| AddReference(void) const | CObject | inline |
| Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive) | CSerialObject | virtual |
| CanBeDeleted(void) const THROWS_NONE | CObject | inline |
| CanGetAnnotatedSites(void) const | CPssmParameters_Base | inline |
| CanGetBitScoreReportingThresh(void) const | CPssmParameters_Base | inline |
| CanGetBitScoreThresh(void) const | CPssmParameters_Base | inline |
| CanGetConstraints(void) const | CPssmParameters_Base | inline |
| CanGetPseudocount(void) const | CPssmParameters_Base | inline |
| CanGetRpsdbparams(void) const | CPssmParameters_Base | inline |
| CDebugDumpable(void) | CDebugDumpable | inline |
| CheckReferenceOverflow(TCount count) const | CObject | private |
| CObject(void) | CObject | |
| CObject(const CObject &src) | CObject | |
| CPssmParameters(void) | CPssmParameters | inline |
| CPssmParameters(const CPssmParameters &value) | CPssmParameters | private |
| CPssmParameters_Base(void) | CPssmParameters_Base | |
| CPssmParameters_Base(const CPssmParameters_Base &) | CPssmParameters_Base | private |
| 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() | CPssmParameters_Base | |
| DeleteThis(void) | CObject | protectedvirtual |
| DoDeleteThisObject(void) | CObject | virtual |
| DoNotDeleteThisObject(void) | CObject | virtual |
| DumpToConsole(void) const | CDebugDumpable | |
| E_memberIndex enum name | CPssmParameters_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 |
| GetAnnotatedSites(void) const | CPssmParameters_Base | inline |
| GetBitScoreReportingThresh(void) const | CPssmParameters_Base | inline |
| GetBitScoreThresh(void) const | CPssmParameters_Base | inline |
| GetConstraints(void) const | CPssmParameters_Base | inline |
| GetNamespaceName(void) const | CSerialObject | |
| GetNamespacePrefix(void) const | CSerialObject | |
| GetPseudocount(void) const | CPssmParameters_Base | inline |
| GetRpsdbparams(void) const | CPssmParameters_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 |
| IsSetAnnotatedSites(void) const | CPssmParameters_Base | inline |
| IsSetBitScoreReportingThresh(void) const | CPssmParameters_Base | inline |
| IsSetBitScoreThresh(void) const | CPssmParameters_Base | inline |
| IsSetConstraints(void) const | CPssmParameters_Base | inline |
| IsSetPseudocount(void) const | CPssmParameters_Base | inline |
| IsSetRpsdbparams(void) const | CPssmParameters_Base | inline |
| m_AnnotatedSites | CPssmParameters_Base | private |
| m_BitScoreReportingThresh | CPssmParameters_Base | private |
| m_BitScoreThresh | CPssmParameters_Base | private |
| m_Constraints | CPssmParameters_Base | private |
| m_Counter | CObject | mutableprivate |
| m_Pseudocount | CPssmParameters_Base | private |
| m_Rpsdbparams | CPssmParameters_Base | private |
| m_set_State | CPssmParameters_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 |
| 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 CPssmParameters &value) | CPssmParameters | 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) | CPssmParameters_Base | virtual |
| ResetAnnotatedSites(void) | CPssmParameters_Base | |
| ResetBitScoreReportingThresh(void) | CPssmParameters_Base | inline |
| ResetBitScoreThresh(void) | CPssmParameters_Base | inline |
| ResetConstraints(void) | CPssmParameters_Base | |
| ResetPseudocount(void) | CPssmParameters_Base | inline |
| ResetRpsdbparams(void) | CPssmParameters_Base | |
| SetAllocFillMode(EAllocFillMode mode) | CObject | static |
| SetAllocFillMode(const string &value) | CObject | static |
| SetAnnotatedSites(TAnnotatedSites &value) | CPssmParameters_Base | |
| SetAnnotatedSites(void) | CPssmParameters_Base | |
| SetBitScoreReportingThresh(TBitScoreReportingThresh value) | CPssmParameters_Base | inline |
| SetBitScoreReportingThresh(void) | CPssmParameters_Base | inline |
| SetBitScoreThresh(TBitScoreThresh value) | CPssmParameters_Base | inline |
| SetBitScoreThresh(void) | CPssmParameters_Base | inline |
| SetConstraints(TConstraints &value) | CPssmParameters_Base | |
| SetConstraints(void) | CPssmParameters_Base | |
| SetPseudocount(TPseudocount value) | CPssmParameters_Base | inline |
| SetPseudocount(void) | CPssmParameters_Base | inline |
| SetRpsdbparams(TRpsdbparams &value) | CPssmParameters_Base | |
| SetRpsdbparams(void) | CPssmParameters_Base | |
| SetVerifyDataGlobal(ESerialVerifyData verify) | CSerialObject | static |
| SetVerifyDataThread(ESerialVerifyData verify) | CSerialObject | static |
| sm_DumpEnabled | CDebugDumpable | privatestatic |
| TAnnotatedSites typedef | CPssmParameters_Base | |
| TBitScoreReportingThresh typedef | CPssmParameters_Base | |
| TBitScoreThresh typedef | CPssmParameters_Base | |
| TConstraints typedef | CPssmParameters_Base | |
| TCount typedef | CObject | |
| TCounter typedef | CObject | |
| 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 | |
| TLockerType typedef | CObject | |
| TmemberIndex typedef | CPssmParameters_Base | |
| Tparent typedef | CPssmParameters | private |
| TPseudocount typedef | CPssmParameters_Base | |
| TRpsdbparams typedef | CPssmParameters_Base | |
| UnassignedByte(void) | CSerialObject | inlinestatic |
| UnassignedString(void) | CSerialObject | inlinestatic |
| UnassignedStringUTF8(void) | CSerialObject | inlinestatic |
| x_GetVerifyData(void) | CSerialObject | privatestatic |
| ~CDebugDumpable(void) | CDebugDumpable | virtual |
| ~CObject(void) | CObject | virtual |
| ~CPssmParameters(void) | CPssmParameters | |
| ~CPssmParameters_Base(void) | CPssmParameters_Base | virtual |
| ~CSerialObject(void) | CSerialObject | virtual |
