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Searched defs:seq_align (Results 1 – 24 of 24) sorted by relevance

/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/phy_tree/unit_test/
H A Dphytree_calc_unit_test.cpp115 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
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/alnmgr/
H A Daln_container.cpp54 CAlnContainer::const_iterator CAlnContainer::insert(const CSeq_align& seq_align) in insert()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/alnmgr/
H A Daln_container.cpp54 CAlnContainer::const_iterator CAlnContainer::insert(const CSeq_align& seq_align) in insert()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/blastfmt/
H A Dguide_tree_app.cpp212 CSeq_align seq_align; in Run() local
H A Dblast_hitmatrix.cpp94 CRef< CSeq_align > seq_align = *iter; in CBlastHitMatrix() local
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/phy_tree/phytree_format/unit_test/
H A Dphytree_format_unit_test.cpp76 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
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/hfilter/
H A Dhitfilter_app.cpp296 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
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/
H A Dasn1.cpp754 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
H A Dgnomon_objmgr.cpp65 Int8 GetModelId(const CSeq_align& seq_align) in GetModelId()
75 CAlignModel::CAlignModel(const CSeq_align& seq_align) : in CAlignModel()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/api/
H A Dremote_search.cpp187 CRef<CSeq_align_set> seq_align = *itr; in s_SplitAlignVectorBySubjects() local
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/api/
H A Dremote_search.cpp187 CRef<CSeq_align_set> seq_align = *itr; in s_SplitAlignVectorBySubjects() local
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/alnmgr/
H A Dseqids_extractor.hpp112 void operator()(const CSeq_align& seq_align, in operator ()()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objtools/alnmgr/
H A Dseqids_extractor.hpp112 void operator()(const CSeq_align& seq_align, in operator ()()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/cobalt/
H A Dseq.cpp276 void CSequence::CreateMsa(const objects::CSeq_align& seq_align, in CreateMsa()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/align/prosplign/
H A Dprosplign.cpp1206 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()
H A DInfo.cpp711 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()
H A Dcompartments.cpp159 CRef<CSeq_align> seq_align(new CSeq_align); in MakeCompartment() local
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/align/util/
H A Dalign_shadow.cpp53 TStrands RetrieveStdStrands(const objects::CSeq_align& seq_align) in RetrieveStdStrands()
65 CAlignShadow::CAlignShadow(const objects::CSeq_align& seq_align, bool save_xcript) in CAlignShadow()
H A Dblast_tabular.cpp51 CBlastTabular::CBlastTabular(const CSeq_align& seq_align, bool save_xcript): in CBlastTabular()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/phy_tree/
H A Dphytree_calc.cpp610 CRef<CSeq_align> seq_align = *iter; in x_InitAlignDS() local
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/unit_tests/api/
H A Dpssmcreate_cdd_unit_test.cpp882 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
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/unit_tests/api/
H A Dpssmcreate_cdd_unit_test.cpp882 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
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/readers/
H A Daln_reader.cpp738 CRef<CSeq_align> seq_align = GetSeqAlign(fasta_flags, pErrorListener); in GetSeqEntry() local
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/readers/
H A Daln_reader.cpp738 CRef<CSeq_align> seq_align = GetSeqAlign(fasta_flags, pErrorListener); in GetSeqEntry() local