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DMAlignedOptimalScore Class Reference

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

+ Inheritance diagram for DMAlignedOptimalScore:
+ Collaboration diagram for DMAlignedOptimalScore:

Public Member Functions

 DMAlignedOptimalScore (EScoreMatrixType type=GLOBAL_DEFAULT_SCORE_MATRIX)
 
void setBlockExtender (BlockExtender *be)
 
virtual bool ComputeMatrix (pProgressFunction pFunc)
 
virtual ~DMAlignedOptimalScore ()
 
- 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 ()
 

Private Member Functions

void convertScoreToDistance ()
 
void initDMAlignedScore (EScoreMatrixType type, int nTermExt, int cTermExt)
 

Private Attributes

BlockExtenderm_blockExtender
 

Static Private Attributes

static const EDistMethod DIST_METHOD = eScoreAlignedOptimal
 

Additional Inherited Members

- Public Types inherited from DistanceMatrix
typedef double TMatType
 
- 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)
 
- 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 60 of file cuDmAlignedOptimalScore.hpp.

Constructor & Destructor Documentation

◆ DMAlignedOptimalScore()

DMAlignedOptimalScore::DMAlignedOptimalScore ( EScoreMatrixType  type = GLOBAL_DEFAULT_SCORE_MATRIX)

Definition at line 50 of file cuDmAlignedOptimalScore.cpp.

References initDMAlignedScore().

◆ ~DMAlignedOptimalScore()

DMAlignedOptimalScore::~DMAlignedOptimalScore ( )
virtual

Definition at line 46 of file cuDmAlignedOptimalScore.cpp.

Member Function Documentation

◆ ComputeMatrix()

bool DMAlignedOptimalScore::ComputeMatrix ( pProgressFunction  pFunc)
virtual

◆ convertScoreToDistance()

void DMAlignedOptimalScore::convertScoreToDistance ( )
private

◆ initDMAlignedScore()

void DMAlignedOptimalScore::initDMAlignedScore ( EScoreMatrixType  type,
int  nTermExt,
int  cTermExt 
)
private

◆ setBlockExtender()

void DMAlignedOptimalScore::setBlockExtender ( BlockExtender be)

Definition at line 68 of file cuDmAlignedOptimalScore.cpp.

References m_blockExtender.

Referenced by TreeFactory::makeTree().

Member Data Documentation

◆ DIST_METHOD

const EDistMethod DMAlignedOptimalScore::DIST_METHOD = eScoreAlignedOptimal
staticprivate

Definition at line 62 of file cuDmAlignedOptimalScore.hpp.

Referenced by initDMAlignedScore().

◆ m_blockExtender

BlockExtender* DMAlignedOptimalScore::m_blockExtender
private

Definition at line 81 of file cuDmAlignedOptimalScore.hpp.

Referenced by ComputeMatrix(), and setBlockExtender().


The documentation for this class was generated from the following files:
Modified on Sat Apr 13 11:47:18 2024 by modify_doxy.py rev. 669887