feature.hpp

ncbi源码

/*
 * ===========================================================================
 * PRODUCTION $Log: feature.hpp,v $
 * PRODUCTION Revision 1000.0  2004/06/01 19:54:56  gouriano
 * PRODUCTION PRODUCTION: IMPORTED [GCC34_MSVC7] Dev-tree R1.4
 * PRODUCTION
 * ===========================================================================
 */

#ifndef GUI_OBJUTILS___FEATURE__HPP
#define GUI_OBJUTILS___FEATURE__HPP

/*  $Id: feature.hpp,v 1000.0 2004/06/01 19:54:56 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:
 *    CLayoutFeat -- utility class to arrange CSeq_feat objects in hierarchical
 *                (tree) order.
 */


#include <corelib/ncbiobj.hpp>
#include <gui/gui.hpp>
#include <gui/objutils/layout.hpp>
#include <objmgr/feat_ci.hpp>
#include <objects/seqfeat/SeqFeatData.hpp>
#include <objects/seqfeat/Seq_feat.hpp>
#include <objects/seqloc/Seq_loc.hpp>

#include <list>

/** @addtogroup GUI_OBJUTILS
 *
 * @{
 */



BEGIN_NCBI_SCOPE


//
// Class for storing a set of nested features.
// A feature describes the genetic location in true gene coordinates of any
// sort of genetic object (gene / protein / RNA / etc).  Each feature has an
// overall extent as well as a series of subregions
//

class NCBI_GUIOBJUTILS_EXPORT CLayoutFeat : public CLayoutObject
{
public:
    typedef vector< CRef<CLayoutFeat> > TFeatList;

    // ctors
    CLayoutFeat(const objects::CMappedFeat& feat);

    //
    // pure virtual requirements
    //

    // Access the feature's remapped location
    const objects::CSeq_loc& GetLocation(void) const;

    // Comparators
    bool LessByPos (const CLayoutObject& obj) const;
    bool LessBySize(const CLayoutObject& obj) const;

    // retrieve the type of this object
    EType GetType() const;

    //
    // type-sepcific accessors
    //

    // Retrieve the feature as an object.  For safety's sake,
    // this returns the remapped feature.
    const CObject* GetObject(TSeqPos pos) const;
    
    bool HasObject(const CObject* obj) const;

    // Access the original feature.  The location on this feature
    // may not be correct, as it hasn't been remapped
    const objects::CSeq_feat&        GetFeature(void) const;

    // Access a new, fully remapped feature
    // This is useful for passing exact features to plugins
    const objects::CMappedFeat&      GetMappedFeature(void) const;

    // Access the size of this feature
    TSeqPos                 size(void) const;

    // Access the sub-intervals in this feature
    const vector<TSeqRange>&   GetIntervals(void) const;

    // Access a text string describing this feature
    //const string&           GetTextId(void) const;

    // Accessors for parent-child relationships in features
    const CLayoutFeat*      GetParent  (void) const;
    const TFeatList&        GetChildren(void) const;

    void                    SetParent(CLayoutFeat* feat);
    TFeatList&              SetChildren(void);

    bool                    IsHiddenLabel(void) const;
    void                    HideLabels();

protected:
    // we store a mapped feature object
    objects::CMappedFeat    m_Feature;
    bool                    m_HideLabel;
    
    // parent / child relationships for this feature
    CLayoutFeat*            m_Parent;
    TFeatList               m_Children;

    // some sort of identifier for this gene
    // this is usually a locus name
    //string                  m_TextId;

    // individual features in this range
    mutable vector<TSeqRange>  m_Intervals;

    // calculate our intervals
    void    x_CalcIntervals(void) const;
};


//
// Predicates for sorting gene info
//

//
// SFeatureBySize()
// arrange features by length of (extent of) feature
//
struct NCBI_GUIOBJUTILS_EXPORT SFeatureBySize
{
    bool operator() (const CLayoutFeat& g0, const CLayoutFeat& g1) const {
        return (g0.size() > g1.size());
    }

    bool operator() (const CLayoutFeat* g0, const CLayoutFeat* g1) const {
        return (g0->size() > g1->size());
    }
};


//
// SFeatureByPos()
// arrange features by position.  in essence, this sorts features as a
// CSeq_feat is sorted
//
struct NCBI_GUIOBJUTILS_EXPORT SFeatureByPos
{
    bool operator() (const CLayoutFeat& g0, const CLayoutFeat& g1) const {
        return (g0.GetFeature().Compare(g1.GetFeature(),
                                        g0.GetLocation(),
                                        g1.GetLocation()) < 0);
    }
    bool operator() (const CLayoutFeat* g0, const CLayoutFeat* g1) const {
        return (*this)(*g0, *g1);
    }
};



inline
bool CLayoutFeat::IsHiddenLabel(void) const
{
    return m_HideLabel;
}


inline
void CLayoutFeat::HideLabels()
{
    m_HideLabel = true;
}


inline
const objects::CSeq_feat& CLayoutFeat::GetFeature(void) const
{
    return m_Feature.GetOriginalFeature();
}


inline
const CObject* CLayoutFeat::GetObject(TSeqPos pos) const
{
    TSeqRange r = GetLocation().GetTotalRange();
    if (pos >= r.GetFrom()  &&  pos <= r.GetTo()) {
        return &m_Feature.GetOriginalFeature();
    }
    return NULL;
}


inline
bool CLayoutFeat::HasObject(const CObject* obj) const
{
    return &m_Feature.GetOriginalFeature() == obj;
}


inline
const objects::CMappedFeat& CLayoutFeat::GetMappedFeature(void) const
{
    return m_Feature;
}


inline
const objects::CSeq_loc& CLayoutFeat::GetLocation(void) const
{
    return m_Feature.GetLocation();
}



inline
TSeqPos CLayoutFeat::size(void) const
{
    return GetLocation().GetTotalRange().GetLength();
}


// Accessors for parent-child relationships in features
inline
const CLayoutFeat* CLayoutFeat::GetParent(void) const
{
    return m_Parent;
}


inline
const CLayoutFeat::TFeatList& CLayoutFeat::GetChildren(void) const
{
    return m_Children;
}


inline
void CLayoutFeat::SetParent(CLayoutFeat* feat)
{
    m_Parent = feat;
}


inline
CLayoutFeat::TFeatList& CLayoutFeat::SetChildren(void)
{
    return m_Children;
}


inline
bool CLayoutFeat::LessByPos(const CLayoutObject& obj) const
{
    const CLayoutFeat* feat = dynamic_cast<const CLayoutFeat*>(&obj);
    if (feat) {
        // two features - we sort in feature order
        SFeatureByPos comp;
        return (comp(*this, *feat));
    } else {
        // default: compare by ranges
        TSeqRange r0 = GetLocation().GetTotalRange();
        TSeqRange r1 = obj.GetLocation().GetTotalRange();
        return (r0.GetFrom() < r1.GetFrom());
    }
}


inline
bool CLayoutFeat::LessBySize(const CLayoutObject& obj) const
{
    TSeqRange r0 = GetLocation().GetTotalRange();
    TSeqRange r1 = obj.GetLocation().GetTotalRange();
    return (r0.GetLength() < r1.GetLength());
}


// Access the sub-intervals in this feature
inline
const vector<TSeqRange>& CLayoutFeat::GetIntervals(void) const
{
    if (m_Intervals.size() == 0) {
        x_CalcIntervals();
    }
    return m_Intervals;
}


inline
CLayoutFeat::EType CLayoutFeat::GetType() const
{
    return eFeat;
}


END_NCBI_SCOPE

/* @} */


/*
 * ===========================================================================
 * $Log: feature.hpp,v $
 * Revision 1000.0  2004/06/01 19:54:56  gouriano
 * PRODUCTION: IMPORTED [GCC34_MSVC7] Dev-tree R1.4
 *
 * Revision 1.4  2004/05/14 14:24:47  dicuccio
 * Added new pure virtual requirement on CLayoutObject(): GetType(), returns enum
 * defined in CLayoutObject
 *
 * Revision 1.3  2004/05/03 13:34:54  dicuccio
 * FIxed include guards, doxygen groups
 *
 * Revision 1.2  2004/05/03 12:41:35  dicuccio
 * Fixed #includes and export specifiers
 *
 * Revision 1.1  2004/04/30 11:52:53  dicuccio
 * Split out from gui/utils
 *
 * Revision 1.24  2004/04/16 14:27:17  dicuccio
 * Added doxygen module tag
 *
 * Revision 1.23  2004/04/15 12:57:43  lebedev
 * Changed GetObject to return NULL or const pointer based on given position
 *
 * Revision 1.22  2004/04/12 16:48:28  dicuccio
 * MOved #include guard
 *
 * Revision 1.21  2004/03/11 17:19:32  dicuccio
 * Use TSeqRange instead of TRange.  Use gui/gui instead of gui/types
 *
 * Revision 1.20  2004/02/24 14:34:49  lebedev
 * Option to hide feature label added
 *
 * Revision 1.19  2003/09/30 19:49:26  dicuccio
 * When requesting the object behind a feature, always return the original feature
 * not remapped to another sequence (solves selection issues in graphical widget)
 *
 * Revision 1.18  2003/09/29 15:20:08  dicuccio
 * Deprecated gui/scope.hpp.  Merged gui/core/types.hpp into gui/types.hpp
 *
 * Revision 1.17  2003/08/22 15:57:11  dicuccio
 * Removed 'USING_SCOPE(objects)'.  Removed export specifier from inline structs
 *
 * Revision 1.16  2003/08/18 14:53:26  dicuccio
 * Changed nales: CFeature -> CLayoutFeat; CAlignment -> CLayoutAlign; CGraph ->
 * CLayoutGraph; CProtProduct -> CLayoutProtProd.
 * Removed USING_SCOPE(objects);
 *
 * Revision 1.15  2003/07/21 19:24:09  dicuccio
 * Changed storage mechanism: CLayoutObject::GetObject() is pure virtual.  Also,
 * CFeature now stores a CMappedFeat object instead of a CSeq_feat / CSeq_loc pair
 *
 * Revision 1.14  2003/07/11 15:24:05  dicuccio
 * Fix compilation error for gcc
 *
 * Revision 1.13  2003/07/11 12:40:01  dicuccio
 * Code clean-ups.  Fixed sorting of features to perform correct feature-order
 * sorting
 *
 * Revision 1.12  2003/07/11 11:46:58  dicuccio
 * Removed dead code
 *
 * Revision 1.11  2003/06/10 13:32:42  dicuccio
 * Rewored CFeature to inherit from CLayoutObject.  Removed a lot fo dead code.
 *
 * Revision 1.10  2003/05/07 17:26:17  dicuccio
 * Removed dead predeclaration; reformatted CVS comments
 *
 * Revision 1.9  2003/05/07 12:30:00  dicuccio
 * Removed CFeature::GetExtent().  Fixed long-standing bug with misreporting of
 * feature locations
 *
 * Revision 1.8  2003/02/25 14:42:48  dicuccio
 * FIxed compilation issue related to API change in CSeq_feat::Compare()
 *
 * Revision 1.7  2003/02/10 18:19:41  dicuccio
 * Fixed compilation errors relating to change in CFeat_CI API
 *
 * Revision 1.6  2003/01/15 20:57:37  dicuccio
 * Dropped private feature sort mechanism in favor of toolkit standard sort.
 *
 * Revision 1.5  2003/01/13 13:11:42  dicuccio
 * Namespace clean-up.  Retired namespace gui -> converted to namespace ncbi.
 * Moved all FLUID-generated code into namespace ncbi.
 *
 * Revision 1.4  2002/12/19 18:13:03  dicuccio
 * Added export specifiers for Win32.
 *
 * Revision 1.3  2002/12/11 19:00:06  dicuccio
 * Re-enabled selection
 *
 * Revision 1.2  2002/12/06 14:08:17  dicuccio
 * Moved feature sorting predicates into feature.[h,c]pp
 *
 * Revision 1.1  2002/11/29 15:28:10  dicuccio
 * Initial revision - moved from gui/core/view/graphic
 *
 * Revision 1.2  2002/11/09 20:57:08  dicuccio
 * Performance improvements:  Implemented smarter widget update (use update
 * flags to specify update conditions); use a more intuitive (and flexible)
 * mechanism to obtain features from the object manager.
 *
 * Revision 1.1  2002/11/07 16:27:26  dicuccio
 * Initial revision
 *
 * ===========================================================================
 */

#endif  // GUI_OBJUTILS___FEATURE__HPP