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

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objects::CSeq_align& align, objects::CScope& scope,

anchor)

(align.CheckNumRows() == 2);

objects::CBioseq_Handle&

try_reverse_dir)

try_reverse_dir)

anchor_direct)

virtual TSeqPos GetSeqStop(TNumrow row) const

virtual TSeqPos GetAlnStart(void) const

virtual TNumrow GetNumRows(void) const

virtual TSeqPos GetSeqLength(TNumrow row) const

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

virtual TSignedRange GetAlnRange(void) const

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

CRef< objects::CScope > m_Scope

virtual string & GetSeqString(string &buffer, TNumrow row, const TSignedRange &seq_rng, const TSignedRange &aln_rng, bool anchor_direct) const

Get sequence string for a given row in sequence range.

virtual TNumrow GetAnchor(void) const

virtual TSeqPos GetSeqStart(TNumrow row) const

IAlnExplorer::TNumrow TNumrow

virtual bool IsRegular() const

virtual TSeqPos GetAlnStop(void) const

map< TNumrow, objects::CBioseq_Handle > m_BioseqHandles

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

virtual TSignedRange GetSeqAlnRange(TNumrow row) const

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

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

CConstRef< objects::CSeq_align > m_Alignment

virtual EPolyATail HasPolyATail() const

Check if there is any unaligned polyA tail.

virtual bool IsPositiveStrand(TNumrow row) const

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

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

CSimpleGraphicDataSource(const objects::CSeq_align &align, objects::CScope &scope, TNumrow anchor)

CSimpleGraphicDataSource.

virtual TSeqPos GetBaseWidth(TNumrow row) const

virtual bool IsNegativeStrand(TNumrow row) const

TSignedRange m_EmptyRange

virtual TSegTypeFlags GetType(void) const

Get current segment type.

virtual const TSignedRange & GetRange(void) const

Get the selected row range.

virtual const TSignedRange & GetAlnRange(void) const

Get alignment range for the segment.

Fake segment iterator that always returns no segment.

virtual bool operator==(const IAlnSegmentIterator &it) const

Compare iterators.

virtual IAlnSegmentIterator & operator++(void)

Advance to the next segment.

virtual IAlnSegmentIterator * Clone(void) const

Create a copy of the iterator.

virtual bool operator!=(const IAlnSegmentIterator &it) const

virtual ~CSimpleSeg_CI(void)

virtual const value_type * operator->(void) const

virtual const value_type & operator*(void) const

CSimpleSeg_CI(void)

Create 'empty' iterator.

ESearchDirection

Position search options.

IAlnExplorer::TSignedRange TSignedRange

IAlnExplorer::TNumrow TNumrow

EPolyATail

Cetantiy of having unaligned polyA tail.

virtual string & GetSeqString(string &buffer, TNumrow row, const TSignedRange &seq_rng, const TSignedRange &aln_rng, bool anchor_direct) const

Get sequence string for a given row in sequence range.

Alignment segment iterator interface.

Alignment segment interface.

@ fInvalid

The iterator is in bad state.

unsigned int TSeqPos

Type for sequence locations and lengths.

int TSignedSeqPos

Type for signed sequence position.

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

USING_SCOPE(ncbi::objects)

#define row(bind, expected)

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