NCBI C++ Toolkit Cross Reference

  C++/include/gui/widgets/seq_graphic/alnvec_graphic_ds.hpp


#ifndef GUI_WIDGETS_SEQ_GRAPHIC___ALNVEC_GRAPHIC_DS__HPP #define GUI_WIDGETS_SEQ_GRAPHIC___ALNVEC_GRAPHIC_DS__HPP /* $Id: alnvec_graphic_ds.hpp 37049 2016-11-30 19:40:50Z shkeda $ * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * Authors: Liangshou Wu * * File Description: */ #include <objtools/alnmgr/alnvec.hpp> #include <objects/seqalign/Seq_align.hpp> #include <gui/utils/event_handler.hpp> #include <gui/widgets/seq_graphic/alngraphic_ds.hpp> BEGIN_NCBI_SCOPE class CAppJobNotification; //////////////////////////////////////////////////////////////////////////////// /// CAlnVecGraphicDataSource - implementation of CAlnGraphicDataSource for /// CAlnVec-based alignments. class NCBI_GUIWIDGETS_SEQGRAPHIC_EXPORT CAlnVecGraphicDataSource : public IAlnGraphicDataSource , public CEventHandler { public: CAlnVecGraphicDataSource(const objects::CAlnVec& aln_mgr); ~CAlnVecGraphicDataSource(); /// @name CAlnGraphicDataSource implementation /// @{ virtual IAlnExplorer::EAlignType GetAlignType() const; virtual TNumrow GetNumRows(void) const; virtual TSeqPos GetAlnStart(void) const; virtual TSeqPos GetAlnStop(void) const; virtual TSeqPos GetSeqStart(TNumrow row) const; virtual TSeqPos GetSeqStop(TNumrow row) const; virtual TSignedRange GetAlnRange(void) const; virtual TSignedRange GetSeqAlnRange(TNumrow row) const; virtual TSeqPos GetSeqLength(TNumrow row) const; virtual TSeqPos GetBaseWidth(TNumrow row) const; virtual TNumrow GetAnchor (void) const; virtual const objects::CSeq_id& GetSeqId(TNumrow row) const; virtual const objects::CBioseq_Handle& GetBioseqHandle(TNumrow row) const; virtual bool IsPositiveStrand(TNumrow row) const; virtual bool IsNegativeStrand(TNumrow row) const; virtual TSignedSeqPos GetSeqPosFromAlnPos(TNumrow for_row, TSeqPos aln_pos, TSearchDirection dir = IAlnExplorer::eNone, bool try_reverse_dir = true) const; 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_range) const; virtual IAlnSegmentIterator* CreateSegmentIterator(TNumrow row, const TSignedRange& range, IAlnSegmentIterator::EFlags flags) const; virtual TSignedSeqPos GetSeqPosFromSeqPos(TNumrow for_row, TNumrow row, TSeqPos seq_pos) const; virtual EPolyATail HasPolyATail() const { return ePolyA_Unknown; }; virtual bool HasCigar() const { return false; } virtual const TCigar* GetCigar() const { return NULL; } /// @} private: // prohibit copying! CAlnVecGraphicDataSource(const CAlnVecGraphicDataSource& ds); CAlnVecGraphicDataSource& operator=(const CAlnVecGraphicDataSource& ds); protected: CConstRef<objects::CAlnVec> m_AlnVec; }; END_NCBI_SCOPE #endif // GUI_WIDGETS_SEQ_GRAPHIC___ALNVEC_GRAPHIC_DS__HPP

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