/dports/biology/seqan1/seqan-1.3.1/seqan/refinement/ |
H A D | graph_algorithm_refine_exact.h | 94 TSeqMap & seq_map, in _refine() 152 TSeqMap & seq_map) in _buildIntervalsForAllSequences() 192 TSeqMap & seq_map, in _createTreesForAllSequences() 284 TSeqMap & seq_map, in _makeRefinedGraphEdges() 361 TSeqMap & seq_map, in _makeAlignmentGraphFromRefinedSegments() 393 TSeqMap & seq_map, in _makeAlignmentGraphFromRefinedSegments() 460 std::map<const void * ,int> seq_map; in matchRefinement() local
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H A D | graph_algorithm_refine_align.h | 49 TMap & seq_map, in _getOtherSequenceAndProject() 87 std::map<const void * ,int> & seq_map, in _getSeqBeginAndEnd()
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H A D | graph_algorithm_refine_exact_iterative.h | 94 TSeqMap & seq_map, in _refine() 167 TSeqMap & seq_map) in _buildIntervalsForAllSequences() 208 TSeqMap & seq_map, in _createTreesForAllSequences() 300 TSeqMap & seq_map, in _makeRefinedGraphEdges() 377 TSeqMap & seq_map, in _makeAlignmentGraphFromRefinedSegments() 409 TSeqMap & seq_map, in _makeAlignmentGraphFromRefinedSegments() 480 std::map<const void * ,int> seq_map; in matchRefinement() local
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H A D | graph_algorithm_refine_inexact.h | 151 TSeqMap & seq_map, in _makeRefinedGraphEdges()
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/graph_align/ |
H A D | graph_algorithm_refine_exact.h | 92 TSeqMap & seq_map, in _refine() 149 TSeqMap & seq_map) in _buildIntervalsForAllSequences() 188 TSeqMap & seq_map, in _createTreesForAllSequences() 278 TSeqMap & seq_map, in _makeRefinedGraphEdges() 354 TSeqMap & seq_map, in _makeAlignmentGraphFromRefinedSegments() 385 TSeqMap & seq_map, in _makeAlignmentGraphFromRefinedSegments() 450 std::map<const void * ,int> seq_map; in matchRefinement() local
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H A D | graph_algorithm_refine_align.h | 49 TMap & seq_map, in _getOtherSequenceAndProject() 93 std::map<const void * ,int> & seq_map, in _getSeqBeginAndEnd()
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H A D | graph_algorithm_refine_exact_iterative.h | 96 TSeqMap & seq_map, in _refine() 170 TSeqMap & seq_map) in _buildIntervalsForAllSequences() 210 TSeqMap & seq_map, in _createTreesForAllSequences() 302 TSeqMap & seq_map, in _makeRefinedGraphEdges() 407 TSeqMap & seq_map, in _makeAlignmentGraphFromRefinedSegments() 438 TSeqMap & seq_map, in _makeAlignmentGraphFromRefinedSegments() 508 std::map<const void * ,int> seq_map; in matchRefinement() local
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H A D | graph_algorithm_refine_inexact.h | 157 TSeqMap & seq_map, in _makeRefinedGraphEdges()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/graph_align/ |
H A D | graph_algorithm_refine_exact.h | 92 TSeqMap & seq_map, in _refine() 149 TSeqMap & seq_map) in _buildIntervalsForAllSequences() 188 TSeqMap & seq_map, in _createTreesForAllSequences() 278 TSeqMap & seq_map, in _makeRefinedGraphEdges() 354 TSeqMap & seq_map, in _makeAlignmentGraphFromRefinedSegments() 385 TSeqMap & seq_map, in _makeAlignmentGraphFromRefinedSegments() 450 std::map<const void * ,int> seq_map; in matchRefinement() local
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H A D | graph_algorithm_refine_align.h | 49 TMap & seq_map, in _getOtherSequenceAndProject() 93 std::map<const void * ,int> & seq_map, in _getSeqBeginAndEnd()
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H A D | graph_algorithm_refine_exact_iterative.h | 96 TSeqMap & seq_map, in _refine() 170 TSeqMap & seq_map) in _buildIntervalsForAllSequences() 210 TSeqMap & seq_map, in _createTreesForAllSequences() 302 TSeqMap & seq_map, in _makeRefinedGraphEdges() 407 TSeqMap & seq_map, in _makeAlignmentGraphFromRefinedSegments() 438 TSeqMap & seq_map, in _makeAlignmentGraphFromRefinedSegments() 508 std::map<const void * ,int> seq_map; in matchRefinement() local
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H A D | graph_algorithm_refine_inexact.h | 157 TSeqMap & seq_map, in _makeRefinedGraphEdges()
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/graph_align/ |
H A D | graph_algorithm_refine_exact.h | 93 TSeqMap & seq_map, in _refine() 151 TSeqMap & seq_map) in _buildIntervalsForAllSequences() 191 TSeqMap & seq_map, in _createTreesForAllSequences() 283 TSeqMap & seq_map, in _makeRefinedGraphEdges() 360 TSeqMap & seq_map, in _makeAlignmentGraphFromRefinedSegments() 392 TSeqMap & seq_map, in _makeAlignmentGraphFromRefinedSegments() 459 std::map<const void * ,int> seq_map; in matchRefinement() local
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H A D | graph_algorithm_refine_exact_iterative.h | 97 TSeqMap & seq_map, in _refine() 172 TSeqMap & seq_map) in _buildIntervalsForAllSequences() 213 TSeqMap & seq_map, in _createTreesForAllSequences() 306 TSeqMap & seq_map, in _makeRefinedGraphEdges() 412 TSeqMap & seq_map, in _makeAlignmentGraphFromRefinedSegments() 444 TSeqMap & seq_map, in _makeAlignmentGraphFromRefinedSegments() 513 std::map<const void * ,int> seq_map; in matchRefinement() local
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H A D | graph_algorithm_refine_align.h | 49 TMap & seq_map, in _getOtherSequenceAndProject() 95 std::map<const void * ,int> & seq_map, in _getSeqBeginAndEnd()
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H A D | graph_algorithm_refine_inexact.h | 161 TSeqMap & seq_map, in _makeRefinedGraphEdges()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/writers/ |
H A D | agp_write.cpp | 135 const CSeqMap& seq_map, in s_AgpWrite() 273 CConstRef<CSeqMap> seq_map; in s_SeqMapForHandle() local 307 const CSeqMap& seq_map, in AgpWrite() 347 const CSeqMap& seq_map, in AgpWrite()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objmgr/ |
H A D | seq_loc_mapper.cpp | 279 CSeq_loc_Mapper::CSeq_loc_Mapper(const CSeqMap& seq_map, in CSeq_loc_Mapper() 321 CSeq_loc_Mapper::CSeq_loc_Mapper(const CSeqMap& seq_map, in CSeq_loc_Mapper() 452 void CSeq_loc_Mapper::x_InitializeSeqMap(const CSeqMap& seq_map, in x_InitializeSeqMap() 460 void CSeq_loc_Mapper::x_InitializeSeqMap(const CSeqMap& seq_map, in x_InitializeSeqMap() 472 void CSeq_loc_Mapper::x_InitializeSeqMap(const CSeqMap& seq_map, in x_InitializeSeqMap()
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H A D | tse_assigner.cpp | 153 CSeqMap& seq_map = const_cast<CSeqMap&>(bioseq->GetSeqMap()); in AddSeq_data() local 257 CSeqMap& seq_map = const_cast<CSeqMap&>(x_GetBioseq(tse, place).GetSeqMap());; in LoadSequence() local
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objmgr/ |
H A D | seq_loc_mapper.cpp | 279 CSeq_loc_Mapper::CSeq_loc_Mapper(const CSeqMap& seq_map, in CSeq_loc_Mapper() 321 CSeq_loc_Mapper::CSeq_loc_Mapper(const CSeqMap& seq_map, in CSeq_loc_Mapper() 452 void CSeq_loc_Mapper::x_InitializeSeqMap(const CSeqMap& seq_map, in x_InitializeSeqMap() 460 void CSeq_loc_Mapper::x_InitializeSeqMap(const CSeqMap& seq_map, in x_InitializeSeqMap() 472 void CSeq_loc_Mapper::x_InitializeSeqMap(const CSeqMap& seq_map, in x_InitializeSeqMap()
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H A D | tse_assigner.cpp | 153 CSeqMap& seq_map = const_cast<CSeqMap&>(bioseq->GetSeqMap()); in AddSeq_data() local 257 CSeqMap& seq_map = const_cast<CSeqMap&>(x_GetBioseq(tse, place).GetSeqMap());; in LoadSequence() local
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objmgr/test/ |
H A D | test_helper.cpp | 881 CConstRef<CSeqMap> seq_map(&handle.GetSeqMap()); in ProcessBioseq() local 929 CConstRef<CSeqMap> seq_map(&handle.GetSeqMap()); in ProcessBioseq() local 975 CConstRef<CSeqMap> seq_map(&handle.GetSeqMap()); in ProcessBioseq() local 1023 CConstRef<CSeqMap> seq_map(&handle.GetSeqMap()); in ProcessBioseq() local
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/ |
H A D | gnomon_engine.cpp | 200 const CAlignMap& seq_map = m_data->m_ss->FrameShiftedSeqMap(); in PartialModelStepBack() local
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H A D | parse.cpp | 550 const CAlignMap& seq_map = m_seqscr.FrameShiftedSeqMap(); in GetGenes() local 711 const CAlignMap& seq_map = m_seqscr.FrameShiftedSeqMap(); in PrintInfo() local
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/dports/security/snort3/snort3-3.1.19.0/tools/snort2lua/rule_states/ |
H A D | rule_unchanged.cc | 239 const ConvertMap* seq_map = &rule_seq; variable
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