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

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41

: m_seqAlignVec(seqAlignVec), m_masterLen(masterSeqLen), m_intersector(0)

62  int

refAlignmentLen = 0;

66

refAlignmentLen =

bm

.getTotalBlockLength();

72

refAlignmentLen =

bm

.getTotalBlockLength();

74

percentages.push_back(100);

83

percentages.push_back(score);

100  int

minAlignedLen = 0;

107

minAlignedLen =

bm

.getTotalBlockLength() * overlappingPercentage/100;

113

minAlignedLen =

bm

.getTotalBlockLength() * overlappingPercentage/100;

130  delete

intersectedBM;

153

list< CRef< CSeq_align > >::iterator lit = seqAlignList.begin();

154  for

(; lit != seqAlignList.end(); lit++)

170

pair<cd_utils::DeltaBlockModel*, bool>

delta

= guide -

bmp

.getMaster();

171

cd_utils::BlockModel& slave =

bmp

.getSlave();

172

pair<cd_utils::BlockModel*, bool> sum = slave + (*

delta

.first);

BlockIntersector * m_intersector

void setReferenceSeqAlign(const CRef< CSeq_align > sa)

int getQualifiedRows(vector< int > &rows)

void formatBlocksForQualifiedRows(list< CRef< CSeq_align > > &seqAlignVec, const set< int > *forcedBreaks=NULL)

vector< CRef< CSeq_align > > & m_seqAlignVec

int getDisqualifiedRows(vector< int > &rows)

CRef< CSeq_align > m_refSeqAlign

int findIntersectingBlocks(int overlappinPercentage=-1)

CRef< CSeq_align > formatOneRow(const BlockModel &guide, CRef< CSeq_align > seqAlign)

void getOverlappingPercentages(vector< int > &percentages)

void addOneAlignment(const BlockModel &bm)

BlockModel * getIntersectedAlignment(double rowFraction=1.0)

void removeOneAlignment(const BlockModel &bm)

int getTotalBlockLength() const

thread_local unique_ptr< FtaMsgPost > bmp

bool Empty(void) const THROWS_NONE

Check if CRef is empty – not pointing to any object, which means having a null value.

#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.

Int4 delta(size_t dimension_, const Int4 *score_)

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