NCBI C++ ToolKit
Public Member Functions | Static Public Member Functions | Private Member Functions | Private Attributes | Static Private Attributes | List of all members
DM_Identities Class Reference

Search Toolkit Book for DM_Identities

#include <algo/structure/cd_utils/cuDmIdentities.hpp>

+ Inheritance diagram for DM_Identities:
+ Collaboration diagram for DM_Identities:

Public Member Functions

 DM_Identities (EScoreMatrixType type, int ext)
 
 DM_Identities (EScoreMatrixType type=GLOBAL_DEFAULT_SCORE_MATRIX, int nTermExt=0, int cTermExt=0)
 
bool UseKimura () const
 
void SetKimura (bool kimura)
 
virtual ~DM_Identities ()
 
virtual bool ComputeMatrix (pProgressFunction pFunc)
 
- Public Member Functions inherited from AlignedDM
 AlignedDM ()
 
void setData (MultipleAlignment *malign)
 
virtual ~AlignedDM ()
 
- Public Member Functions inherited from DistanceMatrix
 DistanceMatrix ()
 
 DistanceMatrix (const int nrows)
 
bool UseAll () const
 
bool UseAligned () const
 
void SetUseAligned (bool useAligned)
 
double ** GetMatrix ()
 
double GetMaxEntry ()
 
double GetMinEntry ()
 
void EnforceSymmetry ()
 
void ReplaceZeroWithTinyValue (const double tiny=TINY_DISTANCE)
 
void SetData (AlignmentCollection *aligns)
 
string GetDistMethodName ()
 
EDistMethod GetDistMethod ()
 
bool ResetMatrixType (EScoreMatrixType newType)
 
string GetMatrixName ()
 
EScoreMatrixType GetMatrixType ()
 
void SetNTermExt (int ext)
 
void SetCTermExt (int ext)
 
int GetNTermExt ()
 
int GetCTermExt ()
 
virtual ~DistanceMatrix ()
 
void printMat (bool triangular=true)
 
- Public Member Functions inherited from AMatrix
 AMatrix ()
 
 AMatrix (const int NumRows, const int NumCols)
 
 AMatrix (const AMatrix &Matrix)
 
AMatrix_baseoperator[] (int RowIndex)
 
- Public Member Functions inherited from AMatrix_base
 AMatrix_base ()
 
 AMatrix_base (const int NumRows, const int NumCols)
 
 AMatrix_base (const AMatrix_base &Matrix)
 
AMatrix_baseoperator= (const AMatrix_base &Matrix)
 
 ~AMatrix_base ()
 
void GetSize (int &NumRows, int &NumCols)
 
int GetNumRows () const
 
int GetNumCols () const
 
double FastGet (const int RowIndex, const int ColIndex) const
 
bool IsColSet (int ColIndex) const
 
bool Shrink (const int NumRows, const int NumCols)
 
void ReSize (const int NumRows, const int NumCols)
 
double & operator[] (int ColIndex)
 
double Get (int RowIndex, int ColIndex)
 
void Set (int RowIndex, int ColIndex, double Val)
 
void LinearTransform (double b, double m, bool ignoreDiagonal=false)
 
void GetExtremalEntries (double &max, double &min, bool ignoreDiagonal=false)
 
void DeAllocate ()
 

Static Public Member Functions

static double GetKimuraDistance (int identities, int alignment_length)
 
static double GetDistance (int identities, int alignment_length)
 
- Static Public Member Functions inherited from DistanceMatrix
static string GetDistMethodName (EDistMethod method)
 
static bool DistMethodUsesScoringMatrix (EDistMethod method)
 
static bool ExtensionsAllowed (EDistMethod method)
 
static bool RequireAlignedBlocks (EDistMethod method)
 
static void readMat (ifstream &ifs, DistanceMatrix &dm, bool triangular)
 
static void writeMat (ofstream &ofs, const DistanceMatrix &dm, bool triangular)
 

Private Member Functions

void GetPercentIdentities (pProgressFunction pFunc)
 
void initDMIdentities (EScoreMatrixType type, int nTermExt, int cTermExt)
 

Private Attributes

bool m_kimura
 

Static Private Attributes

static const double MAX_DISTANCE = 100.0
 
static const EDistMethod DIST_METHOD = ePercentIdentity
 

Additional Inherited Members

- Public Types inherited from DistanceMatrix
typedef double TMatType
 
- Static Public Attributes inherited from DistanceMatrix
static const bool USE_ALIGNED_DEFAULT = true
 
static const int NO_EXTENSION = 0
 
- Protected Types inherited from DistanceMatrix
typedef char * CharPtr
 
- Protected Member Functions inherited from AlignedDM
int GetMaxScoreForAligned ()
 
int GetMaxScore (CharPtr residues)
 
int SetMinScore ()
 
bool GetResidueListsWithShifts ()
 
- Protected Member Functions inherited from DistanceMatrix
virtual void initialize ()
 
void writeMat (ostream &os, bool triangular=true) const
 
- Protected Member Functions inherited from AMatrix_base
int Max (int Val1, int Val2)
 
- Protected Attributes inherited from AlignedDM
CharPtrm_ppAlignedResidues
 
MultipleAlignmentm_maligns
 
- Protected Attributes inherited from DistanceMatrix
std::vector< std::stringm_ConvertedSequences
 
ScoreMatrixm_scoreMatrix
 
EDistMethod m_dMethod
 
bool m_useAligned
 
AlignmentCollectionm_aligns
 
int m_nTermExt
 
int m_cTermExt
 
- Protected Attributes inherited from AMatrix_base
double ** m_Array
 
boolm_ColumnFlags
 
int m_NumRows
 
int m_NumCols
 
int m_RowIndex
 
- Static Protected Attributes inherited from AlignedDM
static const double FRACTIONAL_EXTRA_OFFSET = 0.005
 
- Static Protected Attributes inherited from DistanceMatrix
static const int OUTPUT_PRECISION = 3
 
static const int INITIAL_SCORE_BOUND = kMax_Int
 

Detailed Description

Definition at line 52 of file cuDmIdentities.hpp.

Constructor & Destructor Documentation

◆ DM_Identities() [1/2]

DM_Identities::DM_Identities ( EScoreMatrixType  type,
int  ext 
)

Definition at line 63 of file cuDmIdentities.cpp.

References initDMIdentities().

◆ DM_Identities() [2/2]

DM_Identities::DM_Identities ( EScoreMatrixType  type = GLOBAL_DEFAULT_SCORE_MATRIX,
int  nTermExt = 0,
int  cTermExt = 0 
)

Definition at line 67 of file cuDmIdentities.cpp.

References initDMIdentities().

◆ ~DM_Identities()

DM_Identities::~DM_Identities ( )
virtual

Definition at line 59 of file cuDmIdentities.cpp.

Member Function Documentation

◆ ComputeMatrix()

bool DM_Identities::ComputeMatrix ( pProgressFunction  pFunc)
virtual

◆ GetDistance()

double DM_Identities::GetDistance ( int  identities,
int  alignment_length 
)
static

Definition at line 159 of file cuDmIdentities.cpp.

Referenced by GetPercentIdentities().

◆ GetKimuraDistance()

double DM_Identities::GetKimuraDistance ( int  identities,
int  alignment_length 
)
static

Definition at line 175 of file cuDmIdentities.cpp.

References log, and MAX_DISTANCE.

Referenced by GetPercentIdentities().

◆ GetPercentIdentities()

void DM_Identities::GetPercentIdentities ( pProgressFunction  pFunc)
private

◆ initDMIdentities()

void DM_Identities::initDMIdentities ( EScoreMatrixType  type,
int  nTermExt,
int  cTermExt 
)
private

◆ SetKimura()

void DM_Identities::SetKimura ( bool  kimura)
inline

Definition at line 69 of file cuDmIdentities.hpp.

References ePercIdWithKimura.

◆ UseKimura()

bool DM_Identities::UseKimura ( ) const
inline

Definition at line 65 of file cuDmIdentities.hpp.

Member Data Documentation

◆ DIST_METHOD

const EDistMethod DM_Identities::DIST_METHOD = ePercentIdentity
staticprivate

Definition at line 57 of file cuDmIdentities.hpp.

Referenced by initDMIdentities().

◆ m_kimura

bool DM_Identities::m_kimura
private

Definition at line 90 of file cuDmIdentities.hpp.

Referenced by GetPercentIdentities(), and initDMIdentities().

◆ MAX_DISTANCE

const double DM_Identities::MAX_DISTANCE = 100.0
staticprivate

Definition at line 56 of file cuDmIdentities.hpp.

Referenced by GetKimuraDistance().


The documentation for this class was generated from the following files:
Modified on Wed Apr 17 13:10:45 2024 by modify_doxy.py rev. 669887