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NCBI C++ ToolKit
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This is the complete list of members for CSeq_loc_Mapper_Base, including all inherited members.
| AddReference(void) const | CObject | inline |
| CanBeDeleted(void) const THROWS_NONE | CObject | inline |
| CDebugDumpable(void) | CDebugDumpable | inline |
| CheckReferenceOverflow(TCount count) const | CObject | private |
| CObject(void) | CObject | |
| CObject(const CObject &src) | CObject | |
| CollectSynonyms(const CSeq_id_Handle &id) const | CSeq_loc_Mapper_Base | |
| CollectSynonyms(const CSeq_id_Handle &id, TSynonyms &synonyms) const | CSeq_loc_Mapper_Base | |
| CSeq_align_Mapper_Base class | CSeq_loc_Mapper_Base | friend |
| CSeq_loc_Mapper_Base(CMappingRanges *mapping_ranges, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options()) | CSeq_loc_Mapper_Base | |
| CSeq_loc_Mapper_Base(const CSeq_feat &map_feat, EFeatMapDirection dir, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options()) | CSeq_loc_Mapper_Base | |
| CSeq_loc_Mapper_Base(const CSeq_loc &source, const CSeq_loc &target, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options()) | CSeq_loc_Mapper_Base | |
| CSeq_loc_Mapper_Base(const CSeq_align &map_align, const CSeq_id &to_id, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options()) | CSeq_loc_Mapper_Base | |
| CSeq_loc_Mapper_Base(const CSeq_id &from_id, const CSeq_id &to_id, const CSeq_align &map_align, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options()) | CSeq_loc_Mapper_Base | |
| CSeq_loc_Mapper_Base(const CSeq_align &map_align, const CSeq_id &to_id, TMapOptions opts, IMapper_Sequence_Info *seq_info) | CSeq_loc_Mapper_Base | |
| CSeq_loc_Mapper_Base(const CSeq_align &map_align, size_t to_row, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options()) | CSeq_loc_Mapper_Base | |
| CSeq_loc_Mapper_Base(size_t from_row, size_t to_row, const CSeq_align &map_align, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options()) | CSeq_loc_Mapper_Base | |
| CSeq_loc_Mapper_Base(const CSeq_align &map_align, size_t to_row, TMapOptions opts, IMapper_Sequence_Info *seq_info) | CSeq_loc_Mapper_Base | |
| CSeq_loc_Mapper_Base(const CSeq_loc_Mapper_Base &) | CSeq_loc_Mapper_Base | private |
| CSeq_loc_Mapper_Base(CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options()) | CSeq_loc_Mapper_Base | |
| CTotalRangeSynonymMapper class | CSeq_loc_Mapper_Base | friend |
| DebugDump(CDebugDumpContext ddc, unsigned int depth) const | CObject | virtual |
| DebugDumpFormat(CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const | CDebugDumpable | |
| DebugDumpText(ostream &out, const string &bundle, unsigned int depth) const | CDebugDumpable | |
| DeleteThis(void) | CObject | protectedvirtual |
| DoDeleteThisObject(void) | CObject | virtual |
| DoNotDeleteThisObject(void) | CObject | virtual |
| DumpToConsole(void) const | CDebugDumpable | |
| EAllocFillMode enum name | CObject | |
| eAllocFillNone enum value | CObject | |
| eAllocFillPattern enum value | CObject | |
| eAllocFillZero enum value | CObject | |
| eCounterBitsCanBeDeleted | CObject | static |
| eCounterBitsInPlainHeap | CObject | static |
| eCounterBitsPlaceMask | CObject | static |
| eCounterStateMask | CObject | static |
| eCounterStep | CObject | static |
| eCounterValid | CObject | static |
| EFeatMapDirection enum name | CSeq_loc_Mapper_Base | |
| EGapFlags enum name | CSeq_loc_Mapper_Base | private |
| eGapPreserve enum value | CSeq_loc_Mapper_Base | private |
| eGapRemove enum value | CSeq_loc_Mapper_Base | private |
| eLocationToProduct enum value | CSeq_loc_Mapper_Base | |
| EMapOptions enum name | CSeq_loc_Mapper_Base | |
| eMapped_All enum value | CSeq_loc_Mapper_Base | |
| eMapped_None enum value | CSeq_loc_Mapper_Base | |
| eMapped_Some enum value | CSeq_loc_Mapper_Base | |
| EMapResult enum name | CSeq_loc_Mapper_Base | |
| eMergeAbutting enum value | CSeq_loc_Mapper_Base | private |
| eMergeAll enum value | CSeq_loc_Mapper_Base | private |
| eMergeBySeg enum value | CSeq_loc_Mapper_Base | private |
| eMergeContained enum value | CSeq_loc_Mapper_Base | private |
| EMergeFlags enum name | CSeq_loc_Mapper_Base | private |
| eMergeNone enum value | CSeq_loc_Mapper_Base | private |
| EMiscFlags enum name | CSeq_loc_Mapper_Base | private |
| EnableDebugDump(bool on) | CDebugDumpable | static |
| eProductToLocation enum value | CSeq_loc_Mapper_Base | |
| eSeq_nuc enum value | CSeq_loc_Mapper_Base | |
| eSeq_prot enum value | CSeq_loc_Mapper_Base | |
| eSeq_unknown enum value | CSeq_loc_Mapper_Base | |
| ESeqType enum name | CSeq_loc_Mapper_Base | |
| ESplicedRow enum name | CSeq_loc_Mapper_Base | |
| eSplicedRow_Gen enum value | CSeq_loc_Mapper_Base | |
| eSplicedRow_Prod enum value | CSeq_loc_Mapper_Base | |
| fAlign_Dense_seg_TotalRange enum value | CSeq_loc_Mapper_Base | |
| fAlign_Sparse_ToFirst enum value | CSeq_loc_Mapper_Base | |
| fAlign_Sparse_ToSecond enum value | CSeq_loc_Mapper_Base | |
| fAnnotMap_Both enum value | CSeq_loc_Mapper_Base | |
| fAnnotMap_Default enum value | CSeq_loc_Mapper_Base | |
| fAnnotMap_Location enum value | CSeq_loc_Mapper_Base | |
| fAnnotMap_Product enum value | CSeq_loc_Mapper_Base | |
| fAnnotMap_RemoveNonMapping enum value | CSeq_loc_Mapper_Base | |
| fAnnotMap_ThrowOnFailure enum value | CSeq_loc_Mapper_Base | |
| FAnnotMapFlag enum name | CSeq_loc_Mapper_Base | |
| fCheckStrand enum value | CSeq_loc_Mapper_Base | private |
| fErrorOnPartial enum value | CSeq_loc_Mapper_Base | private |
| FFuzzOption enum name | CSeq_loc_Mapper_Base | |
| fFuzzOption_CStyle enum value | CSeq_loc_Mapper_Base | |
| fFuzzOption_RemoveLimTlOrTr enum value | CSeq_loc_Mapper_Base | |
| fIncludeSrcLocs enum value | CSeq_loc_Mapper_Base | private |
| fKeepNonmapping enum value | CSeq_loc_Mapper_Base | private |
| fMapSingleLevel enum value | CSeq_loc_Mapper_Base | |
| fMixedAlignsAsSpliced enum value | CSeq_loc_Mapper_Base | private |
| fTrimMappedLocation enum value | CSeq_loc_Mapper_Base | |
| fTrimSplicedSegs enum value | CSeq_loc_Mapper_Base | private |
| GetAllocFillMode(void) | CObject | static |
| GetMappingRanges(void) const | CSeq_loc_Mapper_Base | inline |
| GetNonMappingAsNull(void) | CSeq_loc_Mapper_Base | static |
| GetSeqType(const CSeq_id_Handle &idh) const | CSeq_loc_Mapper_Base | protected |
| GetSeqTypeById(const CSeq_id_Handle &idh) const | CSeq_loc_Mapper_Base | inline |
| GetSeqTypeById(const CSeq_id &id) const | CSeq_loc_Mapper_Base | inline |
| GetSequenceLength(const CSeq_id &id) | CSeq_loc_Mapper_Base | protected |
| GetWidthById(const CSeq_id_Handle &idh) const | CSeq_loc_Mapper_Base | inline |
| GetWidthById(const CSeq_id &id) const | CSeq_loc_Mapper_Base | inline |
| IncludeSourceLocs(bool value=true) | CSeq_loc_Mapper_Base | inline |
| InitAlignMapper(const CSeq_align &src_align) | CSeq_loc_Mapper_Base | protectedvirtual |
| InitCounter(void) | CObject | inlineprivate |
| InvalidObject(void) const | CObject | private |
| IsAllocatedInPool(void) const THROWS_NONE | CObject | inline |
| KeepNonmappingRanges(void) | CSeq_loc_Mapper_Base | inline |
| LastIsPartial(void) | CSeq_loc_Mapper_Base | inline |
| m_Counter | CObject | mutableprivate |
| m_CurrentGroup | CSeq_loc_Mapper_Base | protected |
| m_Dst_loc | CSeq_loc_Mapper_Base | protected |
| m_DstRanges | CSeq_loc_Mapper_Base | protected |
| m_FuzzOption | CSeq_loc_Mapper_Base | protected |
| m_GapFlag | CSeq_loc_Mapper_Base | private |
| m_GraphRanges | CSeq_loc_Mapper_Base | private |
| m_LastTruncated | CSeq_loc_Mapper_Base | protected |
| m_LengthMap | CSeq_loc_Mapper_Base | mutableprivate |
| m_MapOptions | CSeq_loc_Mapper_Base | protected |
| m_MappedLocs | CSeq_loc_Mapper_Base | mutableprivate |
| m_Mappings | CSeq_loc_Mapper_Base | protected |
| m_MergeFlag | CSeq_loc_Mapper_Base | private |
| m_MiscFlags | CSeq_loc_Mapper_Base | private |
| m_Partial | CSeq_loc_Mapper_Base | protected |
| m_SeqTypes | CSeq_loc_Mapper_Base | mutableprotected |
| m_SrcLocs | CSeq_loc_Mapper_Base | private |
| m_SynonymMap | CSeq_loc_Mapper_Base | mutableprivate |
| Map(const CSeq_loc &src_loc) | CSeq_loc_Mapper_Base | |
| Map(const CSeq_align &src_align) | CSeq_loc_Mapper_Base | inline |
| Map(const CSeq_align &src_align, size_t row) | CSeq_loc_Mapper_Base | inline |
| Map(const CSeq_graph &src_graph) | CSeq_loc_Mapper_Base | |
| Map(CSeq_annot &annot, TAnnotMapFlags flags=fAnnotMap_Default) | CSeq_loc_Mapper_Base | |
| MapTotalRange(const CSeq_loc &seq_loc) | CSeq_loc_Mapper_Base | |
| MixedAlignsAsSpliced(bool value=true) | CSeq_loc_Mapper_Base | inline |
| ObjectStateCanBeDeleted(TCount count) | CObject | inlineprivatestatic |
| ObjectStateIsAllocatedInPool(TCount count) | CObject | inlineprivatestatic |
| ObjectStateReferenced(TCount count) | CObject | inlineprivatestatic |
| ObjectStateReferencedOnlyOnce(TCount count) | CObject | inlineprivatestatic |
| ObjectStateUnreferenced(TCount count) | CObject | inlineprivatestatic |
| ObjectStateValid(TCount count) | CObject | inlineprivatestatic |
| operator delete(void *ptr) | CObject | |
| operator delete(void *ptr, void *place) | CObject | |
| operator delete(void *ptr, CObjectMemoryPool *place) | CObject | |
| operator delete[](void *ptr) | CObject | |
| operator new(size_t size) | CObject | |
| operator new(size_t size, void *place) | CObject | |
| operator new(size_t size, CObjectMemoryPool *place) | CObject | |
| operator new[](size_t size) | CObject | |
| operator=(const CSeq_loc_Mapper_Base &) | CSeq_loc_Mapper_Base | private |
| CObject::operator=(const CObject &src) THROWS_NONE | CObject | inline |
| Referenced(void) const THROWS_NONE | CObject | inline |
| ReferencedOnlyOnce(void) const THROWS_NONE | CObject | inline |
| ReleaseReference(void) const | CObject | |
| RemoveLastReference(TCount count) const | CObject | private |
| RemoveReference(void) const | CObject | inline |
| SetAllocFillMode(EAllocFillMode mode) | CObject | static |
| SetAllocFillMode(const string &value) | CObject | static |
| SetCheckStrand(bool value=true) | CSeq_loc_Mapper_Base | inline |
| SetErrorOnPartial(bool value=true) | CSeq_loc_Mapper_Base | inline |
| SetFuzzOption(TFuzzOption newOption) | CSeq_loc_Mapper_Base | |
| SetGapPreserve(void) | CSeq_loc_Mapper_Base | inline |
| SetGapRemove(void) | CSeq_loc_Mapper_Base | inline |
| SetMergeAbutting(void) | CSeq_loc_Mapper_Base | inline |
| SetMergeAll(void) | CSeq_loc_Mapper_Base | inline |
| SetMergeBySeg(void) | CSeq_loc_Mapper_Base | inline |
| SetMergeContained(void) | CSeq_loc_Mapper_Base | inline |
| SetMergeNone(void) | CSeq_loc_Mapper_Base | inline |
| SetSeqTypeById(const CSeq_id_Handle &idh, ESeqType seqtype) const | CSeq_loc_Mapper_Base | |
| SetSeqTypeById(const CSeq_id &id, ESeqType seqtype) const | CSeq_loc_Mapper_Base | inline |
| SetTrimSplicedSeg(bool trim) | CSeq_loc_Mapper_Base | inline |
| sm_DumpEnabled | CDebugDumpable | privatestatic |
| sx_GetExonPartLength(const CSpliced_exon_chunk &part) | CSeq_loc_Mapper_Base | privatestatic |
| TAnnotMapFlags typedef | CSeq_loc_Mapper_Base | |
| TCount typedef | CObject | |
| TCounter typedef | CObject | |
| TDendiag typedef | CSeq_loc_Mapper_Base | protected |
| TDstIdMap typedef | CSeq_loc_Mapper_Base | protected |
| TDstRanges typedef | CSeq_loc_Mapper_Base | protected |
| TDstStrandMap typedef | CSeq_loc_Mapper_Base | protected |
| TFuzz typedef | CSeq_loc_Mapper_Base | protected |
| TFuzzOption typedef | CSeq_loc_Mapper_Base | |
| ThrowNullPointerException(void) | CObject | static |
| ThrowNullPointerException(const type_info &type) | CObject | static |
| TLengthMap typedef | CSeq_loc_Mapper_Base | private |
| TLockerType typedef | CObject | |
| TMapOptions typedef | CSeq_loc_Mapper_Base | |
| TMappedRanges typedef | CSeq_loc_Mapper_Base | protected |
| TMiscFlags typedef | CSeq_loc_Mapper_Base | private |
| TRange typedef | CSeq_loc_Mapper_Base | protected |
| TRangeFuzz typedef | CSeq_loc_Mapper_Base | protected |
| TRangeIterator typedef | CSeq_loc_Mapper_Base | protected |
| TRangeMap typedef | CSeq_loc_Mapper_Base | protected |
| TRangesById typedef | CSeq_loc_Mapper_Base | protected |
| TRangesByStrand typedef | CSeq_loc_Mapper_Base | protected |
| TruncateNonmappingRanges(void) | CSeq_loc_Mapper_Base | inline |
| TSeqTypeById typedef | CSeq_loc_Mapper_Base | protected |
| TSortedMappings typedef | CSeq_loc_Mapper_Base | protected |
| TStd typedef | CSeq_loc_Mapper_Base | protected |
| TSynonymMap typedef | CSeq_loc_Mapper_Base | private |
| TSynonyms typedef | CSeq_loc_Mapper_Base | |
| x_AddConversion(const CSeq_id &src_id, TSeqPos src_start, ENa_strand src_strand, const CSeq_id &dst_id, TSeqPos dst_start, ENa_strand dst_strand, TSeqPos length, bool ext_right, int frame, TSeqPos src_bioseq_len, TSeqPos dst_length) | CSeq_loc_Mapper_Base | protected |
| x_AddExonPartsMapping(TSeqPos &mapping_len, ESplicedRow to_row, const CSeq_id &gen_id, TSeqPos &gen_start, TSeqPos &gen_len, ENa_strand gen_strand, const CSeq_id &prod_id, TSeqPos &prod_start, TSeqPos &prod_len, ENa_strand prod_strand) | CSeq_loc_Mapper_Base | private |
| x_AdjustSeqTypesToProt(const CSeq_id_Handle &idh) | CSeq_loc_Mapper_Base | private |
| x_CheckSeqTypes(const CSeq_loc &loc, ESeqType &seqtype, TSeqPos &len) | CSeq_loc_Mapper_Base | private |
| x_FixNonsenseFuzz(CConstRef< CSeq_loc > loc_piece) const | CSeq_loc_Mapper_Base | private |
| x_ForceSeqTypes(const CSeq_loc &loc) const | CSeq_loc_Mapper_Base | private |
| x_GetMappedRanges(const CSeq_id_Handle &id, size_t strand_idx) const | CSeq_loc_Mapper_Base | private |
| x_GetMappedSeq_loc(void) | CSeq_loc_Mapper_Base | private |
| x_GetPrimaryId(const CSeq_id_Handle &synonym) const | CSeq_loc_Mapper_Base | private |
| x_GetRangeLength(const CSeq_loc_CI &it) | CSeq_loc_Mapper_Base | private |
| x_InitAlign(const CDense_diag &diag, size_t to_row, size_t from_row) | CSeq_loc_Mapper_Base | private |
| x_InitAlign(const CDense_seg &denseg, size_t to_row, size_t from_row) | CSeq_loc_Mapper_Base | private |
| x_InitAlign(const CStd_seg &sseg, size_t to_row) | CSeq_loc_Mapper_Base | private |
| x_InitAlign(const CPacked_seg &pseg, size_t to_row, size_t from_row) | CSeq_loc_Mapper_Base | private |
| x_InitializeAlign(const CSeq_align &map_align, const CSeq_id &to_id, const CSeq_id *from_id=nullptr) | CSeq_loc_Mapper_Base | protected |
| x_InitializeAlign(const CSeq_align &map_align, const TSynonyms &to_ids, const TSynonyms *from_ids=nullptr) | CSeq_loc_Mapper_Base | protected |
| x_InitializeAlign(const CSeq_align &map_align, size_t to_row, size_t from_row=size_t(-1)) | CSeq_loc_Mapper_Base | protected |
| x_InitializeFeat(const CSeq_feat &map_feat, EFeatMapDirection dir) | CSeq_loc_Mapper_Base | protected |
| x_InitializeLocs(const CSeq_loc &source, const CSeq_loc &target, int src_frame=0, int dst_frame=0) | CSeq_loc_Mapper_Base | protected |
| x_InitSparse(const CSparse_seg &sparse, size_t to_row) | CSeq_loc_Mapper_Base | private |
| x_InitSpliced(const CSpliced_seg &spliced, const TSynonyms &to_ids) | CSeq_loc_Mapper_Base | private |
| x_InitSpliced(const CSpliced_seg &spliced, ESplicedRow to_row) | CSeq_loc_Mapper_Base | private |
| x_IsSetMiscFlag(EMiscFlags flag) const | CSeq_loc_Mapper_Base | inlineprivate |
| x_IsSynonym(const CSeq_id &id, const TSynonyms &synonyms) const | CSeq_loc_Mapper_Base | private |
| x_IterateExonParts(const CSpliced_exon::TParts &parts, ESplicedRow to_row, const CSeq_id &gen_id, TSeqPos &gen_start, TSeqPos &gen_len, ENa_strand gen_strand, const CSeq_id &prod_id, TSeqPos &prod_start, TSeqPos &prod_len, ENa_strand prod_strand) | CSeq_loc_Mapper_Base | private |
| x_Map_PackedInt_Element(const CSeq_interval &si) | CSeq_loc_Mapper_Base | private |
| x_Map_PackedPnt_Element(const CPacked_seqpnt &pp, TSeqPos p) | CSeq_loc_Mapper_Base | private |
| x_MapInterval(const CSeq_id &src_id, TRange src_rg, bool is_set_strand, ENa_strand src_strand, TRangeFuzz orig_fuzz) | CSeq_loc_Mapper_Base | private |
| x_MapNextRange(const TRange &src_rg, bool is_set_strand, ENa_strand src_strand, const TRangeFuzz &src_fuzz, TSortedMappings &mappings, size_t cvt_idx, TSeqPos *last_src_to) | CSeq_loc_Mapper_Base | private |
| x_MapSeq_align(const CSeq_align &src_align, size_t *row) | CSeq_loc_Mapper_Base | private |
| x_MapSeq_loc(const CSeq_loc &src_loc) | CSeq_loc_Mapper_Base | protected |
| x_NextMappingRange(const CSeq_id &src_id, TSeqPos &src_start, TSeqPos &src_len, ENa_strand src_strand, const CSeq_id &dst_id, TSeqPos &dst_start, TSeqPos &dst_len, ENa_strand dst_strand, const CInt_fuzz *fuzz_from=0, const CInt_fuzz *fuzz_to=0, int frame=0, TSeqPos src_bioseq_len=kInvalidSeqPos) | CSeq_loc_Mapper_Base | protected |
| x_OptimizeSeq_loc(CRef< CSeq_loc > &loc) const | CSeq_loc_Mapper_Base | private |
| x_PreserveDestinationLocs(void) | CSeq_loc_Mapper_Base | protected |
| x_PushLocToDstMix(CRef< CSeq_loc > loc) | CSeq_loc_Mapper_Base | private |
| x_PushMappedRange(const CSeq_id_Handle &id, size_t strand_idx, const TRange &range, const TRangeFuzz &fuzz, bool push_reverse, int group) | CSeq_loc_Mapper_Base | private |
| x_PushNullLoc(void) | CSeq_loc_Mapper_Base | private |
| x_PushRangesToDstMix(void) | CSeq_loc_Mapper_Base | protected |
| x_PushSourceRange(const CSeq_id_Handle &idh, size_t src_strand, size_t dst_strand, const TRange &range, bool push_reverse) | CSeq_loc_Mapper_Base | private |
| x_RangeToSeq_loc(const CSeq_id_Handle &idh, TSeqPos from, TSeqPos to, size_t strand_idx, TRangeFuzz rg_fuzz) | CSeq_loc_Mapper_Base | private |
| x_ReverseRangeOrder(int str) const | CSeq_loc_Mapper_Base | private |
| x_SetLastTruncated(void) | CSeq_loc_Mapper_Base | private |
| x_SetMiscFlag(EMiscFlags flag, bool value) | CSeq_loc_Mapper_Base | private |
| x_StripExtraneousFuzz(CRef< CSeq_loc > &loc) const | CSeq_loc_Mapper_Base | private |
| ~CDebugDumpable(void) | CDebugDumpable | virtual |
| ~CObject(void) | CObject | virtual |
| ~CSeq_loc_Mapper_Base(void) | CSeq_loc_Mapper_Base |
1.9.0
Modified on Tue May 21 10:55:29 2024 by modify_doxy.py rev. 669887