| AddReference(void) const | CObject | inline |
| Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive) | CSerialObject | virtual |
| CanBeDeleted(void) const THROWS_NONE | CObject | inline |
| CanGetDim(void) const | CDense_diag_Base | inline |
| CanGetIds(void) const | CDense_diag_Base | inline |
| CanGetLen(void) const | CDense_diag_Base | inline |
| CanGetScores(void) const | CDense_diag_Base | inline |
| CanGetStarts(void) const | CDense_diag_Base | inline |
| CanGetStrands(void) const | CDense_diag_Base | inline |
| CDebugDumpable(void) | CDebugDumpable | inline |
| CDense_diag(void) | CDense_diag | inline |
| CDense_diag(const CDense_diag &value) | CDense_diag | private |
| CDense_diag_Base(void) | CDense_diag_Base | |
| CDense_diag_Base(const CDense_diag_Base &) | CDense_diag_Base | private |
| CheckNumRows(void) const | CDense_diag | inline |
| CheckReferenceOverflow(TCount count) const | CObject | private |
| CObject(void) | CObject | |
| CObject(const CObject &src) | CObject | |
| CreateRowSeq_interval(TDim row) const | CDense_diag | |
| CSerialObject(void) | CSerialObject | |
| DebugDump(CDebugDumpContext ddc, unsigned int depth) const | CSerialObject | virtual |
| DebugDumpFormat(CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const | CDebugDumpable | |
| DebugDumpText(ostream &out, const string &bundle, unsigned int depth) const | CDebugDumpable | |
| DECLARE_INTERNAL_TYPE_INFO() | CDense_diag_Base | |
| DeleteThis(void) | CObject | protectedvirtual |
| DoDeleteThisObject(void) | CObject | virtual |
| DoNotDeleteThisObject(void) | CObject | virtual |
| DumpToConsole(void) const | CDebugDumpable | |
| E_memberIndex enum name | CDense_diag_Base | |
| 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 |
| Equals(const CSerialObject &object, ESerialRecursionMode how=eRecursive) const | CSerialObject | virtual |
| GetAllocFillMode(void) | CObject | static |
| GetDim(void) const | CDense_diag_Base | inline |
| GetIds(void) const | CDense_diag_Base | inline |
| GetLen(void) const | CDense_diag_Base | inline |
| GetNamespaceName(void) const | CSerialObject | |
| GetNamespacePrefix(void) const | CSerialObject | |
| GetScores(void) const | CDense_diag_Base | inline |
| GetSeqRange(TDim row) const | CDense_diag | inline |
| GetSeqStart(TDim row) const | CDense_diag | inline |
| GetSeqStop(TDim row) const | CDense_diag | inline |
| GetSeqStrand(TDim row) const | CDense_diag | |
| GetStarts(void) const | CDense_diag_Base | inline |
| GetStrands(void) const | CDense_diag_Base | inline |
| GetThisTypeInfo(void) const =0 | CSerialObject | pure virtual |
| HasNamespaceName(void) const | CSerialObject | |
| HasNamespacePrefix(void) const | CSerialObject | |
| InitCounter(void) | CObject | inlineprivate |
| InvalidObject(void) const | CObject | private |
| IsAllocatedInPool(void) const THROWS_NONE | CObject | inline |
| IsSetDim(void) const | CDense_diag_Base | inline |
| IsSetIds(void) const | CDense_diag_Base | inline |
| IsSetLen(void) const | CDense_diag_Base | inline |
| IsSetScores(void) const | CDense_diag_Base | inline |
| IsSetStarts(void) const | CDense_diag_Base | inline |
| IsSetStrands(void) const | CDense_diag_Base | inline |
| m_Counter | CObject | mutableprivate |
| m_Dim | CDense_diag_Base | private |
| m_Ids | CDense_diag_Base | private |
| m_Len | CDense_diag_Base | private |
| m_Scores | CDense_diag_Base | private |
| m_set_State | CDense_diag_Base | private |
| m_Starts | CDense_diag_Base | private |
| m_Strands | CDense_diag_Base | private |
| ms_UnassignedByte | CSerialObject | static |
| ms_UnassignedStr | CSerialObject | static |
| 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 |
| OffsetRow(TDim row, TSignedSeqPos offset) | CDense_diag | |
| 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 CDense_diag &value) | CDense_diag | private |
| CSerialObject::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 |
| Reset(void) | CDense_diag_Base | virtual |
| ResetDim(void) | CDense_diag_Base | inline |
| ResetIds(void) | CDense_diag_Base | |
| ResetLen(void) | CDense_diag_Base | inline |
| ResetScores(void) | CDense_diag_Base | |
| ResetStarts(void) | CDense_diag_Base | |
| ResetStrands(void) | CDense_diag_Base | |
| SetAllocFillMode(EAllocFillMode mode) | CObject | static |
| SetAllocFillMode(const string &value) | CObject | static |
| SetDefaultDim(void) | CDense_diag_Base | inline |
| SetDim(TDim value) | CDense_diag_Base | inline |
| SetDim(void) | CDense_diag_Base | inline |
| SetIds(void) | CDense_diag_Base | inline |
| SetLen(TLen value) | CDense_diag_Base | inline |
| SetLen(void) | CDense_diag_Base | inline |
| SetScores(void) | CDense_diag_Base | inline |
| SetStarts(void) | CDense_diag_Base | inline |
| SetStrands(void) | CDense_diag_Base | inline |
| SetVerifyDataGlobal(ESerialVerifyData verify) | CSerialObject | static |
| SetVerifyDataThread(ESerialVerifyData verify) | CSerialObject | static |
| sm_DumpEnabled | CDebugDumpable | privatestatic |
| TCount typedef | CObject | |
| TCounter typedef | CObject | |
| TDim typedef | CDense_diag_Base | |
| ThrowNullPointerException(void) | CObject | static |
| ThrowNullPointerException(const type_info &type) | CObject | static |
| ThrowUnassigned(TMemberIndex index) const | CSerialObject | |
| ThrowUnassigned(TMemberIndex index, const char *file_name, int file_line) const | CSerialObject | |
| TIds typedef | CDense_diag_Base | |
| TLen typedef | CDense_diag_Base | |
| TLockerType typedef | CObject | |
| TmemberIndex typedef | CDense_diag_Base | |
| Tparent typedef | CDense_diag | private |
| TScores typedef | CDense_diag_Base | |
| TStarts typedef | CDense_diag_Base | |
| TStrands typedef | CDense_diag_Base | |
| UnassignedByte(void) | CSerialObject | inlinestatic |
| UnassignedString(void) | CSerialObject | inlinestatic |
| UnassignedStringUTF8(void) | CSerialObject | inlinestatic |
| Validate() const | CDense_diag | |
| x_GetVerifyData(void) | CSerialObject | privatestatic |
| ~CDebugDumpable(void) | CDebugDumpable | virtual |
| ~CDense_diag(void) | CDense_diag | |
| ~CDense_diag_Base(void) | CDense_diag_Base | virtual |
| ~CObject(void) | CObject | virtual |
| ~CSerialObject(void) | CSerialObject | virtual |
