); in embBtreeGenBankDE()
1745 ajStrAssignSubS(&str,token,0,maxlen-1); in embBtreeGenBankTX()
[all …]
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| H A D | embpatlist.c | 302 ajStrAssignSubS(&seqstr, ajSeqGetSeqS(revseq), pos-1, adj-1); in embPatternRegexSearch()
306 ajStrAssignSubS(&seqstr, ajSeqGetSeqS(seq), pos-1, adj-1); in embPatternRegexSearch()
435 ajStrAssignSubS(&seqstr, ajSeqGetSeqS(revseq), pos-1, adj-1); in embPatternRegexSearchAll()
439 ajStrAssignSubS(&seqstr, ajSeqGetSeqS(seq), pos-1, adj-1); in embPatternRegexSearchAll()
572 ajStrAssignSubS(&seqstr, ajSeqGetSeqS(revseq), in embPatternSeqSearch()
577 ajStrAssignSubS(&seqstr, ajSeqGetSeqS(seq), in embPatternSeqSearch()
718 ajStrAssignSubS(&seqstr, ajSeqGetSeqS(revseq), in embPatternSeqSearchAll()
723 ajStrAssignSubS(&seqstr, ajSeqGetSeqS(seq), in embPatternSeqSearchAll()
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| H A D | embdomain.c | 161 ajStrAssignSubS(pdb, scop, 1, 4); in embScopToPdbid()
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| /dports/biology/emboss/EMBOSS-6.6.0/ajax/core/ |
| H A D | ajobo.c | 377 ajStrAssignSubS(Pdefstr, obo->Def, 1, i); in ajOboGetDef()
387 ajStrAssignSubS(Pdefstr, obo->Def, 0, i); in ajOboGetDef()
541 ajStrAssignSubS(&up, tag->Value, colpos, -1); in ajOboGetParents()
550 ajStrAssignSubS(&up, obo->Replaced, colpos, -1); in ajOboGetParents()
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| H A D | ajpdbio.c | 2640 ajStrAssignSubS(&pdbfile->rtype[i], in pdbioFirstPass()
2655 ajStrAssignSubS(&seqres, pdbfile->lines[i], 14, 18); in pdbioFirstPass()
2663 ajStrAssignSubS(&seqres, pdbfile->lines[i], 19, 70); in pdbioFirstPass()
2794 ajStrAssignSubS(&(pdbfile->compnd), in pdbioFirstPass()
2815 ajStrAssignSubS(&(pdbfile->source), in pdbioFirstPass()
2889 ajStrAssignSubS(&tmpstr, pdbfile->lines[i], 7, 9); in pdbioFirstPass()
2920 ajStrAssignSubS(&tmpstr, pdbfile->lines[i], 38, 39); in pdbioFirstPass()
2947 ajStrAssignSubS(&tmpstr, pdbfile->lines[i], 7, 9); in pdbioFirstPass()
3024 ajStrAssignSubS(&tmpstr, pdbfile->lines[i], 7, 9); in pdbioFirstPass()
4105 ajStrAssignSubS(&pdbfile->atype[i], in pdbioMaskChains()
[all …]
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| H A D | ajcod.c | 935 ajStrAssignSubS(&formatstr, fn, 0, i-1); in ajCodRead()
936 ajStrAssignSubS(&fname, fn, i+1, -1); in ajCodRead()
1552 ajStrAssignSubS(&thys->Species, line, 0, i-1); in codReadCodehop()
1553 ajStrAssignSubS(&tok1, line, i+1, -1); in codReadCodehop()
1571 ajStrAssignSubS(&tok1, line, 0, i-1); in codReadCodehop()
1572 ajStrAssignSubS(&tok2, line, i+1, -1); in codReadCodehop()
1579 ajStrAssignSubS(&thys->Release, tok1, 0, i-1); in codReadCodehop()
1580 ajStrAssignSubS(&thys->Division, tok1, i+1, -1); in codReadCodehop()
1589 ajStrAssignSubS(&tok3, tok2, 0, i-1); in codReadCodehop()
1670 ajStrAssignSubS(&tok1, line, 0, i-1); in codReadGcg()
[all …]
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