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NCBI C++ ToolKit: include/gui/widgets/aln_multiple/alnvec_multi_ds.hpp Source File

(

objects::CSeq_annot& annot,

sync =

,

select_anchor =

);

(

objects::CBioseq_Handle& handle,

sync =

,

select_anchor =

);

sync =

,

select_anchor =

);

TNumrow

(

)

;

objects::CSeq_id&

(TNumrow

)

;

objects::CBioseq_Handle& GetBioseqHandle(TNumrow

)

;

try_reverse_dir =

)

;

try_reverse_dir =

)

;

OnAppJobNotification(

* evt);

s_CleanScope();

x_ClearHandles();

x_CreateHandles();

(objects::CAlnVec& aln_vec);

x_IsJobRunning();

x_DeleteJob();

void x_Assign(CObject_id &dst, const CObject_id &src)

CAlnVecMultiDataSource - implementation of IAlnMultiDataSource for CAlnVec-based alignments.

CAlnVecMultiDataSource(const CAlnVecMultiDataSource &ds)

vector< CAlnVecRowHandle * > THandleVector

virtual void Init(const vector< CConstRef< objects::CSeq_align > > &aligns, bool sync=false, bool select_anchor=false)

CAlnVecMultiDataSource(objects::CScope &scope)

CRef< objects::CScope > m_Scope

CRef< objects::CAlnVec > m_AlnVec

virtual bool IsDataReadSync() const

virtual void SetCreateConsensus(bool b)

CRef< CBuildAlnVecJob > m_Job

CAlnVecMultiDataSource & operator=(const CAlnVecMultiDataSource &ds)

CAppJobNotification Notification send by CAppJobEventTranslator.

CEvent - generic event implementation TODO TODO - Attachments.

IAlignRowHandle provides an abstract way to access alignment row data.

IAlnMultiDataSource - interface to a data source representing an abstract multiple alignment.

virtual IAlnExplorer::EAlignType GetAlignType() const =0

virtual void SetGapChar(TResidue gap_char)=0

virtual void GetAlnFromSeq(TNumrow row, const TRangeColl &seq_coll, TRangeColl &aln_coll) const =0

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

virtual const IAlignRowHandle * GetRowHandle(TNumrow row) const =0

virtual bool IsPositiveStrand(TNumrow row) const =0

virtual TSeqPos GetAlnStart(void) const =0

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

virtual bool CanGetId(TNumrow row) const =0

virtual int GetConsensusRow() const =0

returns index of the Consensus row or -1 if it doesn't exist

virtual bool CanChangeAnchor(void) const =0

virtual void GetSeqFromAln(TNumrow row, const TRangeColl &aln_coll, TRangeColl &seq_coll) const =0

IAlnExplorer::TResidue TResidue

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

virtual TNumrow GetNumRows(void) const =0

number of rows in alignment

virtual TSeqPos GetAlnStop(void) const =0

virtual bool SetAnchor(TNumrow anchor)=0

virtual TSeqPos GetSeqStop(TNumrow row) const =0

virtual TSeqPos GetSeqStart(TNumrow row) const =0

virtual bool IsSetAnchor(void) const =0

Anchoring methods.

virtual TNumrow GetAnchor(void) const =0

virtual bool CanCreateConsensus()=0

virtual bool UnsetAnchor(void)=0

virtual bool IsNegativeStrand(TNumrow row) const =0

virtual bool IsEmpty() const =0

virtual void CreateConsensus()=0

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

Alignment segment iterator interface.

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

virtual int GetGenCode(IAlnExplorer::TNumrow row) const =0

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_ALNMULTIPLE_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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