/dports/biology/py-biopython/biopython-1.79/Tests/ |
H A D | pairwise2_testCases.py | 101 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() [all …]
|
/dports/biology/mummer/mummer-4.0.0beta2-2-g277dac5/src/tigr/ |
H A D | show-diff.cc | 158 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() [all …]
|
/dports/audio/mpz/mpz-1.0.19/app/playlist_ui/ |
H A D | columnsconfig.cpp | 23 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() [all …]
|
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/align/util/ |
H A D | align_sort.cpp | 60 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() [all …]
|
H A D | named_collection_score_impl.cpp | 293 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() [all …]
|
/dports/textproc/lookatme/lookatme-2.3.2/tests/ |
H A D | test_table.py | 27 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 D | fb.t | 136 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 ( $aligns, [ 'c','r','l','r', 'r', 'l', 'c', 'c', ], 'aligns is ok');
|
/dports/sysutils/bacula11-docs/bacula-docs-11.0.5/latex2html/styles/ |
H A D | more_amsmath.perl | 504 local($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 $aligns = &missing_braces unless ( [all …]
|
/dports/sysutils/bacula11-docs/bacula-docs-11.0.5/latex2html-2016/styles/ |
H A D | more_amsmath.perl | 504 local($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 $aligns = &missing_braces unless ( [all …]
|
/dports/textproc/latex2html/latex2html-2016/styles/ |
H A D | more_amsmath.perl | 504 local($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 ( [all …]
|
/dports/net-im/matterhorn/matterhorn-50200.13.0/_cabal_deps/commonmark-extensions-0.2.0.4/src/Commonmark/Extensions/ |
H A D | PipeTable.hs | 48 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 [all …]
|
/dports/textproc/hs-pandoc-crossref/pandoc-crossref-0.3.12.0/_cabal_deps/commonmark-extensions-0.2.0.4/src/Commonmark/Extensions/ |
H A D | PipeTable.hs | 48 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 [all …]
|
/dports/textproc/hs-pandoc/pandoc-2.14.2/_cabal_deps/commonmark-extensions-0.2.1.2/src/Commonmark/Extensions/ |
H A D | PipeTable.hs | 48 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 [all …]
|
/dports/biology/gffread/gffread-0.12.7/examples/ |
H A D | annotation.gff | 3 …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 … [all …]
|
/dports/biology/abyss/abyss-2.3.1/KAligner/ |
H A D | Aligner.cpp | 90 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() [all …]
|
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/align/util/unit_test/ |
H A D | collection_scores_unit_test.cpp | 108 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 D | cuSeqtree.cpp | 496 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() [all …]
|
/dports/biology/abyss/abyss-2.3.1/GapFiller/ |
H A D | gapfill.cpp | 71 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() [all …]
|
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/structure/cd_utils/ |
H A D | cuSeqtree.hpp | 122 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 D | unit_test_alnmgr.cpp | 105 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 [all …]
|
/dports/textproc/py-markdown-it-py/markdown-it-py-2.0.0/markdown_it/rules_block/ |
H A D | table.py | 104 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 D | blast_results.cpp | 487 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() [all …]
|
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/api/ |
H A D | blast_results.cpp | 487 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() [all …]
|
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/ |
H A D | annot.cpp | 100 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 [all …]
|
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/sequence/ |
H A D | align_group.hpp | 74 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,
|