named_collection_score_impl.hpp

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#ifndef __NAMED_ALIGNMENT_COLLECTION_SCORE_IMPL__HPP
#define __NAMED_ALIGNMENT_COLLECTION_SCORE_IMPL__HPP
 
 
/* 
 * ===========================================================================
 *
 *                            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.
 *
 * ===========================================================================
 *
 * Author:  Alex Kotliarov
 *
 * File Description:
 */
 
#include <corelib/ncbiobj.hpp>
 
#include <objmgr/scope.hpp>
 
#include <objects/seq/seq_id_handle.hpp>
#include <objects/seqalign/Seq_align_set.hpp>
 
#include <algo/align/util/named_collection_score.hpp>
 
BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)
 
class CSubjectsSequenceCoverage;
 
class CScoreSeqCoverage : public INamedAlignmentCollectionScore
{
    CScoreSeqCoverage() {}
    static pair<double, bool> MakeScore(CBioseq_Handle const& query_handle, vector<CSeq_align const*>::const_iterator, vector<CSeq_align const*>::const_iterator);
public:
    string GetName() const;
    vector<CScoreValue> Get(CScope& scope, CSeq_align_set const& coll) const;
     void Set(CScope& scope, CSeq_align_set & coll) const;
 
    static const char* Name;    
    static CIRef<INamedAlignmentCollectionScore> Create();
 
    friend class CSubjectsSequenceCoverage;
};
 
class CScoreUniqSeqCoverage : public INamedAlignmentCollectionScore
{
    CScoreUniqSeqCoverage() {}
    static pair<double, bool> MakeScore(CBioseq_Handle const& query_handle, vector<CSeq_align const*>::const_iterator, vector<CSeq_align const*>::const_iterator);
public:
    string GetName() const;   
    vector<CScoreValue> Get(CScope& scope, CSeq_align_set const& coll) const;
    void Set(CScope& scope, CSeq_align_set & coll) const;
 
    static const char* Name;    
    static CIRef<INamedAlignmentCollectionScore> Create();
    
    friend class CSubjectsSequenceCoverage;
};
 
// Adapters that provide ability to compute multiple scores in order to 
// reuse common tasks.
class CSubjectsSequenceCoverage : public INamedAlignmentCollectionScore
{
    typedef pair<double, bool> (*F)(CBioseq_Handle const&, vector<CSeq_align const*>::const_iterator, vector<CSeq_align const*>::const_iterator);
 
    vector<pair<string, F> > m_Calculators;
 
    CSubjectsSequenceCoverage();
    explicit CSubjectsSequenceCoverage(vector<pair<string, F> > const& calculators)
    : m_Calculators(calculators)
    {
    }
 
    static pair<double, bool> MakeScore(CBioseq_Handle const& query_handle, vector<CSeq_align const*>::const_iterator, vector<CSeq_align const*>::const_iterator);
 
public:
    string GetName() const;   
    vector<CScoreValue> Get(CScope& scope, CSeq_align_set const& coll) const;
    void Set(CScope& scope, CSeq_align_set & coll) const;
 
    static const char* Name;    
    static CIRef<INamedAlignmentCollectionScore> Create(vector<string> score_names);
};
 
 
END_SCOPE(objects)
END_NCBI_SCOPE
 
#endif // __NAMED_ALIGNMENT_COLLECTION_SCORE_IMPL__HPP