NCBI C++ ToolKit
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Search Toolkit Book for CPssmInputWithUnnormalizedFreqs
PSSM computation strategy with domains with frequencies that do not sum to 1. More...
Public Member Functions | |
CPssmInputWithUnnormalizedFreqs (void) | |
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CPssmInputWithSingleCD (void) | |
virtual | ~CPssmInputWithSingleCD () |
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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... | |
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virtual | ~IPssmInputCdd () |
virtual const PSIDiagnosticsRequest * | GetDiagnosticsRequest (void) |
Get diagnostics options. More... | |
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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... | |
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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... | |
virtual void | DebugDump (CDebugDumpContext ddc, unsigned int depth) const |
Define method for dumping debug information. 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 |
Additional Inherited Members | |
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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... | |
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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 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... | |
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vector< double > | m_Freqs |
vector< PSICdMsaCellData > | m_MsaData |
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PSICdMsa | m_CdMsa |
PSIMsaDimensions | m_Dimensions |
CPSIBlastOptions | m_Options |
vector< unsigned char > | m_Query |
vector< PSICdMsaCell * > | m_Msa |
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static const int | kQueryLength = 6 |
PSSM computation strategy with domains with frequencies that do not sum to 1.
Definition at line 239 of file pssmcreate_cdd_unit_test.cpp.
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inline |
Definition at line 242 of file pssmcreate_cdd_unit_test.cpp.
References _ASSERT, AMINOACID_TO_NCBISTDAA, and int.