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

m_src(0), m_numRows(0), m_extensibilities(0), m_extendedBlocks(0), m_scoringMatrix(0),

m_nExt(0), m_cExt(0), m_extensionScores(0)

m_src(ma), m_numRows(0), m_extendedBlocks(0), m_scoringMatrix(sm), m_nExt(0), m_cExt(0),

extended =

;

blockExtension = 0;

(

= 0;

< nBlocks;

++)

(blockExtension != 0) {

blockScore = 0.0;

(tmpScore > blockScore)

blockScore = tmpScore;

(tmpScore > blockScore)

blockScore = tmpScore;

extension = -nExt + cExt;

bm1.

()[block].extendSelf(nExt, cExt);

bm2.

()[block].extendSelf(nExt, cExt);

(

= 0;

< term1.first.getLen();

++)

vector<Block>&

=

.getBlocks();

(blockNum >=

.size() || blockNum < 0 ||

.size() == 0)

extFootprintLo =

.getFirstAlignedPosition() -

;

(extFootprintLo < 0)

minStart = (blockNum == 0) ? extFootprintLo :

[blockNum-1].getEnd() + 1;

extFootprintHi =

.getLastAlignedPosition() +

;

maxEnd = (blockNum ==

.size()-1) ? extFootprintHi :

[blockNum+1].getStart() - 1;

= rows.size();

primaryRow = rows[0];

, blockExtension;

nBlocks = primaryBlockModel.

().size();

(

= 1;

<

;

++) {

(

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

score +=

(primaryRow,

, j, primaryBlockModel, secondaryBlockModel, blockExtension);

void GetAllSequences(vector< string > &sequences)

bool setMatrixForExtensionScores(double **matrix, int matrixSize)

MultipleAlignment * m_src

double ** m_extensionScores

int findCommonExtension(const vector< int > &rows)

pair< Block, int > ScoringTerm

BlockModel ** m_extendedBlocks

void setScoringMatrix(ScoreMatrix *sm)

void setCTermExt(int ext)

bool isThisPairExtended(int primaryRow, int secondaryRow) const

bool getScoringTerm(BlockModel &bm, int blockNum, int nExt, int cExt, ScoringTerm &st)

bool extendOnePair(int primaryRow, int secondaryRow)

void setNTermExt(int ext)

double optimizeBlockScore(int row1, int row2, int block, int &extension)

int getTotalLengthExtended(int primaryRow, int secondaryRow) const

void setAlignments(MultipleAlignment *ma)

std::vector< std::string > m_sequences

double scoreBlockPair(const ScoringTerm &term1, const ScoringTerm &term)

ScoreMatrix * m_scoringMatrix

void addOneAlignment(const BlockModel &bm)

BlockModel * getIntersectedAlignment(double rowFraction=1.0)

int getTotalBlockLength() const

vector< Block > & getBlocks()

Block extend(int nExt, int cExt) const

const cd_utils::BlockModel & getBlockModel(int row) 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.

const struct ncbi::grid::netcache::search::fields::SIZE size

static SLJIT_INLINE sljit_ins st(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

#define row(bind, expected)

static DP_BlockInfo * blocks

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