NCBI C++ ToolKit
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CPsiBlastInputFreqRatios Class Reference

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Implements the interface to retrieve data for the last 2 stages of the PSSM creation. More...

#include <algo/blast/api/psi_pssm_input.hpp>

+ Inheritance diagram for CPsiBlastInputFreqRatios:
+ Collaboration diagram for CPsiBlastInputFreqRatios:

Public Member Functions

 CPsiBlastInputFreqRatios (const unsigned char *query, unsigned int query_length, const CNcbiMatrix< double > &freq_ratios, const char *matrix_name=NULL, int gap_existence=0, int gap_extension=0, double impala_scale_factor=0)
 Constructor. More...
 
void Process ()
 No-op as we assume the data is passed in to the constructor. More...
 
unsigned char * GetQuery ()
 @inheritDoc More...
 
unsigned int GetQueryLength ()
 Get the query's length. More...
 
const char * GetMatrixName ()
 Obtain the name of the underlying matrix to use when building the PSSM. More...
 
int GetGapExistence ()
 Obtain the gap existence value to use when building the PSSM. More...
 
int GetGapExtension ()
 Obtain the gap extension value to use when building the PSSM. More...
 
double GetImpalaScaleFactor ()
 Obtain the IMPALA Scale Factor value to use when building the PSSM. More...
 
const CNcbiMatrix< double > & GetData ()
 Obtain a matrix of frequency ratios with this->GetQueryLength() columns and BLASTAA_SIZE rows. More...
 
- Public Member Functions inherited from IPssmInputFreqRatios
virtual ~IPssmInputFreqRatios ()
 virtual destructor More...
 
- Public Member Functions inherited from IPssmInput_Base
virtual ~IPssmInput_Base ()
 virtual destructor 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
 

Private Attributes

unsigned char * m_Query
 Query sequence data. More...
 
unsigned int m_QueryLength
 Length of query sequence data. More...
 
const char * m_MatrixName
 Name of underlying scoring matrix. More...
 
int m_GapExistence
 Gap existence penalty. More...
 
int m_GapExtension
 Gap extension penalty. More...
 
CNcbiMatrix< double > m_FreqRatios
 Frequency ratios. More...
 
double m_ImpalaScaleFactor
 

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...
 

Detailed Description

Implements the interface to retrieve data for the last 2 stages of the PSSM creation.

Note that none of the data is owned by this class, it simply returns pointers to the data it is passed

Definition at line 65 of file psi_pssm_input.hpp.


The documentation for this class was generated from the following file:
Modified on Wed Feb 21 09:54:44 2024 by modify_doxy.py rev. 669887