utils.hpp

来自「ncbi源码」· HPP 代码 · 共 300 行

/*
 * ===========================================================================
 * PRODUCTION $Log: utils.hpp,v $
 * PRODUCTION Revision 1000.0  2004/06/01 19:56:12  gouriano
 * PRODUCTION PRODUCTION: IMPORTED [GCC34_MSVC7] Dev-tree R1.6
 * PRODUCTION
 * ===========================================================================
 */

#ifndef GUI_OBJUTILS___UTILS__HPP
#define GUI_OBJUTILS___UTILS__HPP

/*  $Id: utils.hpp,v 1000.0 2004/06/01 19:56:12 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:
 *    General utility classes for GUI projects.
 */

#include <corelib/ncbistd.hpp>
#include <gui/objutils/feature.hpp>
#include <objmgr/bioseq_handle.hpp>

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


BEGIN_NCBI_SCOPE


//
// Main utilities class
//

class NCBI_GUIOBJUTILS_EXPORT CSeqUtils
{
public:
    // flags controlling feature retrieval
    enum {
        fFeature_LinkFeatures = 0x1,

        fFeature_Default = 0
    };
    typedef int TFeatureFlags;

    // request an annotation selector for a given type
    static objects::SAnnotSelector
    GetAnnotSelector(void);

    static objects::SAnnotSelector
    GetAnnotSelector(objects::SAnnotSelector::TAnnotType choice);

    static objects::SAnnotSelector
    GetAnnotSelector(objects::SAnnotSelector::TFeatType);

    static objects::SAnnotSelector
    GetAnnotSelector(objects::SAnnotSelector::TFeatSubtype);

    // Request a list of landmark features from a bioseq.
    static void GetLandmarkFeatures(const objects::CBioseq_Handle&  handle,
                                    const TSeqRange&          range,
                                    size_t                 max_feats,
                                    CLayoutFeat::TFeatList&   info);

    // Request a list of features from a bioseq.
    static void GetFeatures(const objects::CBioseq_Handle&  handle,
                            const TSeqRange&          range,
                            objects::CSeqFeatData::E_Choice feat_type,
                            CLayoutFeat::TFeatList&   info,
                            TFeatureFlags            flags = fFeature_Default);

    static void GetFeatures(const objects::CBioseq_Handle&  handle,
                            const TSeqRange&         range,
                            objects::SAnnotSelector  sel,
                            CLayoutFeat::TFeatList&  feats,
                            TFeatureFlags            flags = fFeature_Default);

    // Link features into a hierarchical list.  This function will transform a
    // linear, feature-order-sorted list of CLayoutFeat objects into a
    // hierarchically arranged list in which genes are linked to mRNAs, mRNAs
    // to CDSs, etc.
    static void LinkFeatures(CLayoutFeat::TFeatList& features);

    // Request a list of alignments from a bioseq.
    enum EAlignFlags {
        fAlign_LinkMatePairs        = 0x1,
        fAlign_MatedAlignsAsPwAlign = 0x2,

        fAlign_Default = 0x0
    };
    typedef int TAlignFlags;

    static void GetAlignments(const objects::CBioseq_Handle& handle,
                              const TSeqRange&               range,
                              CLayoutEngine::TObjects&       info,
                              TAlignFlags flags = fAlign_Default);

    // Request a list of alignments as smears from a bioseq.  Here, 'window'
    // is the number of bases per bin to place in the smeared alignment
    static void GetAlignmentSmears(const objects::CBioseq_Handle& handle,
                                   const TSeqRange&         range,
                                   TSeqPos                  window,
                                   CLayoutEngine::TObjects& aligns);

    // Request a list of graphs from a bioseq.
    static void GetGraphs(const objects::CBioseq_Handle& handle,
                          const TSeqRange&               range,
                          CLayoutEngine::TObjects&       graphs);

    // remap a location to a parent location.  The child location is split
    // such that all of its relative positions will map correctly to the
    // parent location's positions
    static CRef<objects::CSeq_loc>
    RemapChildToParent(const objects::CSeq_loc& parent,
                       const objects::CSeq_loc& child,
                       objects::CScope* scope = NULL);

    // check to see if two seq-ids are identical.  If provided with a scope,
    // this function will use the synonyms available through a scope to check
    // for identicality.  Note that this may require network access, and may
    // be slow.
    static bool Match(const objects::CSeq_id& id1,
                      const objects::CSeq_id& id2, 
                      objects::CScope* scope = NULL);
};


END_NCBI_SCOPE


/* @} */

/*
 * ===========================================================================
 * $Log: utils.hpp,v $
 * Revision 1000.0  2004/06/01 19:56:12  gouriano
 * PRODUCTION: IMPORTED [GCC34_MSVC7] Dev-tree R1.6
 *
 * Revision 1.6  2004/05/14 14:24:47  dicuccio
 * Added new pure virtual requirement on CLayoutObject(): GetType(), returns enum
 * defined in CLayoutObject
 *
 * Revision 1.5  2004/05/10 00:00:38  dicuccio
 * Added flags to control retrieval of alignments
 *
 * Revision 1.4  2004/05/07 15:44:32  dicuccio
 * Removed GetLabel()
 *
 * 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 1.32  2004/04/16 14:27:17  dicuccio
 * Added doxygen module tag
 *
 * Revision 1.31  2004/04/16 13:30:39  lebedev
 * Do not link features by default
 *
 * Revision 1.30  2004/04/12 16:49:32  dicuccio
 * Dropped getMatePairs() as separate API - folded into GetAlignments()
 *
 * Revision 1.29  2004/04/07 12:40:53  dicuccio
 * Changed GetAnnotSelector() - for feature types, separated feature type and
 * subtype into different functions.  Changed Match() - scope is now an optional
 * (default null) pointer
 *
 * Revision 1.28  2004/04/06 18:28:26  dicuccio
 * Added GetMatePairs().  Cosmetic changes.
 *
 * Revision 1.27  2004/04/02 16:12:59  yazhuk
 * Added Match() function for comparing CSeq_id-s
 *
 * Revision 1.26  2004/03/23 13:36:14  dicuccio
 * Removed lots of dead functions.  Moved #include of alignment_smear.hpp to .cpp
 *
 * Revision 1.25  2004/03/22 16:39:35  rsmith
 * add GetAlignmentSmears()
 *
 * Revision 1.24  2004/03/11 17:20:23  dicuccio
 * Use gui/gui instead of gui/types.  Use TSeqRange instead of TRange
 *
 * Revision 1.23  2004/02/17 17:17:17  dicuccio
 * Added flags to feature retrieval
 *
 * Revision 1.22  2004/02/04 18:05:30  grichenk
 * Added annotation filtering by set of types/subtypes.
 * Renamed *Choice to *Type in SAnnotSelector.
 *
 * Revision 1.21  2004/01/30 17:12:59  dicuccio
 * Added GetLabel() - moved from plugin_utils.[h,c]pp
 *
 * Revision 1.20  2003/10/28 15:23:47  lebedev
 * GetFeatures method that takes a selector added
 *
 * Revision 1.19  2003/10/22 15:40:57  dicuccio
 * Added API to create a dummy seq-entry to wrap a seq-annot
 *
 * Revision 1.18  2003/10/14 15:42:15  dicuccio
 * Changed API for RemapChildToParent() to accept an optional scope
 *
 * Revision 1.17  2003/10/14 12:19:47  dicuccio
 * Added RemapChildToParent() for remapping seq-locs
 *
 * Revision 1.16  2003/09/29 15:20:08  dicuccio
 * Deprecated gui/scope.hpp.  Merged gui/core/types.hpp into gui/types.hpp
 *
 * Revision 1.15  2003/09/24 18:17:23  dicuccio
 * Add additional GetAnnotSelector prototype
 *
 * Revision 1.14  2003/09/17 16:19:25  dicuccio
 * Removed SetResolveDepth().  Added new functions for formatting annotation
 * selectors in standard ways
 *
 * Revision 1.13  2003/08/22 15:57:11  dicuccio
 * Removed 'USING_SCOPE(objects)'.  Removed export specifier from inline structs
 *
 * Revision 1.12  2003/08/18 14:53:26  dicuccio
 * Changed nales: CFeature -> CLayoutFeat; CAlignment -> CLayoutAlign; CGraph ->
 * CLayoutGraph; CProtProduct -> CLayoutProtProd.
 * Removed USING_SCOPE(objects);
 *
 * Revision 1.11  2003/08/15 19:33:11  dicuccio
 * Added SetResolveDepth() for determining the correct depth of annotations
 *
 * Revision 1.10  2003/07/29 13:38:37  lebedev
 * GetGraphs method added
 *
 * Revision 1.9  2003/07/18 13:33:22  lebedev
 * Method to retrieve alignments added
 *
 * Revision 1.8  2003/06/23 13:18:49  dicuccio
 * Merged functionality in from seq_utils.hpp
 *
 * Revision 1.7  2003/06/10 13:32:21  dicuccio
 * Added new API for retrieving landmark features.  Cleaned up a lot of dead code.
 *
 * Revision 1.6  2003/06/02 16:01:30  dicuccio
 * Rearranged include/objects/ subtree.  This includes the following shifts:
 *     - include/objects/alnmgr --> include/objtools/alnmgr
 *     - include/objects/cddalignview --> include/objtools/cddalignview
 *     - include/objects/flat --> include/objtools/flat
 *     - include/objects/objmgr/ --> include/objmgr/
 *     - include/objects/util/ --> include/objmgr/util/
 *     - include/objects/validator --> include/objtools/validator
 *
 * Revision 1.5  2003/01/15 20:58:38  dicuccio
 * Added interface functions for linking and packing features.  Removed old
 * bitmask feature types in favor of toolkit standard CSeqFeatData::E_Choice
 * types.
 *
 * Revision 1.4  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 1.3  2003/01/09 14:48:21  dicuccio
 * Use 'const CBioseq_Handle&' instead of 'CBioseq_Handle&'
 *
 * Revision 1.2  2002/12/19 18:13:03  dicuccio
 * Added export specifiers for Win32.
 *
 * Revision 1.1  2002/11/29 15:28:10  dicuccio
 * Initial revision - moved from gui/core/view/graphic
 *
 * ===========================================================================
 */


#endif  // GUI_OBJUTILS___UTILS__HPP