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NCBI C++ ToolKit: src/gui/widgets/seq_graphic/sparsealn_graphic_ds.cpp Source File

: m_Alignment(sparseAlign)

try_reverse_dir)

try_reverse_dir)

virtual bool IsNegativeStrand(TNumrow row) const

CConstRef< CSparseAln > m_Alignment

virtual TSeqPos GetAlnStart(void) const

virtual TSeqPos GetSeqStart(TNumrow row) const

virtual TSeqPos GetBaseWidth(TNumrow row) const

virtual TNumrow GetAnchor(void) const

IAlnExplorer::TNumrow TNumrow

virtual TSignedSeqPos GetAlnPosFromSeqPos(TNumrow row, TSeqPos seq_pos, IAlnExplorer::ESearchDirection dir=IAlnExplorer::eNone, bool try_reverse_dir=true) const

virtual string & GetAlnSeqString(TNumrow row, string &buffer, const TSignedRange &aln_rng) const

virtual bool IsPositiveStrand(TNumrow row) const

virtual TSeqPos GetSeqStop(TNumrow row) const

CSparseAlnGraphicDataSource(CConstRef< CSparseAln > sparseAlign)

CSparseAlnGraphicDataSource.

virtual const objects::CSeq_id & GetSeqId(TNumrow row) const

virtual TSeqPos GetAlnStop(void) const

virtual IAlnSegmentIterator * CreateSegmentIterator(TNumrow row, const TSignedRange &range, IAlnSegmentIterator::EFlags flag) const

virtual TSignedSeqPos GetSeqPosFromSeqPos(TNumrow for_row, TNumrow row, TSeqPos seq_pos) const

virtual TSignedRange GetAlnRange(void) const

virtual TSeqPos GetSeqLength(TNumrow row) const

virtual TSignedRange GetSeqAlnRange(TNumrow row) const

virtual TSignedSeqPos GetSeqPosFromAlnPos(TNumrow for_row, TSeqPos aln_pos, IAlnExplorer::ESearchDirection dir=IAlnExplorer::eNone, bool try_reverse_dir=true) const

virtual TNumrow GetNumRows(void) const

number of rows in alignment

virtual ~CSparseAlnGraphicDataSource()

virtual const objects::CBioseq_Handle & GetBioseqHandle(TNumrow row) const

TRng GetAlnRange(void) const

Get whole alignment range.

TNumrow GetNumRows(void) const

Synonym of the above.

int GetBaseWidth(TNumrow row) const

Get base width for the sequence (1 for nucleotides, 3 for proteins).

TSeqPos GetSeqStop(TNumrow row) const

virtual IAlnSegmentIterator * CreateSegmentIterator(TNumrow row, const TSignedRange &range, IAlnSegmentIterator::EFlags flags) const

Create segment iterator.

string & GetAlnSeqString(TNumrow row, string &buffer, const TSignedRange &rq_aln_rng, bool force_translation=false) const

Fetch alignment sequence data.

TSignedSeqPos GetAlnPosFromSeqPos(TNumrow row, TSeqPos seq_pos, ESearchDirection dir=eNone, bool try_reverse_dir=true) const

Map sequence position to alignment coordinates.

TSignedSeqPos GetSeqPosFromAlnPos(TNumrow for_row, TSeqPos aln_pos, ESearchDirection dir=eNone, bool try_reverse_dir=true) const

bool IsPositiveStrand(TNumrow row) const

Check direction of the row.

const objects::CBioseq_Handle & GetBioseqHandle(TNumrow row) const

Get bioseq handle for the row.

TNumrow GetAnchor(void) const

Get anchor row index.

TSeqPos GetSeqStart(TNumrow row) const

TSignedRange GetSeqAlnRange(TNumrow row) const

Get sequence range in alignment coords (strand ignored).

bool IsNegativeStrand(TNumrow row) const

const objects::CSeq_id & GetSeqId(TNumrow row) const

Get seq-id for the row.

ESearchDirection

Position search options.

IAlnExplorer::TNumrow TNumrow

Alignment segment iterator interface.

unsigned int TSeqPos

Type for sequence locations and lengths.

int TSignedSeqPos

Type for signed sequence position.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

USING_SCOPE(ncbi::objects)

#define row(bind, expected)

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