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NCBI C++ ToolKit: CPssmIntermediateData_Base Class Reference
Contains the PSSM's intermediate data used to create the PSSM's scores and statistical parameters. More...
CPssmIntermediateData_Base (void) virtual ~CPssmIntermediateData_Base (void) DECLARE_INTERNAL_TYPE_INFO () bool IsSetResFreqsPerPos (void) const observed residue frequencies (or counts) per position of the PSSM (prior to application of pseudocounts) Check if a value has been assigned to ResFreqsPerPos data member. More...
bool CanGetResFreqsPerPos (void) const Check if it is safe to call GetResFreqsPerPos method. More...
void ResetResFreqsPerPos (void) Reset ResFreqsPerPos data member. More...
const TResFreqsPerPos & GetResFreqsPerPos (void) const Get the ResFreqsPerPos member data. More...
TResFreqsPerPos & SetResFreqsPerPos (void) Assign a value to ResFreqsPerPos data member. More...
bool IsSetWeightedResFreqsPerPos (void) const Weighted observed residue frequencies per position of the PSSM. More...
bool CanGetWeightedResFreqsPerPos (void) const Check if it is safe to call GetWeightedResFreqsPerPos method. More...
void ResetWeightedResFreqsPerPos (void) Reset WeightedResFreqsPerPos data member. More...
const TWeightedResFreqsPerPos & GetWeightedResFreqsPerPos (void) const Get the WeightedResFreqsPerPos member data. More...
TWeightedResFreqsPerPos & SetWeightedResFreqsPerPos (void) Assign a value to WeightedResFreqsPerPos data member. More...
bool IsSetFreqRatios (void) const PSSM's frequency ratios Check if a value has been assigned to FreqRatios data member. More...
bool CanGetFreqRatios (void) const Check if it is safe to call GetFreqRatios method. More...
void ResetFreqRatios (void) Reset FreqRatios data member. More...
const TFreqRatios & GetFreqRatios (void) const Get the FreqRatios member data. More...
TFreqRatios & SetFreqRatios (void) Assign a value to FreqRatios data member. More...
bool IsSetInformationContent (void) const Information content per position of the PSSM NOTE: this is needed for diagnostics information only (i.e. More...
bool CanGetInformationContent (void) const Check if it is safe to call GetInformationContent method. More...
void ResetInformationContent (void) Reset InformationContent data member. More...
const TInformationContent & GetInformationContent (void) const Get the InformationContent member data. More...
TInformationContent & SetInformationContent (void) Assign a value to InformationContent data member. More...
bool IsSetGaplessColumnWeights (void) const Relative weight for columns of the PSSM without gaps to pseudocounts NOTE: this is needed for diagnostics information only (i.e. More...
bool CanGetGaplessColumnWeights (void) const Check if it is safe to call GetGaplessColumnWeights method. More...
void ResetGaplessColumnWeights (void) Reset GaplessColumnWeights data member. More...
const TGaplessColumnWeights & GetGaplessColumnWeights (void) const Get the GaplessColumnWeights member data. More...
TGaplessColumnWeights & SetGaplessColumnWeights (void) Assign a value to GaplessColumnWeights data member. More...
bool IsSetSigma (void) const Used in sequence weights computation NOTE: this is needed for diagnostics information only (i.e. More...
bool CanGetSigma (void) const Check if it is safe to call GetSigma method. More...
void ResetSigma (void) Reset Sigma data member. More...
const TSigma & GetSigma (void) const Get the Sigma member data. More...
TSigma & SetSigma (void) Assign a value to Sigma data member. More...
bool IsSetIntervalSizes (void) const Length of the aligned regions per position of the query sequence NOTE: this is needed for diagnostics information only (i.e. More...
bool CanGetIntervalSizes (void) const Check if it is safe to call GetIntervalSizes method. More...
void ResetIntervalSizes (void) Reset IntervalSizes data member. More...
const TIntervalSizes & GetIntervalSizes (void) const Get the IntervalSizes member data. More...
TIntervalSizes & SetIntervalSizes (void) Assign a value to IntervalSizes data member. More...
bool IsSetNumMatchingSeqs (void) const Number of matching sequences per position of the PSSM (including the query) NOTE: this is needed for diagnostics information only (i.e. More...
bool CanGetNumMatchingSeqs (void) const Check if it is safe to call GetNumMatchingSeqs method. More...
void ResetNumMatchingSeqs (void) Reset NumMatchingSeqs data member. More...
const TNumMatchingSeqs & GetNumMatchingSeqs (void) const Get the NumMatchingSeqs member data. More...
TNumMatchingSeqs & SetNumMatchingSeqs (void) Assign a value to NumMatchingSeqs data member. More...
bool IsSetNumIndeptObsr (void) const Number of independent observations per position of the PSSM NOTE: this is needed for building CDD database for DELTA-BLAST Check if a value has been assigned to NumIndeptObsr data member. More...
bool CanGetNumIndeptObsr (void) const Check if it is safe to call GetNumIndeptObsr method. More...
void ResetNumIndeptObsr (void) Reset NumIndeptObsr data member. More...
const TNumIndeptObsr & GetNumIndeptObsr (void) const Get the NumIndeptObsr member data. More...
TNumIndeptObsr & SetNumIndeptObsr (void) Assign a value to NumIndeptObsr data member. More...
virtual void Reset (void) Reset the whole object. More...
CSerialObject (void) virtual ~CSerialObject (void) virtual const CTypeInfo * GetThisTypeInfo (void) const =0 virtual void Assign (const CSerialObject &source, ESerialRecursionMode how=eRecursive) Set object to copy of another one. More...
virtual bool Equals (const CSerialObject &object, ESerialRecursionMode how=eRecursive) const Check if both objects contain the same values. More...
virtual void DebugDump (CDebugDumpContext ddc, unsigned int depth) const Define method for dumping debug information. More...
void ThrowUnassigned (TMemberIndex index) const void ThrowUnassigned (TMemberIndex index, const char *file_name, int file_line) const bool HasNamespaceName (void) const Check if object data type has namespace name. More...
const string & GetNamespaceName (void) const Get namespace name. More...
bool HasNamespacePrefix (void) const Check if data type has namespace prefix. More...
const string & GetNamespacePrefix (void) const Get namespace prefix. More...
CObject (void) Constructor. More...
CObject (const CObject &src) Copy constructor. More...
virtual ~CObject (void) Destructor. More...
CObject & operator= (const CObject &src) THROWS_NONE Assignment operator. More...
bool CanBeDeleted (void) const THROWS_NONE Check if object can be deleted. More...
bool IsAllocatedInPool (void) const THROWS_NONE Check if object is allocated in memory pool (not system heap) More...
bool Referenced (void) const THROWS_NONE Check if object is referenced. More...
bool ReferencedOnlyOnce (void) const THROWS_NONE Check if object is referenced only once. More...
void AddReference (void) const Add reference to object. More...
void RemoveReference (void) const Remove reference to object. More...
void ReleaseReference (void) const Remove reference without deleting object. More...
virtual void DoNotDeleteThisObject (void) Mark this object as not allocated in heap – do not delete this object. More...
virtual void DoDeleteThisObject (void) Mark this object as allocated in heap – object can be deleted. More...
void * operator new (size_t size) Define new operator for memory allocation. More...
void * operator new[] (size_t size) Define new[] operator for 'array' memory allocation. More...
void operator delete (void *ptr) Define delete operator for memory deallocation. More...
void operator delete[] (void *ptr) Define delete[] operator for memory deallocation. More...
void * operator new (size_t size, void *place) Define new operator. More...
void operator delete (void *ptr, void *place) Define delete operator. More...
void * operator new (size_t size, CObjectMemoryPool *place) Define new operator using memory pool. More...
void operator delete (void *ptr, CObjectMemoryPool *place) Define delete operator. More...
CDebugDumpable (void) virtual ~CDebugDumpable (void) void DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const void DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const void DumpToConsole (void) const
Contains the PSSM's intermediate data used to create the PSSM's scores and statistical parameters.
Dimensions and order in which scores are stored must be the same as that specified in Pssm::numRows, Pssm::numColumns, and Pssm::byrow
CPssmIntermediateData_Base –
Definition at line 76 of file PssmIntermediateData_.hpp.
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