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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/diag__hit_8cpp_source.html below:

NCBI C++ ToolKit: src/gui/widgets/hit_matrix/diag_hit.cpp Source File

81

: m_SeqAlign(&seq_align),

84 size_t n

= pr_align.

size

();

86 for

(

size_t i

= 0;

;

++ ) {

112 const

objects::CSeq_align::TScore& scores =

m_SeqAlign

->GetScore();

113 ITERATE

(objects::CSeq_align::TScore, itS, scores) {

114 const

objects::CScore& score = **itS;

117 if

(score.GetId().GetStr() == score_name) {

118 const

objects::CScore::TValue&

val

= score.GetValue();

119 switch

(

val

.Which()) {

120 case

objects::CScore::TValue::e_Real:

return val

.GetReal();

break

;

121 case

objects::CScore::TValue::e_Int:

return val

.GetInt();

break

;

153 _ASSERT

(index < m_Hit->m_Aln->size());

CAlignRange Represents an element of pairwise alignment of two sequences.

virtual ~CDiagHitElement()

virtual TSeqPos GetQueryLength() const

virtual TSeqPos GetSubjectLength() const

virtual objects::ENa_strand GetSubjectStrand() const

virtual objects::ENa_strand GetQueryStrand() const

virtual const IHit & GetHit() const

virtual TSignedSeqPos GetSubjectStart() const

void Init(const CDiagHit *hit, size_t index)

const TAlnRange & x_GetAlnRange() const

virtual TSignedSeqPos GetQueryStart() const

const CPairwiseAln & x_GetAln() const

virtual const IHitElement & GetElem(TDim elem_index) const

virtual const objects::CSeq_align * GetSeqAlign() const

virtual double GetScoreValue(const string &score_name) const

CDiagHit(const objects::CSeq_align &seq_align, const CPairwiseAln &pr_align)

CDiagHit.

virtual TDim GetElemsCount() const

const objects::CSeq_align * m_SeqAlign

A pairwise aln is a collection of ranges for a pair of rows.

USING_SCOPE(ncbi::objects)

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

int TSignedSeqPos

Type for signed sequence position.

position_type GetSecondFrom(void) const

position_type GetFirstFrom(void) const

position_type GetLength(void) const

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

ENa_strand

strand of nucleic acid

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