/*  $Id: cds_fix.hpp 630324 2021-04-30 13:48:31Z 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.
 *
 * ===========================================================================
 *
 * Authors:  Colleen Bollin
 */


#ifndef _CDS_FIX_H_
#define _CDS_FIX_H_

#include <corelib/ncbistd.hpp>

#include <objmgr/scope.hpp>
#include <objmgr/scope.hpp>
#include <objects/seqfeat/Seq_feat.hpp>
#include <objects/seqfeat/Cdregion.hpp>
#include <objects/seqfeat/Genetic_code.hpp>

BEGIN_NCBI_SCOPE

BEGIN_SCOPE(objects)
BEGIN_SCOPE(edit)


NCBI_XOBJEDIT_EXPORT bool SetTranslExcept(objects::CSeq_feat& cds, const string& comment, bool strict, bool extend, objects::CScope& scope);
NCBI_XOBJEDIT_EXPORT void ExtendStop(CSeq_loc& loc, TSeqPos len, CScope& scope);
NCBI_XOBJEDIT_EXPORT bool DoesCodingRegionHaveTerminalCodeBreak(const objects::CCdregion& cdr);
NCBI_XOBJEDIT_EXPORT CRef<CSeq_loc> GetLastCodonLoc(const CSeq_feat& cds, CScope& scope);
NCBI_XOBJEDIT_EXPORT bool AddTerminalCodeBreak(CSeq_feat& cds, CScope& scope);
NCBI_XOBJEDIT_EXPORT bool AdjustProteinFeaturePartialsToMatchCDS(CSeq_feat& new_prot, const CSeq_feat& cds);
NCBI_XOBJEDIT_EXPORT CRef<CSeq_feat> MakemRNAforCDS(const CSeq_feat& cds, CScope& scope);
NCBI_XOBJEDIT_EXPORT CRef<CGenetic_code> GetGeneticCodeForBioseq(CBioseq_Handle bh);
NCBI_XOBJEDIT_EXPORT bool TruncateCDSAtStop(CSeq_feat& cds, CScope& scope);
NCBI_XOBJEDIT_EXPORT bool ExtendCDSToStopCodon (CSeq_feat& cds, CScope& scope);
NCBI_XOBJEDIT_EXPORT void AdjustCDSFrameForStartChange(CCdregion& cds, int change);
NCBI_XOBJEDIT_EXPORT bool DemoteCDSToNucSeq(objects::CSeq_feat_Handle& orig_feat);
NCBI_XOBJEDIT_EXPORT CRef<objects::CSeq_id> GetNewLocalProtId(const string &id_base, CScope &scope, int &offset);
NCBI_XOBJEDIT_EXPORT CRef<objects::CSeq_id> GetNewProtId(objects::CBioseq_Handle bsh, int &offset, string& id_label, bool general_only);
NCBI_XOBJEDIT_EXPORT vector<CRef<objects::CSeq_id> > GetNewProtIdFromExistingProt(objects::CBioseq_Handle bsh, int &offset, string& id_label);
NCBI_XOBJEDIT_EXPORT string GetIdHashOrValue(const string &base, int offset);
NCBI_XOBJEDIT_EXPORT bool IsGeneralIdProtPresent(objects::CSeq_entry_Handle tse);

// these methods are being moved to ncbi::feature namespace
// please modify your usage of them
NCBI_DEPRECATED NCBI_XOBJEDIT_EXPORT bool AdjustProteinMolInfoToMatchCDS(CMolInfo& molinfo, const CSeq_feat& cds);
NCBI_DEPRECATED NCBI_XOBJEDIT_EXPORT bool AdjustForCDSPartials(const CSeq_feat& cds, CSeq_entry_Handle seh);
NCBI_DEPRECATED NCBI_XOBJEDIT_EXPORT CConstRef<CSeq_feat> GetmRNAforCDS(const CSeq_feat& cds, CScope& scope);

class NCBI_XOBJEDIT_EXPORT ApplyCDSFrame
{
public:
    enum ECdsFrame {
        eNotSet,
        eBest,  // choose the frame that produces the longest sequence of aas before a stop codon is produced
        eMatch,  // choose the frame that matches the protein sequence if it can find one
        eOne,
        eTwo,
        eThree
    };

    ~ApplyCDSFrame() {}
    static bool s_SetCDSFrame(CSeq_feat& cds, ECdsFrame frame_type, CScope& scope);
    static CCdregion::TFrame s_FindMatchingFrame(const CSeq_feat& cds, CScope& scope);
    static ECdsFrame s_GetFrameFromName(const string& name);
};



END_SCOPE(edit)
END_SCOPE(objects)
END_NCBI_SCOPE

#endif

