| AddReference(void) const | CObject | inline |
| CanBeDeleted(void) const THROWS_NONE | CObject | inline |
| CCompareSeqRegions(const CSeq_loc &query_loc, CScope *q_scope, CScope *t_scope, ILocMapper &mapper, const SAnnotSelector &q_sel, const SAnnotSelector &t_sel, const CSeq_id &target_id, TComparisonOptions options=fSelectBest|fMergeExons, EScoreMethod score_method=eScore_SymmetricPctOverlap) | CCompareSeqRegions | inline |
| CDebugDumpable(void) | CDebugDumpable | inline |
| CheckReferenceOverflow(TCount count) const | CObject | private |
| CObject(void) | CObject | |
| CObject(const CObject &src) | CObject | |
| 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 | |
| EComparisonOptions enum name | CCompareSeqRegions | |
| eCounterBitsCanBeDeleted | CObject | static |
| eCounterBitsInPlainHeap | CObject | static |
| eCounterBitsPlaceMask | CObject | static |
| eCounterStateMask | CObject | static |
| eCounterStep | CObject | static |
| eCounterValid | CObject | static |
| EnableDebugDump(bool on) | CDebugDumpable | static |
| eScore_Feat1PctOverlap enum value | CCompareSeqRegions | |
| eScore_Feat2PctOverlap enum value | CCompareSeqRegions | |
| eScore_SymmetricPctOverlap enum value | CCompareSeqRegions | |
| EScoreMethod enum name | CCompareSeqRegions | |
| fCreateSentinelGenes enum value | CCompareSeqRegions | |
| fDifferentGenesOnly enum value | CCompareSeqRegions | |
| fMergeExons enum value | CCompareSeqRegions | |
| fSameTypeOnly enum value | CCompareSeqRegions | |
| fSelectBest enum value | CCompareSeqRegions | |
| GetAllocFillMode(void) | CObject | static |
| GetOptions() const | CCompareSeqRegions | inline |
| GetQueryLoc() const | CCompareSeqRegions | inline |
| InitCounter(void) | CObject | inlineprivate |
| InvalidObject(void) const | CObject | private |
| IsAllocatedInPool(void) const THROWS_NONE | CObject | inline |
| m_already_processed_unmatched_targets | CCompareSeqRegions | private |
| m_comp_options | CCompareSeqRegions | private |
| m_Counter | CObject | mutableprivate |
| m_loc_q | CCompareSeqRegions | private |
| m_loc_q_ci | CCompareSeqRegions | private |
| m_mapper | CCompareSeqRegions | private |
| m_scope_q | CCompareSeqRegions | private |
| m_scope_t | CCompareSeqRegions | private |
| m_score_method | CCompareSeqRegions | private |
| m_seen_targets | CCompareSeqRegions | private |
| m_selector_q | CCompareSeqRegions | private |
| m_selector_t | CCompareSeqRegions | private |
| m_self_mapper_q | CCompareSeqRegions | private |
| m_self_mapper_t | CCompareSeqRegions | private |
| m_target_id | CCompareSeqRegions | private |
| NextComparisonGroup(vector< CRef< CCompareFeats > > &v) | CCompareSeqRegions | |
| 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 |
| Rewind() | CCompareSeqRegions | inline |
| s_GetGeneId(const CSeq_feat &feat) | CCompareSeqRegions | static |
| SelectMatches(vector< CRef< CCompareFeats > > &v) | CCompareSeqRegions | |
| SetAllocFillMode(EAllocFillMode mode) | CObject | static |
| SetAllocFillMode(const string &value) | CObject | static |
| SetOptions() | CCompareSeqRegions | inline |
| sm_DumpEnabled | CDebugDumpable | privatestatic |
| TComparisonOptions typedef | CCompareSeqRegions | |
| TCount typedef | CObject | |
| TCounter typedef | CObject | |
| ThrowNullPointerException(void) | CObject | static |
| ThrowNullPointerException(const type_info &type) | CObject | static |
| TLockerType typedef | CObject | |
| x_GetPutativeMatches(vector< CRef< CCompareFeats > > &v, CConstRef< CSeq_feat > q_feat) | CCompareSeqRegions | private |
| x_GetSelfLoc(const CSeq_loc &loc, CScope *scope, bool merge_single_range) | CCompareSeqRegions | private |
| ~CDebugDumpable(void) | CDebugDumpable | virtual |
| ~CObject(void) | CObject | virtual |
