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AlignedDM Class Referenceabstract

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

+ Inheritance diagram for AlignedDM:
+ Collaboration diagram for AlignedDM:

Public Member Functions

 AlignedDM ()
 
void setData (MultipleAlignment *malign)
 
virtual bool ComputeMatrix (pProgressFunction pFunc)=0
 
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 ()
 

Protected Member Functions

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

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

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
 

Private Member Functions

void setData (AlignmentCollection *data)
 

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
 

Detailed Description

Definition at line 43 of file cuAlignedDM.hpp.

Constructor & Destructor Documentation

◆ AlignedDM()

AlignedDM::AlignedDM ( )

Definition at line 9 of file cuAlignedDM.cpp.

◆ ~AlignedDM()

AlignedDM::~AlignedDM ( )
virtual

Definition at line 20 of file cuAlignedDM.cpp.

References i, AMatrix_base::m_NumRows, and m_ppAlignedResidues.

Member Function Documentation

◆ ComputeMatrix()

virtual bool AlignedDM::ComputeMatrix ( pProgressFunction  pFunc)
pure virtual

◆ GetMaxScore()

int AlignedDM::GetMaxScore ( CharPtr  residues)
protected

◆ GetMaxScoreForAligned()

int AlignedDM::GetMaxScoreForAligned ( )
protected

◆ GetResidueListsWithShifts()

bool AlignedDM::GetResidueListsWithShifts ( )
protected

◆ setData() [1/2]

void AlignedDM::setData ( AlignmentCollection data)
inlineprivate

Definition at line 68 of file cuAlignedDM.hpp.

◆ setData() [2/2]

void AlignedDM::setData ( MultipleAlignment malign)

Definition at line 14 of file cuAlignedDM.cpp.

References m_maligns, and DistanceMatrix::SetData().

◆ SetMinScore()

int AlignedDM::SetMinScore ( )
protected

Member Data Documentation

◆ FRACTIONAL_EXTRA_OFFSET

const double AlignedDM::FRACTIONAL_EXTRA_OFFSET = 0.005
staticprotected

◆ m_maligns

MultipleAlignment* AlignedDM::m_maligns
protected

◆ m_ppAlignedResidues

CharPtr* AlignedDM::m_ppAlignedResidues
protected

The documentation for this class was generated from the following files:
Modified on Wed Apr 17 13:10:19 2024 by modify_doxy.py rev. 669887