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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/cuFlexiDm_8cpp_source.html below:

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

50

: m_rows(numRows,

RowContent

()), m_numRows(numRows)

56

vector<char> residues;

59  for

(

unsigned row

= 0;

row

< residues.size();

row

++)

69

seqPair.first.reserve(rc1.size());

70

seqPair.second.reserve(rc2.size());

72  for

(

unsigned int i

= 0;

i

< rc1.size();

i

++)

74  if

(rc1[

i

].aligned && rc2[

i

].aligned)

76

seqPair.first += rc1[

i

].residue;

77

seqPair.second += rc2[

i

].residue;

131  for

(

int i

= 1;

i

< nrows;

i

++)

142  int

Identity, TotalAligned;

144  int

total = (

int

)((

double

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

147  for

(

int

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

152  for

(

int

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

157  for

(

unsigned int i

= 0;

i

< rc1.size();

i

++)

159  if

(rc1[

i

].aligned && rc2[

i

].aligned)

162  if

(rc1[

i

].residue == rc2[

i

].residue)

176  count

+= nrows - (j+1);

177

pFunc(

count

, total);

string GetSequenceForRow(int row)

CRef< CSeq_align > getSeqAlign(int row) const

void getResiduesByRow(vector< char > &residues, bool byNcbiStd=true) const

bool isAligned(char residue, int row) const

ScoreMatrix * m_scoreMatrix

AlignmentCollection * m_aligns

static const EDistMethod DIST_METHOD

bool ComputeMatrix(pProgressFunction pFunc)

FlexiDm(EScoreMatrixType type=GLOBAL_DEFAULT_SCORE_MATRIX, int uniformLength=-1)

static const double MAX_DISTANCE

static double GetDistance(int identities, int alignment_length)

void initDMIdentities(EScoreMatrixType type, int nExt=0, int cExt=0)

void GetPercentIdentities(pProgressFunction pFunc)

bool getAlignedPair(unsigned row1, unsigned row2, pair< string, string > &seqPair)

void read(ColumnResidueProfile &crp)

vector< RowContent > m_rows

RowContent & getRow(int row)

vector< ResidueCell > RowContent

void traverseColumnsOnMaster(ColumnReader &cr)

void addOneRow(BlockModelPair &bmp, const string &mSeq, const string &sSeq)

@ ePercentIdentityRelaxed

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

thread_local unique_ptr< FtaMsgPost > bmp

#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.

#define row(bind, expected)

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