merge_aligner.hpp

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#ifndef NGALIGN_MERGE_ALIGNER__HPP
#define NGALIGN_MERGE_ALIGNER__HPP
 
/*  $Id: merge_aligner.hpp 95346 2021-11-08 14:35:53Z mozese2 $
 * ===========================================================================
 *
 *                            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:  Nathan Bouk
 *
 * File Description:
 *
 */
 
#include <corelib/ncbistd.hpp>
#include <corelib/ncbiobj.hpp>
#include <objects/seqloc/Na_strand.hpp>
 
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objmgr/scope.hpp>
#include <algo/blast/api/blast_types.hpp>
#include <algo/blast/api/bl2seq.hpp>
#include <algo/blast/api/blast_options_handle.hpp>
#include <algo/blast/api/blast_nucl_options.hpp>
#include <objects/seqalign/Seq_align.hpp>
#include <objects/seqalign/Seq_align_set.hpp>
#include <objects/seqalign/Dense_seg.hpp>
 
 
#include <algo/align/ngalign/ngalign_interface.hpp>
#include <algo/align/mergetree/merge_tree.hpp>
 
BEGIN_NCBI_SCOPE
 
BEGIN_SCOPE(objects)
    class CScope;
    class CSeq_align;
    class CSeq_align_set;
    class CSeq_id;
    class CDense_seg;
END_SCOPE(objects)
 
 
 
class CMergeAligner : public IAlignmentFactory
{
public:
    enum EMode {
        /// Use the older (CAlignCleanup) merge algorithm.
        eAlignCleanup,
 
        /// Use the new (CTreeAlignMerger) merge algorithm.
        eTreeAlignMerger,
 
        eDefault = eAlignCleanup
    };
    typedef EMode TMode;
 
    CMergeAligner(int Threshold, TMode mode = eAlignCleanup)
        : m_Threshold(Threshold)
        , m_Mode(mode)
        { }
 
    string GetName() const { return "merge_aligner"; }
 
    TAlignResultsRef GenerateAlignments(objects::CScope& Scope,
                                        ISequenceSet* QuerySet,
                                        ISequenceSet* SubjectSet,
                                        TAlignResultsRef AccumResults);
 
private:
 
    CRef<objects::CSeq_align_set>
    x_MergeAlignments(CQuerySet& QueryAligns, objects::CScope& Scope);
 
    CRef<objects::CSeq_align_set>
    x_MergeSeqAlignSet(objects::CSeq_align_set& InAligns, objects::CScope& Scope);
 
    void x_SortAlignSet(objects::CSeq_align_set& AlignSet, int CompartFlags = 0);
 
    int m_Threshold;
    TMode m_Mode;
    CTreeAlignMerger m_TreeAlignMerger;
};
 
 
END_NCBI_SCOPE
 
#endif