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NCBI C++ ToolKit: src/algo/structure/cd_utils/cuDmAlignedOptimalScore.cpp Source File

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total = (

)((

)nrows * (((double)nrows-1)/2));

(

j=0; j<nrows; j++)

(

k=j+1; k<nrows; k++)

+= nrows - (j+1);

pFunc(

, total);

(

j=0; j<

; ++j)

static const double FRACTIONAL_EXTRA_OFFSET

MultipleAlignment * m_maligns

bool setMatrixForExtensionScores(double **matrix, int matrixSize)

void setScoringMatrix(ScoreMatrix *sm)

void setCTermExt(int ext)

bool extendOnePair(int primaryRow, int secondaryRow)

void setNTermExt(int ext)

void setAlignments(MultipleAlignment *ma)

void setBlockExtender(BlockExtender *be)

virtual ~DMAlignedOptimalScore()

static const EDistMethod DIST_METHOD

DMAlignedOptimalScore(EScoreMatrixType type=GLOBAL_DEFAULT_SCORE_MATRIX)

virtual bool ComputeMatrix(pProgressFunction pFunc)

BlockExtender * m_blockExtender

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

void convertScoreToDistance()

ScoreMatrix * m_scoreMatrix

std::vector< std::string > m_ConvertedSequences

void(* pProgressFunction)(int Num, int Total)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

unsigned int

A callback function used to compare two keys in a database.

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