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

q_index,

s_index,

m_QueryIndex(q_index),

m_SubjectIndex(s_index)

(align.GetSegs().IsStd());

list< CRef< CStd_seg > >

;

& std_list = align.GetSegs().GetStd();

objects::CSeq_align::TScore& scores =

->GetScore();

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

objects::CScore& score = **itS;

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

objects::CScore::TValue&

= score.GetValue();

(

.Which()) {

objects::CScore::TValue::e_Real:

.GetReal();

;

objects::CScore::TValue::e_Int:

.GetInt();

;

m_QueryStrand(q_strand),

m_SubjectStrand(s_strand)

EDirection

Row direction flags.

@ eDirect

Use only sequences whose strand is the same as that of the anchor.

@ eReverse

Use only sequences whose strand is opposite to that of the anchor.

CStdSegHitElement - IHitElement implementation for CStd_seg-based alignments.

virtual TSeqPos GetSubjectLength() const

virtual const IHit & GetHit() const

virtual objects::ENa_strand GetQueryStrand() const

objects::ENa_strand m_SubjectStrand

objects::ENa_strand m_QueryStrand

virtual ~CStdSegHitElement()

virtual objects::ENa_strand GetSubjectStrand() const

virtual TSignedSeqPos GetSubjectStart() const

virtual TSignedSeqPos GetQueryStart() const

virtual TSeqPos GetQueryLength() const

Wraps a CSeq_align containing CStd_seg and provides a simple API for interpreting it as a pairwise al...

static bool HasAlignment(const TStd &std_list, size_t q_index, size_t s_index, TDirection dir)

objects::CSeq_align::TSegs::TStd TStd

virtual double GetScoreValue(const string &score_name) const

CStdSegHit(const objects::CSeq_align &align, int q_index, int s_index)

CConstRef< objects::CSeq_align > m_SeqAlign

virtual const IHitElement & GetElem(TDim elem_index) const

virtual const objects::CSeq_align * GetSeqAlign() const

virtual TDim GetElemsCount() const

CRange< TSignedSeqPos > GetSeqRange(TDim row) const

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.

ENa_strand GetStrand(void) const

Get the location's strand.

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

position_type GetLength(void) const

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

TFrom GetFrom(void) const

Get the From member data.

const TLoc & GetLoc(void) const

Get the Loc member data.

TDim GetDim(void) const

Get the Dim member data.

bool IsEmpty(void) const

Check if variant Empty is selected.

ENa_strand

strand of nucleic acid

static int match(PCRE2_SPTR start_eptr, PCRE2_SPTR start_ecode, uint16_t top_bracket, PCRE2_SIZE frame_size, pcre2_match_data *match_data, match_block *mb)

USING_SCOPE(ncbi::objects)

bool IsStrandGood(ENa_strand strand)

CStdSegHit.

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