/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/phy_tree/unit_test/ |
H A D | phytree_calc_unit_test.cpp | 115 CSeq_align seq_align; in BOOST_AUTO_TEST_CASE() local 176 CSeq_align seq_align; in BOOST_AUTO_TEST_CASE() local 225 CSeq_align seq_align; in BOOST_AUTO_TEST_CASE() local 259 CSeq_align seq_align; in BOOST_AUTO_TEST_CASE() local 297 CSeq_align seq_align; in BOOST_AUTO_TEST_CASE() local 313 CSeq_align seq_align; in BOOST_AUTO_TEST_CASE() local 329 CSeq_align seq_align; in BOOST_AUTO_TEST_CASE() local 346 CSeq_align seq_align; in BOOST_AUTO_TEST_CASE() local 363 CSeq_align seq_align; in BOOST_AUTO_TEST_CASE() local 486 CSeq_align seq_align; in BOOST_AUTO_TEST_CASE() local [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/alnmgr/ |
H A D | aln_container.cpp | 54 CAlnContainer::const_iterator CAlnContainer::insert(const CSeq_align& seq_align) in insert()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/alnmgr/ |
H A D | aln_container.cpp | 54 CAlnContainer::const_iterator CAlnContainer::insert(const CSeq_align& seq_align) in insert()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/blastfmt/ |
H A D | guide_tree_app.cpp | 212 CSeq_align seq_align; in Run() local
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H A D | blast_hitmatrix.cpp | 94 CRef< CSeq_align > seq_align = *iter; in CBlastHitMatrix() local
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/phy_tree/phytree_format/unit_test/ |
H A D | phytree_format_unit_test.cpp | 76 CSeq_align seq_align; in BOOST_AUTO_TEST_CASE() local 92 CSeq_align seq_align; in BOOST_AUTO_TEST_CASE() local 139 CSeq_align seq_align; in BOOST_AUTO_TEST_CASE() local
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/hfilter/ |
H A D | hitfilter_app.cpp | 296 CRef<CSeq_align> seq_align (*ii); in x_ReadInputHits() local 446 CRef<CSeq_align> seq_align (new CSeq_align()); in x_DumpOutput() local 693 CRef<CSeq_align> seq_align = *ii; in x_LoadConstraints() local
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/ |
H A D | asn1.cpp | 754 CRef< CSeq_align > seq_align( new CSeq_align ); in AlignModelToSeqalign() local 949 …CRef<CSeq_align> seq_align = AlignModelToSeqalign(model, *mrna_sid, *contig_sid, is_align, is_alig… in MakeSeqAlign() local 989 …CRef<CSeq_align> seq_align = AlignModelToSeqalign(model, *md.mrna_sid, *contig_sid, false, false, … in model2spliced_seq_align() local 1173 bool IsGnomonConstructed(const CSeq_align& seq_align) in IsGnomonConstructed() 1199 CSeq_align& seq_align = **align_ci; in ExtractSupportModels() local
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H A D | gnomon_objmgr.cpp | 65 Int8 GetModelId(const CSeq_align& seq_align) in GetModelId() 75 CAlignModel::CAlignModel(const CSeq_align& seq_align) : in CAlignModel()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/api/ |
H A D | remote_search.cpp | 187 CRef<CSeq_align_set> seq_align = *itr; in s_SplitAlignVectorBySubjects() local
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/api/ |
H A D | remote_search.cpp | 187 CRef<CSeq_align_set> seq_align = *itr; in s_SplitAlignVectorBySubjects() local
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/alnmgr/ |
H A D | seqids_extractor.hpp | 112 void operator()(const CSeq_align& seq_align, in operator ()()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objtools/alnmgr/ |
H A D | seqids_extractor.hpp | 112 void operator()(const CSeq_align& seq_align, in operator ()()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/cobalt/ |
H A D | seq.cpp | 276 void CSequence::CreateMsa(const objects::CSeq_align& seq_align, in CreateMsa()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/align/prosplign/ |
H A D | prosplign.cpp | 1206 CRef<CSeq_align> seq_align = cpa.MakeSeq_align(*m_protseq, *m_cnseq); in FindGlobalAlignment_stage2() local 1216 CRef<objects::CSeq_align> CProSplign::RefineAlignment(CScope& scope, const CSeq_align& seq_align, C… in RefineAlignment() 1313 void CProSplign::CImplementation::SeekStartStop(CSeq_align& seq_align) in SeekStartStop()
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H A D | Info.cpp | 711 TAliChunkCollection ExtractChunks(CScope& scope, CSeq_align& seq_align) in ExtractChunks() 935 void prosplign::SetScores(objects::CSeq_align& seq_align, objects::CScope& scope, const string& mat… in SetScores() 988 void prosplign::RefineAlignment(CScope& scope, CSeq_align& seq_align, const list<CNPiece>& good_par… in RefineAlignment()
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H A D | compartments.cpp | 159 CRef<CSeq_align> seq_align(new CSeq_align); in MakeCompartment() local
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/align/util/ |
H A D | align_shadow.cpp | 53 TStrands RetrieveStdStrands(const objects::CSeq_align& seq_align) in RetrieveStdStrands() 65 CAlignShadow::CAlignShadow(const objects::CSeq_align& seq_align, bool save_xcript) in CAlignShadow()
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H A D | blast_tabular.cpp | 51 CBlastTabular::CBlastTabular(const CSeq_align& seq_align, bool save_xcript): in CBlastTabular()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/phy_tree/ |
H A D | phytree_calc.cpp | 610 CRef<CSeq_align> seq_align = *iter; in x_InitAlignDS() local
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/unit_tests/api/ |
H A D | pssmcreate_cdd_unit_test.cpp | 882 CRef<CSeq_align> seq_align(new CSeq_align()); in BOOST_AUTO_TEST_CASE() local 1074 CRef<CSeq_align> seq_align(new CSeq_align()); in BOOST_AUTO_TEST_SUITE_END() local
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/unit_tests/api/ |
H A D | pssmcreate_cdd_unit_test.cpp | 882 CRef<CSeq_align> seq_align(new CSeq_align()); in BOOST_AUTO_TEST_CASE() local 1074 CRef<CSeq_align> seq_align(new CSeq_align()); in BOOST_AUTO_TEST_SUITE_END() local
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/readers/ |
H A D | aln_reader.cpp | 738 CRef<CSeq_align> seq_align = GetSeqAlign(fasta_flags, pErrorListener); in GetSeqEntry() local
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/readers/ |
H A D | aln_reader.cpp | 738 CRef<CSeq_align> seq_align = GetSeqAlign(fasta_flags, pErrorListener); in GetSeqEntry() local
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