NCBI C++ ToolKit
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CGeneralScoreMatrix Class Reference

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Score matrix that can take any value. More...

#include <algo/blast/gumbel_params/general_score_matrix.hpp>

+ Inheritance diagram for CGeneralScoreMatrix:
+ Collaboration diagram for CGeneralScoreMatrix:

Public Types

enum  EScoreMatrixName {
  eBlosum45, eBlosum62, eBlosum80, ePam30,
  ePam70, ePam250
}
 Names of standard scoring matrices. More...
 
- 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 CAtomicCounter TCounter
 Counter type is CAtomiCounter. More...
 
typedef TCounter::TValue TCount
 Alias for value type of counter. More...
 

Public Member Functions

 CGeneralScoreMatrix (EScoreMatrixName type, unsigned int sub_size=25)
 Creates a standard score matrix. More...
 
 CGeneralScoreMatrix (const Int4 **matrix, unsigned int size, const char *alphabet=NULL)
 Creates user defined score matrix. More...
 
 CGeneralScoreMatrix (const vector< Int4 > &vals, const char *alphabet=NULL)
 Creates score matrix from values in a given vector. More...
 
 CGeneralScoreMatrix (const CGeneralScoreMatrix &matrix)
 Copy constructor. More...
 
 ~CGeneralScoreMatrix ()
 Destructor. More...
 
const Int4 ** GetMatrix (void) const
 Access matrix values. More...
 
const char * GetResidueOrder (void) const
 Get order of residues in the score matrix. More...
 
unsigned int GetNumResidues (void) const
 Get number of residues. More...
 
Int4 GetScore (Uint4 i, Uint4 j) const
 Get score matrix entry for at specified position. More...
 
Int4 GetScore (char a, char b) const
 Return score matrix entry for a given pair of residues. 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
 

Protected Attributes

Int4 ** m_ScoreMatrix
 
char * m_ResidueOrder
 
unsigned int m_NumResidues
 

Private Member Functions

CGeneralScoreMatrixoperator= (const CGeneralScoreMatrix &)
 Forbid assignment operator. More...
 

Additional Inherited Members

- Static Public Member Functions inherited from CObject
static NCBI_NORETURN void ThrowNullPointerException (void)
 Define method to throw null pointer exception. More...
 
static NCBI_NORETURN 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

Score matrix that can take any value.

Definition at line 51 of file general_score_matrix.hpp.

Member Enumeration Documentation

Names of standard scoring matrices.

Enumerator
eBlosum45 
eBlosum62 
eBlosum80 
ePam30 
ePam70 
ePam250 

Definition at line 56 of file general_score_matrix.hpp.

Constructor & Destructor Documentation

CGeneralScoreMatrix::CGeneralScoreMatrix ( CGeneralScoreMatrix::EScoreMatrixName  type,
unsigned int  sub_size = 25 
)

Creates a standard score matrix.

Parameters
typeStandard score matrix type [in]
sub_sizeNumber of rows and columns to copy [in]

Definition at line 48 of file general_score_matrix.cpp.

References eBlosum45, eBlosum62, eBlosum80, ePam250, ePam30, ePam70, i, m_NumResidues, m_ResidueOrder, m_ScoreMatrix, min(), NCBI_THROW, NCBISM_Blosum45, NCBISM_Blosum62, NCBISM_Blosum80, NCBISM_Pam250, NCBISM_Pam30, NCBISM_Pam70, NCBISM_Unpack(), SNCBIFullScoreMatrix::s, and SNCBIPackedScoreMatrix::symbols.

CGeneralScoreMatrix::CGeneralScoreMatrix ( const Int4 **  matrix,
unsigned int  size,
const char *  alphabet = NULL 
)

Creates user defined score matrix.

Matrix and alphabet are copied.

Parameters
matrixMatrix values [in]
sizeNumber of alphabet elements [in]
alphabetAlphabel symbols [in]

Definition at line 102 of file general_score_matrix.cpp.

References i, m_NumResidues, m_ResidueOrder, m_ScoreMatrix, and NULL.

CGeneralScoreMatrix::CGeneralScoreMatrix ( const vector< Int4 > &  vals,
const char *  alphabet = NULL 
)

Creates score matrix from values in a given vector.

Parameters
valsValues for the score matrix as consecutive rows [in]
alphabetOrder of residues for the score matrix or NULL

Definition at line 125 of file general_score_matrix.cpp.

References _ASSERT, i, m_NumResidues, m_ResidueOrder, m_ScoreMatrix, and NULL.

CGeneralScoreMatrix::CGeneralScoreMatrix ( const CGeneralScoreMatrix matrix)

Copy constructor.

Parameters
matrixScore matrix

Definition at line 149 of file general_score_matrix.cpp.

References GetResidueOrder(), i, m_NumResidues, m_ResidueOrder, m_ScoreMatrix, and NULL.

CGeneralScoreMatrix::~CGeneralScoreMatrix ( )

Destructor.

Definition at line 171 of file general_score_matrix.cpp.

References m_ResidueOrder, m_ScoreMatrix, and NULL.

Member Function Documentation

const Int4** CGeneralScoreMatrix::GetMatrix ( void  ) const
inline

Access matrix values.

Returns
Pointer to matrix values

Definition at line 97 of file general_score_matrix.hpp.

unsigned int CGeneralScoreMatrix::GetNumResidues ( void  ) const
inline

Get number of residues.

Returns
Number of residues

Definition at line 107 of file general_score_matrix.hpp.

Referenced by BOOST_AUTO_TEST_CASE(), and CGumbelParamsOptions::Validate().

const char* CGeneralScoreMatrix::GetResidueOrder ( void  ) const
inline

Get order of residues in the score matrix.

Returns
Pointer to alphabet symbols

Definition at line 102 of file general_score_matrix.hpp.

Referenced by BOOST_AUTO_TEST_CASE(), and CGeneralScoreMatrix().

Int4 CGeneralScoreMatrix::GetScore ( Uint4  i,
Uint4  j 
) const

Get score matrix entry for at specified position.

Throws exception if index out of bounds

Parameters
iMatrix row number [in]
jMatrix column number [in]
Returns
Score matrix value at position i, j

Definition at line 183 of file general_score_matrix.cpp.

References i, m_NumResidues, m_ScoreMatrix, and NCBI_THROW.

Referenced by BOOST_AUTO_TEST_CASE(), and CGumbelParamsOptions::Validate().

Int4 CGeneralScoreMatrix::GetScore ( char  a,
char  b 
) const

Return score matrix entry for a given pair of residues.

Throws exception for illegal residues

Parameters
aResidue 1 [in]
bResidue 2 [in]
Returns
Score matrix value for a given pair of residues

Definition at line 193 of file general_score_matrix.cpp.

References rapidjson::a, b, i, m_NumResidues, m_ResidueOrder, m_ScoreMatrix, and NCBI_THROW.

CGeneralScoreMatrix& CGeneralScoreMatrix::operator= ( const CGeneralScoreMatrix )
private

Forbid assignment operator.

Member Data Documentation

unsigned int CGeneralScoreMatrix::m_NumResidues
protected

Definition at line 132 of file general_score_matrix.hpp.

Referenced by CGeneralScoreMatrix(), and GetScore().

char* CGeneralScoreMatrix::m_ResidueOrder
protected

Definition at line 131 of file general_score_matrix.hpp.

Referenced by CGeneralScoreMatrix(), GetScore(), and ~CGeneralScoreMatrix().

Int4** CGeneralScoreMatrix::m_ScoreMatrix
protected

Definition at line 130 of file general_score_matrix.hpp.

Referenced by CGeneralScoreMatrix(), GetScore(), and ~CGeneralScoreMatrix().


The documentation for this class was generated from the following files:
Modified on Tue Jul 07 15:24:05 2015 by modify_doxy.py rev. 426318