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NCBI C++ ToolKit
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This is the complete list of members for CSeq_align_Mapper, 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 | |
| Convert(CSeq_loc_Conversion_Set &cvts) | CSeq_align_Mapper | private |
| CSeq_align_Mapper_Base::Convert(void) | CSeq_align_Mapper_Base | |
| CSeq_align_Mapper_Base::Convert(size_t row) | CSeq_align_Mapper_Base | |
| CreateSubAlign(const CSeq_align &align) | CSeq_align_Mapper | protectedvirtual |
| CreateSubAlign(const CSpliced_seg &spliced, const CSpliced_exon &exon) | CSeq_align_Mapper | protectedvirtual |
| CSeq_align_Mapper(const CSeq_align &align, CSeq_loc_Mapper_Base &loc_mapper) | CSeq_align_Mapper | |
| CSeq_align_Mapper(CSeq_loc_Mapper_Base &loc_mapper) | CSeq_align_Mapper | private |
| CSeq_align_Mapper_Base(const CSeq_align &align, CSeq_loc_Mapper_Base &loc_mapper) | CSeq_align_Mapper_Base | |
| CSeq_align_Mapper_Base(CSeq_loc_Mapper_Base &loc_mapper) | CSeq_align_Mapper_Base | protected |
| CSeq_loc_Conversion_Set class | CSeq_align_Mapper | 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 | |
| eAlign_Empty enum value | CSeq_align_Mapper_Base | protected |
| eAlign_MultiDim enum value | CSeq_align_Mapper_Base | protected |
| eAlign_MultiId enum value | CSeq_align_Mapper_Base | protected |
| eAlign_Normal enum value | CSeq_align_Mapper_Base | protected |
| EAlignFlags enum name | CSeq_align_Mapper_Base | protected |
| 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 |
| EnableDebugDump(bool on) | CDebugDumpable | static |
| GetAllocFillMode(void) | CObject | static |
| GetDim(void) const | CSeq_align_Mapper_Base | inline |
| GetDstAlign(void) const | CSeq_align_Mapper_Base | |
| GetLocMapper(void) const | CSeq_align_Mapper_Base | inlineprotected |
| GetMaxDim(void) const | CSeq_align_Mapper_Base | inlineprotected |
| GetRowId(size_t idx) const | CSeq_align_Mapper_Base | |
| GetSegments() const | CSeq_align_Mapper_Base | inline |
| InitCounter(void) | CObject | inlineprivate |
| InitExon(const CSpliced_seg &spliced, const CSpliced_exon &exon) | CSeq_align_Mapper_Base | protected |
| InvalidObject(void) const | CObject | private |
| IsAllocatedInPool(void) const THROWS_NONE | CObject | inline |
| m_AlignFlags | CSeq_align_Mapper_Base | protected |
| m_AlignScores | CSeq_align_Mapper_Base | private |
| m_Counter | CObject | mutableprivate |
| m_Dim | CSeq_align_Mapper_Base | private |
| m_DstAlign | CSeq_align_Mapper_Base | mutableprotected |
| m_GroupScores | CSeq_align_Mapper_Base | private |
| m_HaveStrands | CSeq_align_Mapper_Base | private |
| m_LocMapper | CSeq_align_Mapper_Base | private |
| m_OrigAlign | CSeq_align_Mapper_Base | private |
| m_OrigExon | CSeq_align_Mapper_Base | private |
| m_ScoresInvalidated | CSeq_align_Mapper_Base | private |
| m_Segs | CSeq_align_Mapper_Base | mutableprotected |
| m_SegsScores | CSeq_align_Mapper_Base | private |
| m_SubAligns | CSeq_align_Mapper_Base | protected |
| 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 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 |
| sm_DumpEnabled | CDebugDumpable | privatestatic |
| TConvByIndex typedef | CSeq_align_Mapper | private |
| TCount typedef | CObject | |
| TCounter typedef | CObject | |
| TDendiag typedef | CSeq_align_Mapper_Base | |
| ThrowNullPointerException(void) | CObject | static |
| ThrowNullPointerException(const type_info &type) | CObject | static |
| TIdMap typedef | CSeq_align_Mapper | private |
| TLockerType typedef | CObject | |
| TRange typedef | CSeq_align_Mapper | private |
| TRangeMap typedef | CSeq_align_Mapper | private |
| TScores typedef | CSeq_align_Mapper_Base | private |
| TScoresGroups typedef | CSeq_align_Mapper_Base | private |
| TSegments typedef | CSeq_align_Mapper_Base | |
| TStd typedef | CSeq_align_Mapper_Base | |
| TStrands typedef | CSeq_align_Mapper_Base | private |
| TSubAligns typedef | CSeq_align_Mapper_Base | protected |
| x_ConvertAlign(size_t *row) | CSeq_align_Mapper_Base | private |
| x_ConvertAlignCvt(CSeq_loc_Conversion_Set &cvts) | CSeq_align_Mapper | private |
| x_ConvertRow(size_t row) | CSeq_align_Mapper_Base | private |
| x_ConvertRowCvt(CSeq_loc_Conversion &cvt, size_t row) | CSeq_align_Mapper | private |
| x_ConvertRowCvt(TIdMap &cvts, size_t row) | CSeq_align_Mapper | private |
| x_ConvertSegment(TSegments::iterator &seg_it, size_t row) | CSeq_align_Mapper_Base | private |
| x_ConvertSegmentCvt(TSegments::iterator &seg_it, CSeq_loc_Conversion &cvt, size_t row) | CSeq_align_Mapper | private |
| x_ConvertSegmentCvt(TSegments::iterator &seg_it, TIdMap &id_map, size_t row) | CSeq_align_Mapper | private |
| x_ConvToDstDisc(CRef< CSeq_align > &dst) const | CSeq_align_Mapper_Base | private |
| x_FillKnownStrands(TStrands &strands) const | CSeq_align_Mapper_Base | private |
| x_GetDstDendiag(CRef< CSeq_align > &dst) const | CSeq_align_Mapper_Base | private |
| x_GetDstDenseg(CRef< CSeq_align > &dst) const | CSeq_align_Mapper_Base | private |
| x_GetDstDisc(CRef< CSeq_align > &dst) const | CSeq_align_Mapper_Base | private |
| x_GetDstExon(CSpliced_seg &spliced, TSegments::const_iterator &seg, CSeq_id_Handle &gen_id, CSeq_id_Handle &prod_id, ENa_strand &gen_strand, ENa_strand &prod_strand, bool &last_exon_partial, const CSeq_id_Handle &last_gen_id, const CSeq_id_Handle &last_prod_id) const | CSeq_align_Mapper_Base | private |
| x_GetDstPacked(CRef< CSeq_align > &dst) const | CSeq_align_Mapper_Base | private |
| x_GetDstSparse(CRef< CSeq_align > &dst) const | CSeq_align_Mapper_Base | private |
| x_GetDstSpliced(CRef< CSeq_align > &dst) const | CSeq_align_Mapper_Base | private |
| x_GetDstSplicedSubAlign(CSpliced_seg &spliced, const CSeq_align_Mapper_Base &sub_align, bool &last_exon_partial, CSeq_id_Handle &gen_id, CSeq_id_Handle &last_gen_id, bool &single_gen_id, ENa_strand &gen_strand, bool &single_gen_str, CSeq_id_Handle &prod_id, CSeq_id_Handle &last_prod_id, bool &single_prod_id, ENa_strand &prod_strand, bool &single_prod_str, bool &partial) const | CSeq_align_Mapper_Base | private |
| x_GetDstStd(CRef< CSeq_align > &dst) const | CSeq_align_Mapper_Base | private |
| x_GetPartialDenseg(CRef< CSeq_align > &dst, size_t start_seg) const | CSeq_align_Mapper_Base | private |
| x_HaveMixedSeqTypes(void) const | CSeq_align_Mapper_Base | private |
| x_HaveMixedStrand(void) const | CSeq_align_Mapper_Base | private |
| x_Init(const CSeq_align &align) | CSeq_align_Mapper_Base | protected |
| x_Init(const TDendiag &diags) | CSeq_align_Mapper_Base | private |
| x_Init(const CDense_seg &denseg) | CSeq_align_Mapper_Base | private |
| x_Init(const TStd &sseg) | CSeq_align_Mapper_Base | private |
| x_Init(const CPacked_seg &pseg) | CSeq_align_Mapper_Base | private |
| x_Init(const CSeq_align_set &align_set) | CSeq_align_Mapper_Base | private |
| x_Init(const CSpliced_seg &spliced) | CSeq_align_Mapper_Base | private |
| x_Init(const CSparse_seg &sparse) | CSeq_align_Mapper_Base | private |
| x_InsertSeg(TSegments::iterator &where, int len, size_t dim, bool reverse) | CSeq_align_Mapper_Base | protected |
| x_InvalidateScores(SAlignment_Segment *seg=NULL) | CSeq_align_Mapper_Base | protected |
| x_IsEmpty(void) const | CSeq_align_Mapper_Base | private |
| x_PushExonPart(CRef< CSpliced_exon_chunk > &last_part, CSpliced_exon_chunk::E_Choice part_type, int part_len, CSpliced_exon &exon) const | CSeq_align_Mapper_Base | private |
| x_PushSeg(int len, size_t dim, ENa_strand strand=eNa_strand_unknown) | CSeq_align_Mapper_Base | private |
| ~CDebugDumpable(void) | CDebugDumpable | virtual |
| ~CObject(void) | CObject | virtual |
| ~CSeq_align_Mapper(void) | CSeq_align_Mapper | |
| ~CSeq_align_Mapper_Base(void) | CSeq_align_Mapper_Base |
1.9.0
Modified on Tue May 28 05:51:55 2024 by modify_doxy.py rev. 669887