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

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123

ppScores =

new int

*[256];

124  for

(j=0; j<256; j++) {

125

ppScores[j] =

new int

[256];

127  for

(j=0; j<256; j++) {

128  for

(k=0; k<256; k++) {

135  int

total = (

int

)((

double

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

136  for

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

139  for

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

143  count

+= nrows - (j+1);

144

pFunc(

count

, total);

152  for

(j=0; j<256; j++) {

153  delete

[]ppScores[j];

165  double

pairwiseScore = 0;

166  unsigned int

res1, res2;

170  for

(

int i

=0;

i

<alignLen;

i

++) {

171

res1 = (

unsigned int

) residuesRow1[

i

];

172

res2 = (

unsigned int

) residuesRow2[

i

];

173  if

(res1 == 0 || res2 == 0) {

176

pairwiseScore += ppScores[res1][res2];

178  return

pairwiseScore;

196  for

(

int

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

197  for

(

int

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

int Max(int Val1, int Val2)

static const double FRACTIONAL_EXTRA_OFFSET

CharPtr * m_ppAlignedResidues

MultipleAlignment * m_maligns

bool GetResidueListsWithShifts()

int GetAlignmentLength(int row=0) const

virtual ~DM_AlignedScore()

double GetScore(CharPtr residuesRow1, CharPtr residuesRow2, int **ppScores)

DM_AlignedScore(EScoreMatrixType type, int ext)

void CalcPairwiseScores(pProgressFunction pFunc)

void ConvertScoresToDistances()

static const EDistMethod DIST_METHOD

virtual bool ComputeMatrix(pProgressFunction pFunc)

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

ScoreMatrix * m_scoreMatrix

int GetScore(char i, char j)

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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