| /dports/math/SCIP/scip-7.0.3/check/coverage/settings/ |
| H A D | lns_exp3.set | 5 heuristics/alns/banditalgo = e
7 heuristics/alns/freq = 15
9 heuristics/alns/rewardcontrol = 1.0
11 heuristics/alns/uselocalredcost = TRUE
12 heuristics/alns/usepscost = TRUE
14 heuristics/alns/fixtol = 0.15
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| H A D | lns_epsgreedy_vanilla.set | 23 # frequency for calling primal heuristic <alns> (-1: never, 0: only at depth freqofs)
25 heuristics/alns/freq = 10
29 heuristics/alns/banditalgo = g
33 heuristics/alns/rewardcontrol = 0
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| H A D | usebenders.set | 11 # frequency for calling primal heuristic <alns> (-1: never, 0: only at depth freqofs)
13 heuristics/alns/freq = -1
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| H A D | usebenders-cutstrengthen.set | 11 # frequency for calling primal heuristic <alns> (-1: never, 0: only at depth freqofs)
13 heuristics/alns/freq = -1
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| H A D | benders-qp.set | 23 # frequency for calling primal heuristic <alns> (-1: never, 0: only at depth freqofs)
25 heuristics/alns/freq = -1
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| /dports/biology/stacks/stacks-2.4/src/ |
| H A D | GappedAln.h | 349 for (uint i = alns[n].query_pos + 1; i <= alns[n].query_pos + alns[n].aln_len; i++) { in align_constrained()
350 for (uint j = alns[n].subj_pos + 1; j <= alns[n].subj_pos + alns[n].aln_len; j++) { in align_constrained()
373 q_start = 1 + alns[n].query_pos + alns[n].aln_len; in align_constrained()
375 s_start = 1 + alns[n].subj_pos + alns[n].aln_len; in align_constrained()
387 if (alns.back().query_pos + alns.back().aln_len != query.length()) { in align_constrained()
388 q_start = 1 + alns.back().query_pos + alns.back().aln_len; in align_constrained()
394 q = 1 + alns.back().subj_pos + alns.back().aln_len; in align_constrained()
781 sort(alns.begin(), alns.end(), compare_alignres); in trace_global_alignment()
782 this->_aln = alns[0]; in trace_global_alignment()
927 sort(alns.begin(), alns.end(), compare_alignres); in trace_local_alignment()
[all …]
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| H A D | mstack.h | 46 …vector<Aln> alns; // Vector describing gapped alignments between this stack and oth… variable
96 , alns (move(o.alns)) in MergedStack()
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| H A D | gstacks.cc | 1280 vector<STAln> alns, final_alns; in align_reads_to_contig() local
1309 if (alns.size() == 0) in align_reads_to_contig()
1315 if (alns.size() == 1 && alns[0].aln_len == query.length()) { in align_reads_to_contig()
1344 sort(alns.begin(), alns.end(), [](STAln a, STAln b) in suffix_tree_hits_to_dag()
1367 end_pos = alns[i].subj_pos + alns[i].aln_len - 1; in suffix_tree_hits_to_dag()
1373 if (alns[j].query_pos > alns[i].query_pos && in suffix_tree_hits_to_dag()
1374 alns[j].subj_pos > alns[i].subj_pos && in suffix_tree_hits_to_dag()
1387 if (alns[j].max._index == j || score > alns[j].max._score) in suffix_tree_hits_to_dag()
1474 if (alns.size() == 0) { in find_locus_overlap()
1493 size_t query_stop = alns.front().query_pos + alns.front().aln_len - 1; in find_locus_overlap()
[all …]
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| H A D | ustacks.cc | 285 sort(tag_1->alns.begin(), tag_1->alns.end(), rank_alignments); in merge_gapped_alns()
291 if (tag_1->masked || tag_1->alns.size() == 0) in merge_gapped_alns()
293 if (tag_1->alns.size() > 1 && tag_1->alns[0].pct_id == tag_1->alns[1].pct_id) in merge_gapped_alns()
300 tag_2 = merged[tag_1->alns[0].id]; in merge_gapped_alns()
301 sort(tag_2->alns.begin(), tag_2->alns.end(), rank_alignments); in merge_gapped_alns()
303 if (tag_2->masked || tag_2->alns.size() == 0) in merge_gapped_alns()
305 if (tag_2->alns.size() > 1 && tag_2->alns[0].pct_id == tag_2->alns[1].pct_id) in merge_gapped_alns()
308 if (tag_1->id != (int)tag_2->alns[0].id) in merge_gapped_alns()
311 cigar_1 = invert_cigar(tag_1->alns[0].cigar); in merge_gapped_alns()
312 cigar_2 = tag_2->alns[0].cigar; in merge_gapped_alns()
[all …]
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| H A D | SuffixTree.cc | 53 SuffixTree::align(const char *query, vector<pair<size_t, size_t> > &alns) in align() argument
121 alns.push_back(make_pair(aln_pos, qcnt)); in align()
139 alns.push_back(make_pair(dists[i] + query_start - qcnt + 1, qcnt)); in align()
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| /dports/biology/stacks/stacks-2.4/scripts/ |
| H A D | integrate_alignments.py | 94 def parse_catalog_alignments(aln_path, alns): argument
113 alns[locus] = (chr, bp, "-");
115 alns[locus] = (chr, bp, "+");
121 def convert_sample(path, file, out_path, alns): argument
176 if cat_locus not in alns:
179 (chr, bp, strand) = alns[cat_locus]
301 (chr, bp, strand) = alns[cat_locus]
340 if cat_locus not in alns:
343 (chr, bp, strand) = alns[cat_locus]
410 alns = {} variable
[all …]
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| /dports/biology/p5-BioPerl-Run/BioPerl-Run-1.007003/scripts/ |
| H A D | bp_blast2tree.pl | 63 my (@alns,@seqs);
83 push @alns, $aln_factory->align(\@seqs);
90 $out->write_aln(@alns);
113 foreach my $aln ( @alns ) {
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/sra/readers/bam/test/ |
| H A D | samtools.hpp | 96 TAlignments& alns, size_t limit_count = 0);
98 TAlignments& alns, size_t limit_count = 0) in Fetch() argument
100 Fetch(GetRefSeqIndex(id), from, to, alns, limit_count); in Fetch()
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| H A D | samtools.cpp | 274 TAlignments& alns, size_t limit_count) in Fetch() argument
280 params.m_Alns = &alns; in Fetch()
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| /dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/Align/ |
| H A D | Utilities.pm | 268 my ( @alns, $i );
291 push @alns, $newaln;
293 return \@alns;
321 my ( @alns, $i );
345 push @alns, $newaln;
347 return \@alns;
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/seqqa/ |
| H A D | blastp_tests.cpp | 101 const list<CRef<CSeq_align> >& alns = annot->GetData().GetAlign(); in RunTest() local
102 if (alns.size() == 0) { in RunTest()
114 = *alns.front()->GetSegs().GetDenseg().GetIds()[0]; in RunTest()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/align/contig_assembly/demo/ |
| H A D | demo_contig_assembly.cpp | 108 vector<CRef<CSeq_align> > alns; in Run() local
116 alns = CContigAssembly::Align(id1, id2, blast_params, min_frac_ident, in Run()
122 ITERATE (vector<CRef<CSeq_align> >, aln, alns) { in Run()
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| /dports/science/py-pymol/pymol-open-source-2.4.0/modules/pymol/ |
| H A D | seqalign.py | 29 alns = pairwise2.align.globalcs(s1, s2,
34 a.add_sequence("s1", alns[0][0])
35 a.add_sequence("s2", alns[0][1])
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| /dports/biology/py-biopython/biopython-1.79/Tests/ |
| H A D | test_codonalign.py | 148 alns = []
171 alns.append(caln)
172 self.alns = alns
175 self.assertEqual(len(self.alns), 6)
177 for n, i in enumerate(self.alns):
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| /dports/biology/mothur/mothur-1.46.1/source/commands/ |
| H A D | chimeravsearchcommand.h | 50 string accnos, alns, formattedFastaFilename, templatefile, vsearchLocation; member
69 alns = al; in vsearchData()
121 … groups2Files, string outputFName, string filename, string accnos, string alns, string newCountFil…
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| H A D | chimerauchimecommand.cpp | 315 string accnos, alns, formattedFastaFilename, templatefile, uchimeLocation; member
334 alns = al; in uchimeData()
1126 …params->setDriverNames((params->outputFName + thisGroup), (params->alns+thisGroup), (params->accno… in driverGroups()
1174 …lns) { params->util.appendFiles((params->alns+thisGroup), params->alns); params->util.mothurRemove… in driverGroups()
1189 … groups2Files, string outputFName, string filename, string accnos, string alns, vector<string> gro… in createProcessesGroups() argument
1228 …emplatefile, filename+extension, fastafile, countfile, accnos+extension, alns+extension, thisGrou… in createProcessesGroups()
1244 …ame, uchimeLocation, templatefile, filename, fastafile, countfile, accnos, alns, thisGroups, vars); in createProcessesGroups()
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| /dports/biology/p5-BioPerl-Run/BioPerl-Run-1.007003/lib/Bio/Tools/Run/Alignment/ |
| H A D | Proda.pm | 340 my @alns;
342 push @alns, $aln;
344 return @alns;
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/cddalignview/ |
| H A D | cav_function.cpp | 406 const SeqAnnotList *alns; in CAV_DisplayMultiple() local
407 int retval = LoadASNFromIstream(asnIstrstream, &seqs, &alns); in CAV_DisplayMultiple()
415 auto_ptr<const SeqAnnotList> alignments(alns); in CAV_DisplayMultiple()
417 return CAV_DisplayMultiple(*seqs, *alns, options, paragraphWidth, conservationThreshhold, in CAV_DisplayMultiple()
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| /dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/AlignIO/ |
| H A D | po.pm | 231 my @alns = @_;
243 foreach $aln (@alns) {
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/align/contig_assembly/ |
| H A D | contig_assembly.cpp | 627 CRef<CSeq_align_set> alns; in Align() local
629 alns = Blastn(id0, id1, blast_params, scope); in Align()
639 NON_CONST_ITERATE (CSeq_align_set::Tdata, aln, alns->Set()) { in Align()
664 if (alns->Get().empty()) { in Align()
673 FindDiagFromAlignSet(*alns, scope, diag_finding_window, strand, diag); in Align()
728 NON_CONST_ITERATE (CSeq_align_set::Tdata, aln, alns->Set()) { in Align()
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