NCBI C++ ToolKit
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CPssmInputWithUnnormalizedFreqs Class Reference

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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 PSICdMsaGetData (void)
 Get CD data for PSSM computation. More...
 
virtual const PSIBlastOptionsGetOptions (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 PSIDiagnosticsRequestGetDiagnosticsRequest (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...
 
CObjectoperator= (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< Uint8TCounter
 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< PSICdMsaCellDatam_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()

CPssmInputWithUnnormalizedFreqs::CPssmInputWithUnnormalizedFreqs ( void  )
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:
Modified on Sat Feb 24 07:48:55 2024 by modify_doxy.py rev. 669887