gff_feature_record.hpp

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/*  $Id: gff_feature_record.hpp 93574 2021-04-30 16:19:19Z stakhovv $
 * ===========================================================================
 *
 *                            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: Frank Ludwig
 *
 * File Description:
 *   GFF3 transient data structures
 *
 */
 
#ifndef OBJTOOLS_WRITERS___GFF_FEATURE_RECORD__HPP
#define OBJTOOLS_WRITERS___GFF_FEATURE_RECORD__HPP
 
#include <objmgr/mapped_feat.hpp>
#include <objtools/writers/gff_base_record.hpp>
 
BEGIN_NCBI_SCOPE
BEGIN_objects_SCOPE // namespace ncbi::objects::
 
//  ============================================================================
class NCBI_XOBJWRITE_EXPORT CGffFeatureRecord
//  ============================================================================
    : public CGffBaseRecord
{
public:
    CGffFeatureRecord(
        const string& id="");
    CGffFeatureRecord(
        const CGffFeatureRecord& other);
    virtual ~CGffFeatureRecord();
 
    void InitLocation(
        const CSeq_loc&);
    void SetLocation(
        const CSeq_interval&,
        unsigned int,
        unsigned int =0);
    void SetEndpoints(
        unsigned int start,
        unsigned int stop,
        ENa_strand strand);
    const CSeq_loc& Location() const {
        return *m_pLoc;
    };
    void SetGbKeyFrom(
        CMappedFeat);
 
protected:
};
 
//  ============================================================================
class NCBI_XOBJWRITE_EXPORT CGffSourceRecord
//  ============================================================================
    : public CGffBaseRecord
{
public:
    CGffSourceRecord(
        const string& id=""): CGffBaseRecord(id) {};
};
 
//  ============================================================================
class NCBI_XOBJWRITE_EXPORT CGffAlignRecord
//  ============================================================================
    : public CGffBaseRecord
{
public:
    CGffAlignRecord(
        const string& id="");
 
    void
    AddInsertion(
        unsigned int);
    void
    AddForwardShift(
        unsigned int);
    void
    AddReverseShift(
        unsigned int);
    void
    AddDeletion(
        unsigned int);
    void
    AddMatch(
        unsigned int);
 
    void
    FinalizeMatches();
 
    string StrId() const { return mRecordId; };
    string StrTarget() const;
    string StrGap() const;
    string StrAttributes() const;
 
protected:
    string mRecordId;
    string mAttrGap;
    bool mGapIsTrivial;
    unsigned int mAccumulatedMatches;
};
 
END_objects_SCOPE
END_NCBI_SCOPE
 
#endif // OBJTOOLS_WRITERS___GFF_FEATURE_RECORD__HPP