NCBI C++ ToolKit
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Search Toolkit Book for CPssmIntermediateData_Base
Contains the PSSM's intermediate data used to create the PSSM's scores and statistical parameters. More...
#include <objects/scoremat/PssmIntermediateData_.hpp>
Public Member Functions | |
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... | |
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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... | |
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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... | |
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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 |
Private Types | |
typedef CSerialObject | Tparent |
Private Member Functions | |
CPssmIntermediateData_Base (const CPssmIntermediateData_Base &) | |
CPssmIntermediateData_Base & | operator= (const CPssmIntermediateData_Base &) |
Private Attributes | |
Uint4 | m_set_State [1] |
list< int > | m_ResFreqsPerPos |
list< double > | m_WeightedResFreqsPerPos |
list< double > | m_FreqRatios |
list< double > | m_InformationContent |
list< double > | m_GaplessColumnWeights |
list< double > | m_Sigma |
list< int > | m_IntervalSizes |
list< int > | m_NumMatchingSeqs |
list< double > | m_NumIndeptObsr |
Additional Inherited Members | |
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static void | SetVerifyDataThread (ESerialVerifyData verify) |
static void | SetVerifyDataGlobal (ESerialVerifyData verify) |
static string | UnassignedString (void) |
static CStringUTF8 | UnassignedStringUTF8 (void) |
static char | UnassignedByte (void) |
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static NCBI_XNCBI_EXPORT void | ThrowNullPointerException (void) |
Define method to throw null pointer exception. More... | |
static NCBI_XNCBI_EXPORT void | ThrowNullPointerException (const type_info &type) |
static EAllocFillMode | GetAllocFillMode (void) |
static void | SetAllocFillMode (EAllocFillMode mode) |
static void | SetAllocFillMode (const string &value) |
Set mode from configuration parameter value. More... | |
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static void | EnableDebugDump (bool on) |
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static const char * | ms_UnassignedStr = "<*unassigned*>" |
static const char | ms_UnassignedByte = char(0xcd) |
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static const TCount | eCounterBitsCanBeDeleted = 1 << 0 |
Define possible object states. More... | |
static const TCount | eCounterBitsInPlainHeap = 1 << 1 |
Heap signature was found. More... | |
static const TCount | eCounterBitsPlaceMask |
Mask for 'in heap' state flags. More... | |
static const int | eCounterStep = 1 << 2 |
Skip over the "in heap" bits. More... | |
static const TCount | eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2) |
Minimal value for valid objects (reference counter is zero) Must be a single bit value. More... | |
static const TCount | eCounterStateMask |
Valid object, and object in heap. More... | |
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virtual void | DeleteThis (void) |
Virtual method "deleting" this object. More... | |
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
Definition at line 76 of file PssmIntermediateData_.hpp.