| /dports/biology/abyss/abyss-2.3.1/GapFiller/ |
| H A D | gapfill.cpp | 71 unsigned long long aligns; member
104 static void readAlignments(const char* path, Alignments& aligns, in readAlignments()
206 const Alignments& aligns) in alignReadsToGapFlanks()
275 static void fillGaps(Scaffolds& scaffs, const Alignments& aligns) in fillGaps()
340 Alignments aligns; in main() local
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/structure/cd_utils/ |
| H A D | cuSeqtree.cpp | 488 void SeqTree::selectByGI(const AlignmentCollection& aligns, const vector<CRef<CSeq_id> >& gis) in selectByGI()
531 void SeqTree::fixRowName(AlignmentCollection& aligns, SeqNameMode mode) in fixRowName()
584 void SeqTree::fixRowNumber(AlignmentCollection& aligns) in fixRowNumber()
603 void SeqTree::addSelectionFields(AlignmentCollection& aligns) in addSelectionFields()
621 void SeqTree::updateSeqCounts(const AlignmentCollection& aligns) in updateSeqCounts()
639 bool SeqTree::isSequenceCompositionSame(AlignmentCollection& aligns) in isSequenceCompositionSame()
677 void SeqTree::getSequenceComposition(AlignmentCollection& aligns, in getSequenceComposition()
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| /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()
128 CRef<TScopeAlnStats> InitAlnStats(const CAlnContainer& 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
971 CAlnContainer aligns; in BOOST_AUTO_TEST_CASE() local
|
| /dports/devel/pear-ezc_ConsoleTools/ConsoleTools-1.6.1/docs/ |
| H A D | tutorial_example_11_progressmonitor.php | 16 $output->outputLine();
|
| /dports/audio/mpz/mpz-1.0.19/app/playlist_ui/ |
| H A D | columnsconfig.h | 39 QVector<Qt::Alignment> aligns; variable
|
| /dports/biology/mummer/mummer-4.0.0beta2-2-g277dac5/examples/ |
| H A D | align.py | 17 aligns = mummer.align_sequences(ref, qry, o) variable
|
| /dports/textproc/hs-pandoc-crossref/pandoc-crossref-0.3.12.0/_cabal_deps/pandoc-2.11.4/src/Text/Pandoc/Readers/ |
| H A D | CSV.hs | 45 aligns = replicate numcols AlignDefault function
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/readers/ |
| H A D | psl_reader.cpp | 72 auto& aligns = annot.SetData().SetAlign(); in xProcessData() local
|
| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/readers/ |
| H A D | psl_reader.cpp | 72 auto& aligns = annot.SetData().SetAlign(); in xProcessData() local
|
| /dports/biology/mummer/mummer-4.0.0beta2-2-g277dac5/examples/align_cpp/ |
| H A D | align.cpp | 19 auto aligns = mummer::nucmer::align_sequences(ref.c_str(), ref.size(), in main() local
|
| /dports/games/vultures-eye/vulture-2.3.67/slashem/win/gl/ |
| H A D | gl_text.c | 41 static int find_aligns(unsigned short *aligns, char *line) in find_aligns()
91 static int choose_best_align(unsigned short *aligns, int cut_off) in choose_best_align()
219 unsigned short aligns[MAX_ALGN]; in do_scan_text() local
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/ |
| H A D | annot.cpp | 92 double CGnomonAnnotator::TryWithoutObviouslyBadAlignments(TGeneModelList& aligns, TGeneModelList& s… in TryWithoutObviouslyBadAlignments()
189 TGeneModelList aligns(il, ir); in Predict() local
343 …SaveWallModel(auto_ptr<CGeneModel>& wall_model, TNestedGenes& nested_genes, TGeneModelList& aligns) in SaveWallModel()
354 void FindPartials(TGeneModelList& models, TGeneModelList& aligns, EStrand strand) in FindPartials()
661 TGeneModelList aligns; in Predict() local
|
| /dports/textproc/hs-pandoc/pandoc-2.14.2/src/Text/Pandoc/Readers/ |
| H A D | CSV.hs | 45 aligns = replicate numcols AlignDefault function
|
| /dports/biology/abyss/abyss-2.3.1/KAligner/ |
| H A D | Aligner.cpp | 90 AlignmentSet& aligns, const Sequence& seq, in alignKmer()
128 AlignmentSet aligns; in getAlignmentsInternal() local
|
| /dports/biology/py-bx-python/bx-python-0.8.13/lib/bx/align/ |
| H A D | score_tests.py | 16 aligns = [("CCACTAGTTTTTAAATAATCTACTATCAAATAAAAGATTTGTTAATAATAAATTTTAAATCATTAACACTT", variable
|
| /dports/biology/sim4/sim4.2003-09-21/ |
| H A D | sim4.init.c | 474 edit_script_list *head, *aligns; in print_align_blk() local
522 edit_script_list *head, *aligns; in print_align_lat() local
700 static void add_offset_aligns(edit_script_list *aligns, int offset) in add_offset_aligns()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/api/ |
| H A D | magicblast.cpp | 409 TSeqAlignVector aligns; in x_BuildSeqAlignSet() local
465 CRef<CSeq_align_set> aligns(x_CreateSeqAlignSet(chains, query_data, in x_BuildResultSet() local
520 CRef<CSeq_align_set> aligns, in CMagicBlastResults()
535 CRef<CSeq_align_set> aligns, in CMagicBlastResults()
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| H A D | blast_results.cpp | 487 TSeqAlignVector aligns, in CSearchResultSet()
501 CSearchResultSet::CSearchResultSet(TSeqAlignVector aligns, in CSearchResultSet()
559 TSeqAlignVector aligns, in x_Init()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/api/ |
| H A D | magicblast.cpp | 409 TSeqAlignVector aligns; in x_BuildSeqAlignSet() local
465 CRef<CSeq_align_set> aligns(x_CreateSeqAlignSet(chains, query_data, in x_BuildResultSet() local
520 CRef<CSeq_align_set> aligns, in CMagicBlastResults()
535 CRef<CSeq_align_set> aligns, in CMagicBlastResults()
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| H A D | blast_results.cpp | 487 TSeqAlignVector aligns, in CSearchResultSet()
501 CSearchResultSet::CSearchResultSet(TSeqAlignVector aligns, in CSearchResultSet()
559 TSeqAlignVector aligns, in x_Init()
|
| /dports/multimedia/pipewire/pipewire-0.3.43/test/ |
| H A D | test-spa-buffer.c | 87 uint32_t aligns[2]; in PWTEST() local
|
| /dports/textproc/hs-pandoc/pandoc-2.14.2/test/Tests/Writers/ |
| H A D | ConTeXt.hs | 106 aligns = [ (AlignRight, ColWidthDefault) function
|
| /dports/textproc/hs-pandoc-crossref/pandoc-crossref-0.3.12.0/_cabal_deps/pandoc-2.11.4/test/Tests/Writers/ |
| H A D | ConTeXt.hs | 102 …aligns = [(AlignRight, ColWidthDefault), (AlignLeft, ColWidthDefault), (AlignCenter, ColWidthDefau… function
|
| /dports/www/tikiwiki/tiki-21.2/lib/wiki-plugins/ |
| H A D | wikiplugin_fancytable.php | 363 function process_section($data, $type, $line_sep, $cellbeg, $cellend, $widths, $aligns, $valigns)
|
| /dports/net-im/matterhorn/matterhorn-50200.13.0/_cabal_deps/commonmark-extensions-0.2.0.4/src/Commonmark/Extensions/ |
| H A D | PipeTable.hs | 108 let aligns = pipedAligns ++ unpipedAlign function
204 let aligns = pipeTableAlignments tabledata function
|