alnmulti_ds.hpp

ncbi源码

/*
 * ===========================================================================
 * PRODUCTION $Log: alnmulti_ds.hpp,v $
 * PRODUCTION Revision 1000.3  2004/04/12 18:15:52  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.12
 * PRODUCTION
 * ===========================================================================
 */

#ifndef GUI_WIDGETS_ALN_MULTIPLE___ALN_MULTI_DS__HPP
#define GUI_WIDGETS_ALN_MULTIPLE___ALN_MULTI_DS__HPP

/*  $Id: alnmulti_ds.hpp,v 1000.3 2004/04/12 18:15:52 gouriano Exp $
 * ===========================================================================
 *
 *                            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:  Mike DiCuccio
 *
 * File Description:
 *
 */

#include <corelib/ncbistd.hpp>
#include <corelib/ncbiobj.hpp>

#include <objects/seqloc/Seq_loc.hpp>
#include <gui/widgets/aln_data/align_ds.hpp>

BEGIN_NCBI_SCOPE
USING_SCOPE(ncbi::objects);

/// IAlignRowHandle provides an abstract way to access alignment row data.
///
/// IAlignRowHandle-inherited classes are supposed to provide proprietary
/// interface depending on the nature of data being represented.
class NCBI_GUIWIDGETS_ALNMULTIPLE_EXPORT IAlignRowHandle
{
protected:
    virtual ~IAlignRowHandle() {}
};


/// IAlnMultiDataSource - interface to a data source representing abstract
/// multiple alignment.
class NCBI_GUIWIDGETS_ALNMULTIPLE_EXPORT IAlnMultiDataSource
{
public:
    typedef CAlnVec::TNumrow   TNumrow;
    typedef CAlnVec::TResidue  TResidue;
    typedef CAlnMap                   TSearchDirection;
    typedef CAlnMap::ESearchDirection ESearchDirection;

public:
    /// number of rows in alignment
    virtual TNumrow  GetNumRows (void) const = 0;    
    virtual TSeqPos  GetAlnStart (void) const = 0; 
    virtual TSeqPos  GetAlnStop (void) const = 0;

    /// returns index of the Consensus row or -1 if it doesn't exist
    virtual int     GetConsensusRow() const = 0;
    virtual const IAlignRowHandle*  GetRowHandle(TNumrow row) const = 0;
    
    /// Anchoring methods 
    virtual bool  IsSetAnchor (void) const = 0;
    virtual TNumrow  GetAnchor (void) const = 0; 
    virtual void  SetAnchor (TNumrow anchor) = 0; 
    virtual void  UnsetAnchor (void) = 0;
    
    virtual bool    CanGetId(TNumrow row) const = 0;
    virtual const CSeq_id&  GetSeqId(TNumrow row) const = 0;
    
    virtual TSignedSeqPos  GetSeqPosFromAlnPos(TNumrow for_row, TSeqPos aln_pos,
                                ESearchDirection dir=TSearchDirection::eNone,
                                bool try_reverse_dir=true) const = 0;
    
    virtual TSignedSeqPos  GetAlnPosFromSeqPos(TNumrow row, TSeqPos seq_pos, 
                                ESearchDirection dir=TSearchDirection::eNone,
                                bool try_reverse_dir=true) const = 0;
};

END_NCBI_SCOPE

/*
 * ===========================================================================
 * $Log: alnmulti_ds.hpp,v $
 * Revision 1000.3  2004/04/12 18:15:52  gouriano
 * PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.12
 *
 * Revision 1.12  2003/12/10 19:03:20  yazhuk
 * Added const specifier to CanGetId() and GetSeqId().
 *
 * Revision 1.11  2003/12/10 17:04:36  yazhuk
 * Changed row identification from mandatory CBioseqHandle to optional CSeq_id.
 * Clean-up
 *
 * Revision 1.10  2003/11/26 16:52:53  johnson
 * switch IAlnMultiDataSource to use CAlnMap::ESearchDirection instead of it's
 * own ESearchDirection
 *
 * Revision 1.9  2003/11/17 21:12:46  yazhuk
 * Moved SetGapChar() to CAlnVecMultiDataSource
 *
 * Revision 1.8  2003/10/29 23:27:05  yazhuk
 * Replaced CAlnMultiDataSource with IAlnMultiDataSource
 *
 * Revision 1.7  2003/09/25 20:43:47  yazhuk
 * Moved consensus row support to CAlignDataSource
 *
 * Revision 1.6  2003/09/24 18:19:50  dicuccio
 * Inherit data source from generic data source, removing many redundant data
 * members / functions
 *
 * Revision 1.5  2003/09/23 21:53:44  yazhuk
 * Added support for consensus row
 *
 * Revision 1.4  2003/09/16 14:37:13  dicuccio
 * Cleaned up and clarified export specifiers - added a new specifier for each
 * library
 *
 * Revision 1.3  2003/09/12 12:59:14  dicuccio
 * Added export specifiers.  Inlined virtual dtors for interface classes
 *
 * Revision 1.2  2003/08/28 18:23:47  yazhuk
 * Modified to be used with new CAlnMultiWidget
 *
 * Revision 1.1  2003/07/14 17:37:18  dicuccio
 * Initial revision
 *
 * ===========================================================================
 */

#endif  // GUI_WIDGETS_ALN_MULTIPLE___ALN_MULTI_DS__HPP