| /dports/biology/abyss/abyss-2.3.1/vendor/nthash/ |
| H A D | sttest.cpp | 32 for(string seq, hseq; good;) { in main() local
33 good = static_cast<bool>(getline(in, hseq)); in main()
35 good = static_cast<bool>(getline(in, hseq)); in main()
36 good = static_cast<bool>(getline(in, hseq)); in main()
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| /dports/biology/emboss/EMBOSS-6.6.0/emboss/ |
| H A D | edialign.c | 6749 char **hseq = NULL; in edialign_ali_arrange() local
6781 if((hseq = (char **) calloc(seqnum , sizeof(char *))) == NULL) in edialign_ali_arrange()
7002 if( (hseq[hv] = calloc( (maxlen+1), sizeof(char) )) == NULL ) in edialign_ali_arrange()
7019 hseq[hv][i] = tolower((int)seq[hv][i]); in edialign_ali_arrange()
7025 hseq[ fragments[hv].s[k]][ii] = seq[fragments[hv].s[k]][ii]; in edialign_ali_arrange()
7029 endseq[hv][ shift[hv][ii] ] = hseq[hv][ii]; in edialign_ali_arrange()
7424 AJFREE(hseq[hv]); in edialign_ali_arrange()
7447 AJFREE (hseq); in edialign_ali_arrange()
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| /dports/biology/jalview/jalview/src/jalview/datamodel/ |
| H A D | AlignmentView.java | 835 SequenceI hseq = sequences[s].getSeq(gapCharacter) in getUpdatedView() local
839 alignment[s] = hseq; in getUpdatedView()
844 + hseq.getSequenceAsString()); in getUpdatedView()
845 if (hseq.getEnd() >= hseq.getStart()) in getUpdatedView()
847 alignment[s].setEnd(hseq.getEnd()); in getUpdatedView()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objects/blastxml/ |
| H A D | blastxml.asn | 79 hseq VisibleString, -- alignment string for subject (with gaps)
|
| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objects/blastxml2/ |
| H A D | blastxml2.asn | 123 hseq VisibleString, -- alignment string for subject (with gaps)
|
| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objects/blastxml/ |
| H A D | blastxml.asn | 79 hseq VisibleString, -- alignment string for subject (with gaps)
|
| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objects/blastxml2/ |
| H A D | blastxml2.asn | 123 hseq VisibleString, -- alignment string for subject (with gaps)
|
| /dports/biology/ncbi-toolkit/ncbi/network/wwwblast/Src/XML/ |
| H A D | blstxml.asn | 116 hseq VisibleString, -- alignment string for subject (with gaps)
|
| /dports/biology/ncbi-toolkit/ncbi/tools/ |
| H A D | blstxml.asn | 79 hseq VisibleString, -- alignment string for subject (with gaps)
|
| H A D | bxmlobj.c | 1226 MemFree(ptr -> hseq); in HspFree()
1418 ptr -> hseq = av.ptrvalue; in HspAsnRead()
1526 if (ptr -> hseq != NULL) { in HspAsnWrite()
1527 av.ptrvalue = ptr -> hseq; in HspAsnWrite()
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| H A D | bxmlobj.h | 208 CharPtr hseq; member
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| H A D | xmlblast.c | 190 hsp->hseq = MemNew(length+1); in BXMLGetSeqLineForDenseDiag()
233 hsp->hseq[i] = t_res; in BXMLGetSeqLineForDenseDiag()
274 hsp->hseq = MemNew(length+1); in BXMLGetSeqLineForDenseSeg()
316 hsp->hseq[abs_index] = '-'; in BXMLGetSeqLineForDenseSeg()
327 hsp->hseq[abs_index] = t_res; in BXMLGetSeqLineForDenseSeg()
338 hsp->hseq[abs_index] = t_res; in BXMLGetSeqLineForDenseSeg()
383 hsp->hseq = MemNew(length+1); in BXMLGetSeqLineForStdSeg()
424 hsp->hseq[abs_index] = residue1; in BXMLGetSeqLineForStdSeg()
453 hsp->hseq[abs_index] = residue1; in BXMLGetSeqLineForStdSeg()
494 hsp->hseq[abs_index] = residue1; in BXMLGetSeqLineForStdSeg()
[all …]
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| /dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/Search/Tiling/ |
| H A D | MapTiling.pm | 355 $hstart ||= $hseq->start;
372 $hseq = $aln->get_seq_by_pos(2);
374 $hinc = $hseq->length - $hseq->num_gaps($Bio::LocatableSeq::GAP_SYMBOLS);
392 -strand => $hseq->strand,
396 -tag => { subject_id => $hseq->id,
397 subject_desc => $hseq->desc,
398 subject_start => $hstart + (($hseq->strand && $hseq->strand < 0) ? -1 : 1)*$hlen,
399 subject_end => $hstart + (($hseq->strand && $hseq->strand < 0) ? -1 : 1)*($hlen+$hinc-1)
403 $hit_string .= $hseq->seq;
416 $hseq->add_SeqFeature(@hfeats);
[all …]
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| /dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/SearchIO/ |
| H A D | infernal.pm | 544 $csline, $qseq, $midline, $hseq, $pline) = @$hsp;
564 'Hsp_hseq' => $hseq,
|
| /dports/biology/p5-BioPerl/BioPerl-1.7.7/t/SearchIO/ |
| H A D | gmap_f9.t | 39 hseq => 'GGAGGAGGTGGAGGAGGAGG', # ditto
75 hseq => 'TAGCTGTTTTCCAAAATATA', # ditto
128 is(substr($hsp->hit_string, 0, 20), $info->{hseq}, 'Hit sequence');
|
| /dports/biology/py-biopython/biopython-1.79/Bio/SearchIO/BlastIO/ |
| H A D | blast_text.py | 99 hseq = ""
107 hseq += hchar
109 frag.query, frag.hit = qseq, hseq
|
| /dports/biology/py-biopython/biopython-1.79/Bio/SearchIO/ |
| H A D | BlatIO.py | 354 hseq = "" if not hseqlist else hseqlist[idx]
357 frag = HSPFragment(hid, qid, hit=hseq, query=qseq)
|
| /dports/biology/py-biopython/biopython-1.79/Bio/SearchIO/ExonerateIO/ |
| H A D | _base.py | 129 hseq = str(frag.hit.seq)
130 h_triplets_pre, h_triplets, h_triplets_post = _make_triplets(hseq, phase)
246 hseq = "" if hseqlist is None else hseqlist[idx]
249 frag = HSPFragment(hid, qid, hit=hseq, query=qseq)
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| /dports/biology/py-biopython/biopython-1.79/Bio/SearchIO/_model/ |
| H A D | hsp.py | 846 hseq = self.hit.seq
848 hseq = "?"
861 lines.append("%10s - %s" % ("Hit", hseq))
872 lines.append("%10s - %s%s%s" % ("Hit", hseq[:59], cont, hseq[-5:]))
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| /dports/biology/readseq/rez/ |
| H A D | rseq.notes | 381 %hseq = (); %count = ();
404 %hseq=(); # keep only last iteration
441 if (!$hseq{$name}) {
446 if ($npad>0) { $hseq{$name} = $pad }
450 if ($m==4) { $hseq{$name} .= $line[2] }
451 if ($m==6) { $hseq{$name} .= $line[1] }
470 $hlen = length($hseq{$name});
474 if ($npad>0) { $hseq{$name} .= $pad }
476 $hitlen = length($hseq{$name});
480 if ($format eq "fasta") { $hseq{$name} =~ s/\-/X/g }
[all …]
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| /dports/cad/ghdl/ghdl-1.0.0/testsuite/synth/issue662/ |
| H A D | tb_psl_stable.vhdl | 24 procedure hseq (s : string; signal clk : std_logic; signal o : out std_logic_vector(3 downto 0)) procedure
50 end hseq;
66 SEQ_D : hseq ("011006660000000", clk, d);
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| /dports/chinese/gcin-gtk3/gcin-2.9.0/data/ |
| H A D | NewCJ3.cin | 106062 hseq; 生長激素
|
| /dports/chinese/gcin-qt5/gcin-2.9.0/data/ |
| H A D | NewCJ3.cin | 106062 hseq; 生長激素
|
| /dports/chinese/gcin/gcin-2.9.0/data/ |
| H A D | NewCJ3.cin | 106062 hseq; 生長激素
|
| /dports/databases/timescaledb/timescaledb-2.5.1/tsl/src/nodes/ |
| H A D | data_node_dispatch.c | 584 HASH_SEQ_STATUS hseq; in flush_data_nodes() local
588 hash_seq_init(&hseq, sds->nodestates); in flush_data_nodes()
590 for (ss = hash_seq_search(&hseq); ss != NULL; ss = hash_seq_search(&hseq)) in flush_data_nodes()
1016 HASH_SEQ_STATUS hseq; in data_node_dispatch_end() local
1018 hash_seq_init(&hseq, sds->nodestates); in data_node_dispatch_end()
1020 for (ss = hash_seq_search(&hseq); ss != NULL; ss = hash_seq_search(&hseq)) in data_node_dispatch_end()
|