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/dports/biology/py-biopython/biopython-1.79/Tests/
H A Dpairwise2_testCases.py101 aligns.sort()
129 aligns.sort()
165 aligns.sort()
315 aligns.sort()
343 aligns.sort()
423 aligns.sort()
466 aligns.sort()
507 aligns.sort()
557 aligns.sort()
607 aligns.sort()
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/dports/biology/mummer/mummer-4.0.0beta2-2-g277dac5/src/tigr/
H A Dshow-diff.cc158 aligns.clear(); in PrintDiff()
174 sort(aligns.begin(), aligns.end(), EdgeletIdQLoQCmp_t()); in PrintDiff()
176 aligns[i]->stpc = aligns[i]->isQLIS ? j++ : -1; in PrintDiff()
179 sort(aligns.begin(), aligns.end(), EdgeletLoRCmp_t()); in PrintDiff()
180 assert ( aligns[0] == &lpad && aligns[nAligns-1] == &rpad ); in PrintDiff()
189 A = aligns[i]; in PrintDiff()
256 aligns.clear(); in PrintDiff()
270 sort(aligns.begin(), aligns.end(), EdgeletIdRLoRCmp_t()); in PrintDiff()
272 aligns[i]->stpc = aligns[i]->isRLIS ? j++ : -1; in PrintDiff()
274 sort(aligns.begin(), aligns.end(), EdgeletLoQCmp_t()); in PrintDiff()
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/dports/audio/mpz/mpz-1.0.19/app/playlist_ui/
H A Dcolumnsconfig.cpp23 aligns.append(Qt::AlignVCenter); in ColumnsConfig()
24 aligns.append(Qt::AlignVCenter); in ColumnsConfig()
25 aligns.append(Qt::AlignVCenter); in ColumnsConfig()
26 aligns.append(Qt::AlignVCenter | Qt::AlignRight); in ColumnsConfig()
27 aligns.append(Qt::AlignVCenter | Qt::AlignRight); in ColumnsConfig()
36 QVector<Qt::Alignment> aligns; in deserialize() local
51 result.setAligns(aligns); in deserialize()
70 …if (widths.size() == stretches.size() && stretches.size() == aligns.size() && aligns.size() == fie… in vaidate()
93 return aligns.at(col - 1); in align()
150 aligns.clear(); in setAligns()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/align/util/
H A Dalign_sort.cpp60 CLocalAlignSource(const TList& aligns) in CLocalAlignSource() argument
61 : m_Aligns(aligns) in CLocalAlignSource()
320 TAlignments aligns; in SortAlignments() local
340 aligns.push_back(val); in SortAlignments()
358 std::sort(aligns.begin(), aligns.end(), m_Predicate); in SortAlignments()
377 aligns.clear(); in SortAlignments()
387 if (aligns.size()) { in SortAlignments()
388 std::sort(aligns.begin(), aligns.end(), m_Predicate); in SortAlignments()
407 aligns.clear(); in SortAlignments()
419 std::sort(aligns.begin(), aligns.end(), m_Predicate); in SortAlignments()
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H A Dnamed_collection_score_impl.cpp293 vector<CSeq_align const*> aligns; in MakeSubjectScores() local
295 aligns.reserve(coll.Get().size()); in MakeSubjectScores()
298 aligns.push_back(i->GetNonNullPointer()); in MakeSubjectScores()
301 std::sort(aligns.begin(), aligns.end(), Compare); in MakeSubjectScores()
303 for ( vector<CSeq_align const*>::const_iterator i = aligns.begin(); i != aligns.end(); ) { in MakeSubjectScores()
310 for ( ; j != aligns.end(); ++j ) { in MakeSubjectScores()
333 vector<CSeq_align const*> aligns; in MakeSubjectScores() local
335 aligns.reserve(coll.Get().size()); in MakeSubjectScores()
341 std::sort(aligns.begin(), aligns.end(), Compare); in MakeSubjectScores()
343 for ( vector<CSeq_align const*>::const_iterator i = aligns.begin(); i != aligns.end(); ) { in MakeSubjectScores()
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/dports/textproc/lookatme/lookatme-2.3.2/tests/
H A Dtest_table.py27 aligns = ["left", "center", "right"]
33 table = lookatme.widgets.table.Table(rows, headers=headers, aligns=aligns)
115 aligns = ["left", "center", "right"]
121 table = lookatme.widgets.table.Table(rows, headers=headers, aligns=aligns)
141 aligns = ["left", "center", "right"]
148 table = lookatme.widgets.table.Table(rows, headers=headers, aligns=aligns)
/dports/graphics/p5-Graph-Easy/Graph-Easy-0.76/t/
H A Dfb.t136 my ($lines,$aligns) = $node->_aligned_label();
140 is_deeply ( $aligns, [ 'c', 'r', 'l', 'c', 'c', ], 'aligns is ok');
145 ($lines,$aligns) = $node->_aligned_label();
149 is_deeply ( $aligns, [ 'c', 'r', 'l', 'c', 'c', ], 'aligns is ok');
154 ($lines,$aligns) = $node->_aligned_label();
158 is_deeply ( $aligns, [ 'c', 'r', 'r', 'l', 'c', 'c', ], 'aligns is ok');
163 ($lines,$aligns) = $node->_aligned_label();
167 is_deeply ( $aligns, [ 'c','r','l','r', 'r', 'l', 'c', 'c', ], 'aligns is ok');
/dports/sysutils/bacula11-docs/bacula-docs-11.0.5/latex2html/styles/
H A Dmore_amsmath.perl504 local($aligns);
505 $aligns = &missing_braces unless (
517 local($aligns);
518 $aligns = &missing_braces unless (
530 local($aligns);
531 $aligns = &missing_braces unless (
543 local($aligns);
544 $aligns = &missing_braces unless (
556 local($aligns);
557 $aligns = &missing_braces unless (
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/dports/sysutils/bacula11-docs/bacula-docs-11.0.5/latex2html-2016/styles/
H A Dmore_amsmath.perl504 local($aligns);
505 $aligns = &missing_braces unless (
517 local($aligns);
518 $aligns = &missing_braces unless (
530 local($aligns);
531 $aligns = &missing_braces unless (
543 local($aligns);
544 $aligns = &missing_braces unless (
556 local($aligns);
557 $aligns = &missing_braces unless (
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/dports/textproc/latex2html/latex2html-2016/styles/
H A Dmore_amsmath.perl504 local($aligns);
505 $aligns = &missing_braces unless (
517 local($aligns);
518 $aligns = &missing_braces unless (
530 local($aligns);
531 $aligns = &missing_braces unless (
543 local($aligns);
544 $aligns = &missing_braces unless (
556 local($aligns);
557 $aligns = &missing_braces unless (
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/dports/net-im/matterhorn/matterhorn-50200.13.0/_cabal_deps/commonmark-extensions-0.2.0.4/src/Commonmark/Extensions/
H A DPipeTable.hs48 pipeTable aligns headerCells rows =
53 toRow "th" aligns headerCells) <>
57 mconcat (map (toRow "td" aligns) rows))
75 pipeTable aligns headerCells rows = do
108 let aligns = pipedAligns ++ unpipedAlign function
109 guard $ not (null aligns)
112 return $! aligns
188 try (do aligns <- pDividers
189 guard $ length aligns ==
204 let aligns = pipeTableAlignments tabledata function
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/dports/textproc/hs-pandoc-crossref/pandoc-crossref-0.3.12.0/_cabal_deps/commonmark-extensions-0.2.0.4/src/Commonmark/Extensions/
H A DPipeTable.hs48 pipeTable aligns headerCells rows =
53 toRow "th" aligns headerCells) <>
57 mconcat (map (toRow "td" aligns) rows))
75 pipeTable aligns headerCells rows = do
108 let aligns = pipedAligns ++ unpipedAlign function
109 guard $ not (null aligns)
112 return $! aligns
188 try (do aligns <- pDividers
189 guard $ length aligns ==
204 let aligns = pipeTableAlignments tabledata function
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/dports/textproc/hs-pandoc/pandoc-2.14.2/_cabal_deps/commonmark-extensions-0.2.1.2/src/Commonmark/Extensions/
H A DPipeTable.hs48 pipeTable aligns headerCells rows =
53 toRow "th" aligns headerCells) <>
57 mconcat (map (toRow "td" aligns) rows))
75 pipeTable aligns headerCells rows = do
108 let aligns = pipedAligns ++ unpipedAlign function
109 guard $ not (null aligns)
112 return $! aligns
188 try (do aligns <- pDividers
189 guard $ length aligns ==
204 let aligns = pipeTableAlignments tabledata function
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/dports/biology/gffread/gffread-0.12.7/examples/
H A Dannotation.gff3 …Genbank:NM_004668.2,HGNC:HGNC:7043,MIM:154360;Note=The RefSeq transcript aligns at 64%25 coverage …
4 …Genbank:NM_004668.2,HGNC:HGNC:7043,MIM:154360;Note=The RefSeq transcript aligns at 64%25 coverage …
5 …Genbank:NM_004668.2,HGNC:HGNC:7043,MIM:154360;Note=The RefSeq transcript aligns at 64%25 coverage …
6 …Genbank:NM_004668.2,HGNC:HGNC:7043,MIM:154360;Note=The RefSeq transcript aligns at 64%25 coverage …
7 …Genbank:NM_004668.2,HGNC:HGNC:7043,MIM:154360;Note=The RefSeq transcript aligns at 64%25 coverage …
8 …Genbank:NM_004668.2,HGNC:HGNC:7043,MIM:154360;Note=The RefSeq transcript aligns at 64%25 coverage …
9 …Genbank:NM_004668.2,HGNC:HGNC:7043,MIM:154360;Note=The RefSeq transcript aligns at 64%25 coverage …
10 …Genbank:NM_004668.2,HGNC:HGNC:7043,MIM:154360;Note=The RefSeq transcript aligns at 64%25 coverage …
11 …Genbank:NM_004668.2,HGNC:HGNC:7043,MIM:154360;Note=The RefSeq transcript aligns at 64%25 coverage …
12 …Genbank:NM_004668.2,HGNC:HGNC:7043,MIM:154360;Note=The RefSeq transcript aligns at 64%25 coverage …
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/dports/biology/abyss/abyss-2.3.1/KAligner/
H A DAligner.cpp90 AlignmentSet& aligns, const Sequence& seq, in alignKmer() argument
118 aligns[ctgIndex].push_back(align); in alignKmer()
128 AlignmentSet aligns; in getAlignmentsInternal() local
135 return aligns; in getAlignmentsInternal()
138 alignKmer(aligns, seq, isRC, good, 0, seqLen); in getAlignmentsInternal()
141 return aligns; in getAlignmentsInternal()
144 alignKmer(aligns, seq, isRC, good, last_kmer, seqLen); in getAlignmentsInternal()
149 AlignmentSet::const_iterator ctgIter = aligns.begin(); in getAlignmentsInternal()
162 return aligns; in getAlignmentsInternal()
168 alignKmer(aligns, seq, isRC, good, i, seqLen); in getAlignmentsInternal()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/align/util/unit_test/
H A Dcollection_scores_unit_test.cpp108 CRef<CSeq_align_set> aligns(new CSeq_align_set); in BOOST_AUTO_TEST_CASE() local
126 aligns->Set() = coll; in BOOST_AUTO_TEST_CASE()
129 BOOST_CHECK( 120 == aligns->Get().size()); in BOOST_AUTO_TEST_CASE()
134 vector<CScoreValue> qcovs = score->Get("seq_percent_coverage", *aligns); in BOOST_AUTO_TEST_CASE()
146 vector<CScoreValue> qcovus = score->Get("uniq_seq_percent_coverage", *aligns); in BOOST_AUTO_TEST_CASE()
159 vector<CScoreValue> all = score->Get("subjects-sequence-coverage-group", score_names, *aligns); in BOOST_AUTO_TEST_CASE()
180 score->Set("subjects-sequence-coverage-group", score_names, *aligns); in BOOST_AUTO_TEST_CASE()
182 …for (list<CRef<CSeq_align> >::const_iterator i = aligns->Get().begin(); i != aligns->Get().end(); … in BOOST_AUTO_TEST_CASE()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/structure/cd_utils/
H A DcuSeqtree.cpp496 aligns.GetRowsWithSeqID(seqId, rowsForOne); in selectByGI()
533 int num = aligns.GetNumRows(); in fixRowName()
539 CCdCore* cd = aligns.GetScopedLeafCD(cursor->rowID); in fixRowName()
545 …sprintf(loc, "[%d~%d]", aligns.GetLowerBound(cursor->rowID), aligns.GetUpperBound(cursor->rowID)); in fixRowName()
546 aligns.Get_GI_or_PDB_String_FromAlignment(cursor->rowID, gi); in fixRowName()
548 aligns.GetSpeciesForRow(cursor->rowID, species); in fixRowName()
584 void SeqTree::fixRowNumber(AlignmentCollection& aligns) in fixRowNumber() argument
603 void SeqTree::addSelectionFields(AlignmentCollection& aligns) in addSelectionFields() argument
621 void SeqTree::updateSeqCounts(const AlignmentCollection& aligns) in updateSeqCounts() argument
643 getSequenceComposition(aligns, cdComposition); in isSequenceCompositionSame()
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/dports/biology/abyss/abyss-2.3.1/GapFiller/
H A Dgapfill.cpp71 unsigned long long aligns; member
120 if (++stats.aligns % 10000000 == 0 && opt::verbose) in readAlignments()
122 << "out of " << stats.aligns << ".\n"; in readAlignments()
132 aligns.insert(make_pair(rec.rname, rec)); in readAlignments()
206 const Alignments& aligns) in alignReadsToGapFlanks() argument
210 tie(start, end) = aligns.equal_range(cid); in alignReadsToGapFlanks()
280 alignReadsToGapFlanks(sit->second, aligns); in fillGaps()
340 Alignments aligns; in main() local
341 readAlignments(argv[argc-1], aligns, scaffs); in main()
343 cerr << "aligns: " << stats.aligns << "\tsplit: " in main()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/structure/cd_utils/
H A DcuSeqtree.hpp122 void selectByGI(const AlignmentCollection& aligns,const vector< CRef <CSeq_id> >& gis);
138 void fixRowName(AlignmentCollection& aligns, SeqNameMode mode);
139 void fixRowNumber(AlignmentCollection& aligns);
140 void addSelectionFields(AlignmentCollection& aligns);
141 void updateSeqCounts(const AlignmentCollection& aligns);
142 bool isSequenceCompositionSame(AlignmentCollection& aligns);
145 void getSequenceComposition(AlignmentCollection& aligns,
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/alnmgr/unit_test/
H A Dunit_test_alnmgr.cpp105 CAlnContainer& aligns, in LoadAligns() argument
114 aligns.insert(*align); in LoadAligns()
134 ITERATE(CAlnContainer, aln_it, aligns) { in InitAlnStats()
442 CAlnContainer aligns; in BOOST_AUTO_TEST_CASE() local
490 CAlnContainer aligns; in BOOST_AUTO_TEST_CASE() local
579 CAlnContainer aligns; in BOOST_AUTO_TEST_CASE() local
695 CAlnContainer aligns; in BOOST_AUTO_TEST_CASE() local
749 CAlnContainer aligns; in BOOST_AUTO_TEST_CASE() local
825 CAlnContainer aligns; in BOOST_AUTO_TEST_CASE() local
896 CAlnContainer aligns; in BOOST_AUTO_TEST_CASE() local
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/dports/textproc/py-markdown-it-py/markdown-it-py-2.0.0/markdown_it/rules_block/
H A Dtable.py104 aligns = []
119 aligns.append("center" if charCodeAt(t, 0) == 0x3A else "right")
121 aligns.append("left")
123 aligns.append("")
139 if columnCount == 0 or columnCount != len(aligns):
163 if aligns[i]:
164 token.attrs = {"style": "text-align:" + aligns[i]}
211 if aligns[i]:
212 token.attrs = {"style": "text-align:" + aligns[i]}
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/api/
H A Dblast_results.cpp487 TSeqAlignVector aligns, in CSearchResultSet() argument
496 ancillary_data.resize(aligns.size()); in CSearchResultSet()
501 CSearchResultSet::CSearchResultSet(TSeqAlignVector aligns, in CSearchResultSet() argument
509 for(size_t i = 0; i < aligns.size(); i++) { in CSearchResultSet()
510 queries.push_back(s_ExtractSeqId(aligns[i])); in CSearchResultSet()
565 _ASSERT(queries.size() == aligns.size()); in x_Init()
566 _ASSERT(aligns.size() == msg_vec.size()); in x_Init()
567 _ASSERT(aligns.size() == ancillary_data.size()); in x_Init()
592 m_Results.resize(aligns.size()); in x_Init()
594 for(size_t i = 0; i < aligns.size(); i++) { in x_Init()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/api/
H A Dblast_results.cpp487 TSeqAlignVector aligns, in CSearchResultSet() argument
496 ancillary_data.resize(aligns.size()); in CSearchResultSet()
501 CSearchResultSet::CSearchResultSet(TSeqAlignVector aligns, in CSearchResultSet() argument
509 for(size_t i = 0; i < aligns.size(); i++) { in CSearchResultSet()
510 queries.push_back(s_ExtractSeqId(aligns[i])); in CSearchResultSet()
565 _ASSERT(queries.size() == aligns.size()); in x_Init()
566 _ASSERT(aligns.size() == msg_vec.size()); in x_Init()
567 _ASSERT(aligns.size() == ancillary_data.size()); in x_Init()
592 m_Results.resize(aligns.size()); in x_Init()
594 for(size_t i = 0; i < aligns.size(); i++) { in x_Init()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/
H A Dannot.cpp100 for(TGeneModelList::iterator it = aligns.begin(); it != aligns.end(); it++) { in TryWithoutObviouslyBadAlignments()
108 for(TGeneModelList::iterator it = aligns.begin(); it != aligns.end(); ) { in TryWithoutObviouslyBadAlignments()
122 it = aligns.erase(it); in TryWithoutObviouslyBadAlignments()
189 TGeneModelList aligns(il, ir); in Predict() local
204 RemoveShortHolesAndRescore(aligns); in Predict()
210 ITERATE(TGeneModelList, it_c, aligns) { in Predict()
346 aligns.push_back(*wall_model); in SaveWallModel()
349 aligns.push_back(nested->second); in SaveWallModel()
402 aligns.splice(aligns.end(), models, ir); in FindPartials()
661 TGeneModelList aligns; in Predict() local
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/sequence/
H A Dalign_group.hpp74 void GroupByTaxIds(const TAlignList& aligns,
83 void GroupByLikeTaxIds(const TAlignList& aligns,
107 void GroupBySequenceType(const TAlignList& aligns,
120 void GroupBySeqIds(const TAlignList& aligns,
127 void GroupByStrand(const TAlignList& aligns,

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