Search Toolkit Book for CPssmInputWithUnnormalizedFreqs
PSSM computation strategy with domains with frequencies that do not sum to 1. More...
Inheritance diagram for CPssmInputWithUnnormalizedFreqs:
Collaboration diagram for CPssmInputWithUnnormalizedFreqs:
Public Member Functions | |
| CPssmInputWithUnnormalizedFreqs (void) | |
| Public Member Functions inherited from CPssmInputWithSingleCD | |
| CPssmInputWithSingleCD (void) | |
| virtual | ~CPssmInputWithSingleCD () |
| Public Member Functions inherited from CPssmInputWithNoCDs | |
| CPssmInputWithNoCDs (void) | |
| virtual | ~CPssmInputWithNoCDs () |
| virtual PSICdMsa * | GetData (void) |
| Get CD data for PSSM computation. More... | |
| virtual const PSIBlastOptions * | GetOptions (void) |
| Get CDD-related PSI-BLAST options. More... | |
| virtual void | Process (void) |
| Pre-process CDs used for PSSM computation. More... | |
| virtual unsigned char * | GetQuery (void) |
| Get the query sequence used as master for the multiple sequence alignment in ncbistdaa encoding. More... | |
| virtual unsigned int | GetQueryLength (void) |
| Get the query's length. More... | |
| Public Member Functions inherited from IPssmInputCdd | |
| virtual | ~IPssmInputCdd () |
| virtual const PSIDiagnosticsRequest * | GetDiagnosticsRequest (void) |
| Get diagnostics options. More... | |
| Public Member Functions inherited from IPssmInput_Base | |
| virtual | ~IPssmInput_Base () |
| virtual destructor More... | |
| virtual const char * | GetMatrixName () |
| Obtain the name of the underlying matrix to use when building the PSSM. More... | |
| virtual int | GetGapExistence () |
| Obtain the gap existence value for the underlying matrix used to build the PSSM. More... | |
| virtual int | GetGapExtension () |
| Obtain the gap extension value for the underlying matrix used to build the PSSM. More... | |
| virtual CRef< objects::CBioseq > | GetQueryForPssm () |
| Get a CBioseq object for attachment into the CPssmWithParameters that CPssmEngine produces (only attached if it's not NULL). 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... | |
| virtual void | DebugDump (CDebugDumpContext ddc, unsigned int depth) const |
| Define method for dumping debug information. 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 |
Additional Inherited Members | |
| 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 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 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... | |
| Protected Attributes inherited from CPssmInputWithSingleCD | |
| vector< double > | m_Freqs |
| vector< PSICdMsaCellData > | m_MsaData |
| Protected Attributes inherited from CPssmInputWithNoCDs | |
| PSICdMsa | m_CdMsa |
| PSIMsaDimensions | m_Dimensions |
| CPSIBlastOptions | m_Options |
| vector< unsigned char > | m_Query |
| vector< PSICdMsaCell * > | m_Msa |
| Static Protected Attributes inherited from CPssmInputWithNoCDs | |
| static const int | kQueryLength = 6 |
Detailed Description
PSSM computation strategy with domains with frequencies that do not sum to 1.
Definition at line 239 of file pssmcreate_cdd_unit_test.cpp.
Constructor & Destructor Documentation
◆ CPssmInputWithUnnormalizedFreqs()
|
inline |
Definition at line 242 of file pssmcreate_cdd_unit_test.cpp.
References _ASSERT, AMINOACID_TO_NCBISTDAA, and int.
The documentation for this class was generated from the following file:
- src/algo/blast/unit_tests/api/pssmcreate_cdd_unit_test.cpp
