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

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total = (

)((

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

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

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

(

=0;

<alignLen;

++) {

(Res1 == Res2 && Res1 != 0) {

+= nrows - (j+1);

pFunc(

, total);

(alignLen > 0.0) {

p = 1.0 - p - 0.2*p*p;

int Max(int Val1, int Val2)

CharPtr * m_ppAlignedResidues

MultipleAlignment * m_maligns

bool GetResidueListsWithShifts()

int GetAlignmentLength(int row=0) const

void GetPercentIdentities(pProgressFunction pFunc)

virtual bool ComputeMatrix(pProgressFunction pFunc)

static const double MAX_DISTANCE

static const EDistMethod DIST_METHOD

static double GetKimuraDistance(int identities, int alignment_length)

DM_Identities(EScoreMatrixType type, int ext)

static double GetDistance(int identities, int alignment_length)

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

ScoreMatrix * m_scoreMatrix

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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