1 #ifndef GUI_WIDGETS_ALN_MULTIPLE___ALNVEC_MULTI_DS__HPP
2 #define GUI_WIDGETS_ALN_MULTIPLE___ALNVEC_MULTI_DS__HPP
59 virtual void Init(
const objects::CSeq_annot& annot,
bool sync =
false,
bool select_anchor =
false);
60 virtual void Init(
const objects::CBioseq_Handle& handle,
bool sync =
false,
bool select_anchor =
false);
62 bool sync =
false,
bool select_anchor =
false);
96 virtual const objects::CSeq_id&
GetSeqId(TNumrow
row)
const;
97 virtual const objects::CBioseq_Handle& GetBioseqHandle(TNumrow
row)
const;
107 bool try_reverse_dir =
true)
const;
110 bool try_reverse_dir =
true)
const;
133 void OnAppJobNotification(
CEvent* evt);
135 static void s_CleanScope();
139 virtual void x_ClearHandles();
140 virtual void x_CreateHandles();
141 virtual void x_Assign(objects::CAlnVec& aln_vec);
143 virtual bool x_IsJobRunning();
144 virtual void 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
range(_Ty, _Ty) -> range< _Ty >
static bool GetSeqId(const T &d, set< string > &labels, const string name="", bool detect=false, bool found=false)
#define row(bind, expected)