hit_matrix_ds.hpp

ncbi源码

/*
 * ===========================================================================
 * PRODUCTION $Log: hit_matrix_ds.hpp,v $
 * PRODUCTION Revision 1000.2  2004/04/12 18:16:43  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.6
 * PRODUCTION
 * ===========================================================================
 */

#ifndef GUI_WIDGETS_HIT_MATRIX___HIT_MATRIX_DS__HPP
#define GUI_WIDGETS_HIT_MATRIX___HIT_MATRIX_DS__HPP

/*  $Id: hit_matrix_ds.hpp,v 1000.2 2004/04/12 18:16:43 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:  Andrey Yazhuk
 *
 * File Description:
 *
 */

#include <corelib/ncbistd.hpp>

#include <objects/seq/Seq_annot.hpp>
#include <objmgr/scope.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objmgr/bioseq_handle.hpp>
#include <objects/seqalign/Seq_align_set.hpp>
#include <objects/seqalign/Dense_seg.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objects/seqalign/Score.hpp>
#include <serial/iterator.hpp>
#include <gui/widgets/hit_matrix/hit_data_adapter.hpp>

BEGIN_NCBI_SCOPE
USING_SCOPE(objects);

/// CHitMatrixDataSource implements Adapter design pattern. It adapts given 
/// CSeq_annot ot CSeq_align_set object by providing standard interface 
/// representing data as plain list of pair-wise alignments.

class NCBI_GUIWIDGETS_HIT_MATRIX_EXPORT CHitMatrixDataSource
    : public CObject
{
public:
    typedef CConstRef<CSeq_id>  TIdRef;
    typedef vector<TIdRef>        TIdRefCont;
    typedef deque<CHitDataAdapter>  THitAdapterCont;
    

    CHitMatrixDataSource(const CSeq_align_set& aset, CScope& scope);
    CHitMatrixDataSource(const CSeq_annot& annot, CScope& scope);
    virtual ~CHitMatrixDataSource();

    /// returns list of all seq ids in the Data Source
    const TIdRefCont& GetSeqIDs();

    /// selects query and subject from the set of available sequences
    bool    SelectIds(const TIdRef& q_id, const TIdRef& s_id);   
    
    CScope&     GetScope();
    TIdRef      GetQueryId()    const;
    TIdRef      GetSubjectId()  const;
    CBioseq_Handle      GetQueryHandle();
    CBioseq_Handle      GetSubjectHandle();
    
    int     GetScoresCount()    const;
    const   CObject_id&  GetScoreId(size_t index)    const;
        
    const THitAdapterCont&  GetHits()   const;

    TSeqRange   GetQueryHitsRange();
    TSeqRange   GetSubjectHitsRange();
protected:
    void    x_Init(CTypeConstIterator<CSeq_align>& it);

protected:
    typedef vector<const CObject_id*> TObjectIdVector;    

    CConstRef<CSeq_annot>       m_Annot;
    CConstRef<CSeq_align_set>   m_Set;
    CRef<CScope>           m_Scope;
    
    TIdRefCont   m_SeqIds; /// list of Ids for all sequences
    TObjectIdVector     m_ScoreIds;

    TIdRef      m_QueryID;
    TIdRef      m_SubjectID;

    THitAdapterCont m_HitAdapters;

    TSeqRange   m_QueryHitsRange;
    TSeqRange   m_SubjectHitsRange;
};


END_NCBI_SCOPE

/*
 * ===========================================================================
 * $Log: hit_matrix_ds.hpp,v $
 * Revision 1000.2  2004/04/12 18:16:43  gouriano
 * PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.6
 *
 * Revision 1.6  2004/02/12 21:02:06  yazhuk
 * Added data members for storing hit ranges and functions for accessing them
 *
 * Revision 1.5  2003/12/05 17:36:58  yazhuk
 * Added construction from CSeq_Annot, changed API to use const refs instead of CRefs
 *
 * Revision 1.4  2003/12/01 17:01:52  yazhuk
 * Seriously redesigned  CHitMatrixDataSource
 *
 * Revision 1.3  2003/11/18 17:56:06  yazhuk
 * Fixed GCC warnings
 *
 * Revision 1.2  2003/11/18 00:06:42  yazhuk
 * GCC compilation fixes
 *
 * Revision 1.1  2003/11/17 21:00:13  yazhuk
 * Initial revision
 *
 * ===========================================================================
 */

#endif  // GUI_WIDGETS_HIT_MATRIX___HIT_MATRIX_DS__HPP