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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/cuAlignedDM_8cpp_source.html below:

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

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39  int

firstAligned, lastAligned;

66  for

(

int i

=0;

i

<nrows;

i

++) {

85  for

(

int i

= 0;

i

<nrows; ++

i

) {

92  for

(

int i

= 0;

i

<nrows; ++

i

) {

102  for

(

int i

= 0;

i

<nrows; ++

i

) {

111  for

(

int i

= 0;

i

<nrows; ++

i

) {

135  for

(

int i

=0;

i

<nrows;

i

++) {

142  for

(

int i

=0;

i

<nrows; ++

i

) {

144  if

(rowVal > maxVal) {

166  for

(

int i

=0;

i

<alignLen;

i

++) {

167

Res1 = residues[

i

];

int Max(int Val1, int Val2)

int GetMaxScoreForAligned()

static const double FRACTIONAL_EXTRA_OFFSET

CharPtr * m_ppAlignedResidues

int GetMaxScore(CharPtr residues)

MultipleAlignment * m_maligns

bool GetResidueListsWithShifts()

void setData(MultipleAlignment *malign)

void GetAllSequences(vector< string > &sequences)

int GetAlignmentLength(int row=0) const

void GetAlignedResiduesForAll(char **&ppAlignedResidues, bool forceRecompute)

int GetLowerBound(int row) const

int GetUpperBound(int row) const

ScoreMatrix * m_scoreMatrix

AlignmentCollection * m_aligns

std::vector< std::string > m_ConvertedSequences

static const int INITIAL_SCORE_BOUND

void SetData(AlignmentCollection *aligns)

EScoreMatrixType GetType() const

int GetScore(char i, char j)

#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.

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