Search Toolkit Book for CPssmIntermediateData
CPssmIntermediateData –. More...
#include <objects/scoremat/PssmIntermediateData.hpp>
Inheritance diagram for CPssmIntermediateData:
Collaboration diagram for CPssmIntermediateData:
Public Member Functions | |
| CPssmIntermediateData (void) | |
| ~CPssmIntermediateData (void) | |
| Public Member Functions inherited from CPssmIntermediateData_Base | |
| 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... | |
| Public Member Functions inherited from CSerialObject | |
| 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... | |
| Public Member Functions inherited from CObject | |
| 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... | |
| Public Member Functions inherited from CDebugDumpable | |
| 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 CPssmIntermediateData_Base | Tparent |
Private Member Functions | |
| CPssmIntermediateData (const CPssmIntermediateData &value) | |
| CPssmIntermediateData & | operator= (const CPssmIntermediateData &value) |
Additional Inherited Members | |
| Public Types inherited from CPssmIntermediateData_Base | |
| enum class | E_memberIndex { e__allMandatory = 0 , e_resFreqsPerPos , e_weightedResFreqsPerPos , e_freqRatios , e_informationContent , e_gaplessColumnWeights , e_sigma , e_intervalSizes , e_numMatchingSeqs , e_numIndeptObsr } |
| typedef list< int > | TResFreqsPerPos |
| typedef list< double > | TWeightedResFreqsPerPos |
| typedef list< double > | TFreqRatios |
| typedef list< double > | TInformationContent |
| typedef list< double > | TGaplessColumnWeights |
| typedef list< double > | TSigma |
| typedef list< int > | TIntervalSizes |
| typedef list< int > | TNumMatchingSeqs |
| typedef list< double > | TNumIndeptObsr |
| typedef Tparent::CMemberIndex< E_memberIndex, 10 > | TmemberIndex |
| Public Types inherited from CObject | |
| enum | EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern } |
| Control filling of newly allocated memory. More... | |
| typedef CObjectCounterLocker | TLockerType |
| Default locker type for CRef. More... | |
| typedef atomic< Uint8 > | TCounter |
| Counter type is CAtomiCounter. More... | |
| typedef Uint8 | TCount |
| Alias for value type of counter. More... | |
| Static Public Member Functions inherited from CSerialObject | |
| static void | SetVerifyDataThread (ESerialVerifyData verify) |
| static void | SetVerifyDataGlobal (ESerialVerifyData verify) |
| static string | UnassignedString (void) |
| static CStringUTF8 | UnassignedStringUTF8 (void) |
| static char | UnassignedByte (void) |
| Static Public Member Functions inherited from CObject | |
| 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... | |
| Static Public Member Functions inherited from CDebugDumpable | |
| static void | EnableDebugDump (bool on) |
| Static Public Attributes inherited from CSerialObject | |
| static const char * | ms_UnassignedStr = "<*unassigned*>" |
| static const char | ms_UnassignedByte = char(0xcd) |
| Static Public Attributes inherited from CObject | |
| 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... | |
| Protected Member Functions inherited from CObject | |
| virtual void | DeleteThis (void) |
| Virtual method "deleting" this object. More... | |
Detailed Description
Definition at line 65 of file PssmIntermediateData.hpp.
The documentation for this class was generated from the following files:
- include/objects/scoremat/PssmIntermediateData.hpp
- src/objects/scoremat/PssmIntermediateData.cpp
