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/dports/biology/seqan1/seqan-1.3.1/seqan/refinement/
H A Dgraph_algorithm_refine_exact.h94 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
H A Dgraph_algorithm_refine_align.h49 TMap & seq_map, in _getOtherSequenceAndProject()
87 std::map<const void * ,int> & seq_map, in _getSeqBeginAndEnd()
H A Dgraph_algorithm_refine_exact_iterative.h94 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
H A Dgraph_algorithm_refine_inexact.h151 TSeqMap & seq_map, in _makeRefinedGraphEdges()
/dports/biology/seqan/seqan-library-2.4.0/include/seqan/graph_align/
H A Dgraph_algorithm_refine_exact.h92 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
H A Dgraph_algorithm_refine_align.h49 TMap & seq_map, in _getOtherSequenceAndProject()
93 std::map<const void * ,int> & seq_map, in _getSeqBeginAndEnd()
H A Dgraph_algorithm_refine_exact_iterative.h96 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
H A Dgraph_algorithm_refine_inexact.h157 TSeqMap & seq_map, in _makeRefinedGraphEdges()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/graph_align/
H A Dgraph_algorithm_refine_exact.h92 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
H A Dgraph_algorithm_refine_align.h49 TMap & seq_map, in _getOtherSequenceAndProject()
93 std::map<const void * ,int> & seq_map, in _getSeqBeginAndEnd()
H A Dgraph_algorithm_refine_exact_iterative.h96 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
H A Dgraph_algorithm_refine_inexact.h157 TSeqMap & seq_map, in _makeRefinedGraphEdges()
/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/graph_align/
H A Dgraph_algorithm_refine_exact.h93 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
H A Dgraph_algorithm_refine_exact_iterative.h97 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
H A Dgraph_algorithm_refine_align.h49 TMap & seq_map, in _getOtherSequenceAndProject()
95 std::map<const void * ,int> & seq_map, in _getSeqBeginAndEnd()
H A Dgraph_algorithm_refine_inexact.h161 TSeqMap & seq_map, in _makeRefinedGraphEdges()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/writers/
H A Dagp_write.cpp135 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()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objmgr/
H A Dseq_loc_mapper.cpp279 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()
H A Dtse_assigner.cpp153 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
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objmgr/
H A Dseq_loc_mapper.cpp279 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()
H A Dtse_assigner.cpp153 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
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objmgr/test/
H A Dtest_helper.cpp881 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
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/
H A Dgnomon_engine.cpp200 const CAlignMap& seq_map = m_data->m_ss->FrameShiftedSeqMap(); in PartialModelStepBack() local
H A Dparse.cpp550 const CAlignMap& seq_map = m_seqscr.FrameShiftedSeqMap(); in GetGenes() local
711 const CAlignMap& seq_map = m_seqscr.FrameShiftedSeqMap(); in PrintInfo() local
/dports/security/snort3/snort3-3.1.19.0/tools/snort2lua/rule_states/
H A Drule_unchanged.cc239 const ConvertMap* seq_map = &rule_seq; variable

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