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NCBI C++ ToolKit: include/gui/widgets/seq_graphic/alnvec_graphic_ds.hpp Source File

try_reverse_dir =

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;

try_reverse_dir =

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;

CAlnVecGraphicDataSource - implementation of CAlnGraphicDataSource for CAlnVec-based alignments.

virtual const TCigar * GetCigar() const

Get CIGAR vector.

virtual bool HasCigar() const

Check if there is a CIGAR string.

CConstRef< objects::CAlnVec > m_AlnVec

CAlnVecGraphicDataSource(const CAlnVecGraphicDataSource &ds)

CAlnVecGraphicDataSource & operator=(const CAlnVecGraphicDataSource &ds)

virtual EPolyATail HasPolyATail() const

Check if there is any unaligned polyA tail.

CAppJobNotification Notification send by CAppJobEventTranslator.

ESearchDirection

Position search options.

IAlnGraphicDataSource - interface to a data source representing an abstract alignment used in graphic...

vector< TCigarPair > TCigar

virtual TSignedRange GetAlnRange(void) const =0

virtual TSignedSeqPos GetSeqPosFromSeqPos(TNumrow for_row, TNumrow row, TSeqPos seq_pos) const =0

virtual IAlnExplorer::EAlignType GetAlignType() const

virtual bool IsNegativeStrand(TNumrow row) const =0

virtual const objects::CBioseq_Handle & GetBioseqHandle(IAlnExplorer::TNumrow row) const =0

IAlnExplorer::TNumrow TNumrow

EPolyATail

Cetantiy of having unaligned polyA tail.

virtual TSeqPos GetSeqStart(TNumrow row) const =0

virtual TSignedRange GetSeqAlnRange(TNumrow row) const =0

virtual bool IsPositiveStrand(TNumrow row) const =0

virtual TSeqPos GetSeqStop(TNumrow row) const =0

virtual TSignedSeqPos GetAlnPosFromSeqPos(TNumrow row, TSeqPos seq_pos, IAlnExplorer::ESearchDirection dir=IAlnExplorer::eNone, bool try_reverse_dir=true) const =0

Alignment segment iterator interface.

virtual TSeqPos GetAlnStart() const =0

virtual TSeqPos GetBaseWidth(IAlnExplorer::TNumrow) const =0

virtual TSeqPos GetAlnStop() const =0

virtual string & GetAlnSeqString(IAlnExplorer::TNumrow row, string &buffer, const IAlnExplorer::TSignedRange &aln_range) const =0

virtual IAlnExplorer::TNumrow GetNumRows() const =0

virtual IAlnExplorer::TNumrow GetAnchor() const =0

virtual IAlnSegmentIterator * CreateSegmentIterator(IAlnExplorer::TNumrow, const IAlnExplorer::TSignedRange &, IAlnSegmentIterator::EFlags) const =0

virtual TSignedSeqPos GetSeqPosFromAlnPos(IAlnExplorer::TNumrow for_row, TSeqPos aln_pos, IAlnExplorer::ESearchDirection dir=IAlnExplorer::eNone, bool try_reverse_dir=true) const =0

int GetSeqLength(const CBioseq &bioseq)

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.

#define NCBI_GUIWIDGETS_SEQGRAPHIC_EXPORT

static bool GetSeqId(const T &d, set< string > &labels, const string name="", bool detect=false, bool found=false)

#define row(bind, expected)

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