#ifndef NEWCLEANUP__HPP
#define NEWCLEANUP__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: Robert Smith, Jonathan Kans, Michael Kornbluh
*
* File Description:
*   Basic and Extended Cleanup of CSeq_entries.
*
* ===========================================================================
*/

#include <stack>

#include <objects/seqfeat/OrgMod.hpp>
#include <objects/seqfeat/SeqFeatData.hpp>
#include <objects/seqfeat/Seq_feat.hpp>
#include <objects/seq/MolInfo.hpp>
#include <objects/seqblock/GB_block.hpp>

#include <objtools/cleanup/cleanup_change.hpp>

BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)

class CSeq_entry;
class CSeq_submit;
class CBioseq;
class CBioseq_set;
class CSeq_annot;
class CSeq_feat;
class CSeqFeatData;
class CSeq_descr;
class CSeqdesc;
class CSeq_loc;
class CSeq_loc_mix;
class CGene_ref;
class CProt_ref;
class CRNA_ref;
class CImp_feat;
class CGb_qual;
class CDbtag;
class CUser_field;
class CUser_object;
class CObject_id;
class CGB_block;
class CMolInfo;
class CEMBL_block;
class CPubdesc;
class CPub_equiv;
class CPub;
class CCit_gen;
class CCit_sub;
class CCit_art;
class CCit_book;
class CCit_pat;
class CCit_let;
class CId_pat;
class CCit_proc;
class CCit_jour;
class CPubMedId;
class CAuth_list;
class CAuthor;
class CAffil;
class CPerson_id;
class CName_std;
class CBioSource;
class COrg_ref;
class COrgName;
class CSubSource;
class CMolInfo;
class CCdregion;
class CDate;
class CDate_std;
class CImprint;
class CSubmit_block;
class CSeq_align;
class CDense_diag;
class CDense_seg;
class CStd_seg;
class CMedline_entry;
class CPub_set;
class CTrna_ext;
class CPCRPrimerSet;
class CPCRReactionSet;

class CSeq_entry_Handle;
class CBioseq_Handle;
class CBioseq_set_Handle;
class CSeq_annot_Handle;
class CSeq_feat_Handle;

class CObjectManager;
class CScope;

class CNewCleanup_imp
{
public:

    static const int NCBI_CLEANUP_VERSION = 1;

    // some cleanup functions will return a value telling you whether
    // to erase the cleaned value ( or whatever action may be
    // required ).
    enum EAction {
        eAction_Nothing = 1,
        eAction_Erase
    };

    // Constructor
    CNewCleanup_imp (CRef<CCleanupChange> changes, Uint4 options = 0);

    // Destructor
    virtual ~CNewCleanup_imp ();

    /// Main methods

    void SetScope(CScope& scope) { m_Scope.Reset(&scope); }

    /// Basic Cleanup methods

    void BasicCleanupSeqEntry (
        CSeq_entry& se
    );

    void BasicCleanupSeqSubmit (
        CSeq_submit& ss
    );

    void BasicCleanupSubmitblock(CSubmit_block& sb);

    void BasicCleanupSeqAnnot (
        CSeq_annot& sa
    );

    void BasicCleanupBioseq (
        CBioseq& bs
    );

    void BasicCleanupBioseqSet (
        CBioseq_set& bss
    );

    void BasicCleanupSeqFeat (
        CSeq_feat& sf
    );

    void BasicCleanupBioSource (
        CBioSource& src
    );

    void BasicCleanupSeqEntryHandle (
        CSeq_entry_Handle& seh
    );

    void BasicCleanupBioseqHandle (
        CBioseq_Handle& bsh
    );

    void BasicCleanupBioseqSetHandle (
        CBioseq_set_Handle& bssh
    );

    void BasicCleanupSeqAnnotHandle (
        CSeq_annot_Handle& sah
    );

    void BasicCleanupSeqFeatHandle (
        CSeq_feat_Handle& sfh
    );

    void BasicCleanup(CPubdesc& pd, bool strip_serial);

    void BasicCleanup(CSeqdesc& desc);

    /// Extended Cleanup methods

    void ExtendedCleanupSeqEntry (
        CSeq_entry& se
    );

    void ExtendedCleanupSeqSubmit (
        CSeq_submit& ss
    );

    void ExtendedCleanupSeqAnnot (
        CSeq_annot& sa
    );

    void ExtendedCleanupSeqEntryHandle (
        CSeq_entry_Handle& seh
    );

    void ExtendedCleanup(CSeq_entry_Handle& seh) { ExtendedCleanupSeqEntryHandle(seh);  }

    void ExtendedCleanup(CBioSource& biosrc);

    static bool ShouldRemoveAnnot(const CSeq_annot& annot);

    static void AddNcbiCleanupObject(CSeq_descr& descr);

private:

    // many more methods and variables ...

    // We do not include the usual "x_" prefix for private functions
    // because we want to be able to distinguish between higher-level
    // functions like those just below, and the lower-level
    // functions like those farther below.

    void ChangeMade (CCleanupChange::EChanges e);

    void EnteringEntry(CSeq_entry& se);
    void LeavingEntry (CSeq_entry& se);

    void SetGeneticCode (CBioseq& bs);

    void SubmitblockBC (CSubmit_block& sb);

    void SeqsetBC (CBioseq_set& bss);
    void ProtSeqBC (CBioseq& bs);

    void SeqIdBC( CSeq_id &seq_id );

    void GBblockOriginBC( string& str);
    void GBblockBC (CGB_block& gbk);
    void EMBLblockBC (CEMBL_block& emb);

    void BiosourceFeatBC (CBioSource& biosrc, CSeq_feat & seqfeat);
    void BiosourceBC (CBioSource& bsc);
    void OrgrefModBC (string& str);
    void OrgrefBC (COrg_ref& org);
    void x_MovedNamedValuesInStrain(COrgName& orgname);
    void x_MovedNamedValuesInStrain(COrgName& orgname, COrgMod::ESubtype stype, const string& prefix);
    void OrgnameBC (COrgName& onm, COrg_ref &org_ref);
    void OrgmodBC (COrgMod& omd);

    void DbtagBC (CDbtag& dbt);

    void PubdescBC (CPubdesc& pub);
    void PubSetBC( CPub_set &pub_set );

    void ImpFeatBC( CSeq_feat& sf );

    void SiteFeatBC( const CSeqFeatData::ESite &site, CSeq_feat& sf );

    void SeqLocBC( CSeq_loc &loc );
    void ConvertSeqLocWholeToInt( CSeq_loc &loc );
    void SeqLocMixBC( CSeq_loc_mix & loc_mix );

    void SeqfeatBC (CSeq_feat& sf);

    void GBQualBC (CGb_qual& gbq);
    void Except_textBC (string& except_text);

    void GenerefBC (CGene_ref& gr);
    void ProtNameBC (  std::string & str );
    void ProtActivityBC (  std::string & str );
    void ProtrefBC (CProt_ref& pr);
    void RnarefBC (CRNA_ref& rr);
    void RnarefGenBC(CRNA_ref& rr);

    void GeneFeatBC (CGene_ref& gr, CSeq_feat& sf);
    void ProtFeatfBC (CProt_ref& pr, CSeq_feat& sf);
    void PostProtFeatfBC (CProt_ref& pr);
    void RnaFeatBC (CRNA_ref& rr, CSeq_feat& sf);
    void CdregionFeatBC (CCdregion& cds, CSeq_feat& seqfeat);

    static bool x_IsCommentRedundantWithEC(const CSeq_feat& seqfeat, CScope& scope);

    void DeltaExtBC( CDelta_ext & delta_ext, CSeq_inst &seq_inst );

    void UserObjectBC( CUser_object &user_object );

    void PCRReactionSetBC( CPCRReactionSet &pcr_reaction_set );
    void SubSourceListBC(CBioSource& biosrc);

    void MolInfoBC( CMolInfo &molinfo );
    void CreateMissingMolInfo( CBioseq& seq );

    static bool IsInternalTranscribedSpacer(const string& name);
    static bool TranslateITSName( string &in_out_name );


    // Extended Cleanup functions
    void BioSourceEC ( CBioSource& biosrc );
    void AddProteinTitles (CBioseq& seq);
    void ProtRefEC( CProt_ref& pr);
    void CdRegionEC( CSeq_feat& sf);
    bool x_FixParentPartials(const CSeq_feat& sf, CSeq_feat& parent);
    void x_ExtendFeatureToCoverSequence(CSeq_feat_Handle fh, const CBioseq& seq);
    void x_ExtendProteinFeatureOnProteinSeq(CBioseq& seq);
    void x_ExtendSingleGeneOnMrna(CBioseq& seq);
    static bool IsSyntheticConstruct(const CBioSource& src);

    void MoveDbxrefs(CSeq_feat& sf);
    void MoveStandardName(CSeq_feat& sf);
    void CreatePubFromFeat(CSeq_feat& sf);
    void ResynchProteinPartials ( CSeq_feat& feat );
    void ResynchPeptidePartials( CBioseq& seq );
    void x_SetPartialsForProtein(CBioseq& prot, bool partial5, bool partial3, bool feat_partial);
    void RemoveBadProteinTitle(CBioseq& seq);
    void MoveCitationQuals(CBioseq& seq);
    void x_RemoveUnseenTitles(CSeq_descr& seq_descr);
    void KeepLatestDateDesc(CSeq_descr & seq_descr);
    void x_SingleSeqSetToSeq(CBioseq_set& set);
    void x_MergeDupBioSources(CSeq_descr & seq_descr);

    // void XxxxxxBC (Cxxxxx& xxx);

    // Prohibit copy constructor & assignment operator
    CNewCleanup_imp (const CNewCleanup_imp&);
    CNewCleanup_imp& operator= (const CNewCleanup_imp&);

private:

    // data structures used for post-processing

    // recorded by x_NotePubdescOrAnnotPubs
    typedef std::map<int, int> TMuidToPmidMap;
    TMuidToPmidMap m_MuidToPmidMap;
    // recorded by x_RememberMuidThatMightBeConvertibleToPmid
    typedef std::vector< CRef<CPub> > TMuidPubContainer;
    TMuidPubContainer m_MuidPubContainer;
    // m_OldLabelToPubMap and m_PubToNewPubLabelMap work together.
    // They supply "old_label -> node" and "node -> new_label", respectively,
    // so together we can get a mapping of "old_label -> new_label".
    // m_OldLabelToPubMap is a multimap because a node's address may change as we do our cleaning, and
    // at least one should remain so we can make the "old_label -> new_label" connection.
    typedef std::multimap< string, CRef<CPub> > TOldLabelToPubMap;
    TOldLabelToPubMap m_OldLabelToPubMap;
    // remember label changes
    typedef std::map< CRef<CPub>, string > TPubToNewPubLabelMap;
    TPubToNewPubLabelMap m_PubToNewPubLabelMap;
    // remember all Seq-feat CPubs so we remember to change them later
    typedef std::vector< CRef<CPub> > TSeqFeatCitPubContainer;
    TSeqFeatCitPubContainer m_SeqFeatCitPubContainer;
    // note all Pubdesc/annot cit-gen labels
    typedef std::vector<string> TPubdescCitGenLabelVec;
    TPubdescCitGenLabelVec m_PubdescCitGenLabelVec;

    enum EGBQualOpt {
        eGBQualOpt_normal,
        eGBQualOpt_CDSMode
    };

    // Gb_qual cleanup.
    void x_ConvertGoQualifiers(CSeq_feat& sf);
    void x_CleanSeqFeatQuals(CSeq_feat& sf);
    EAction GBQualSeqFeatBC(CGb_qual& gbq, CSeq_feat& seqfeat);

    void x_AddNcbiCleanupObject( CSeq_entry &seq_entry );


    // for rpt_unit and replace GenBank qualifiers
    bool x_CleanupRptUnit(CGb_qual& gbq);
    bool x_CleanupRptUnitRange(string& val);
    static bool x_IsBaseRange(const string& val);
    static bool x_IsDotBaseRange(const string& val);
    static bool x_IsHyphenBaseRange(const string& val);


    void x_ChangeTransposonToMobileElement(CGb_qual& gbq);
    void x_ChangeInsertionSeqToMobileElement(CGb_qual& gbq);
    void x_ExpandCombinedQuals(CSeq_feat::TQual& quals);
    EAction x_GeneGBQualBC( CGene_ref& gene, const CGb_qual& gb_qual );
    EAction x_SeqFeatCDSGBQualBC(CSeq_feat& feat, CCdregion& cds, const CGb_qual& gb_qual);
    EAction x_HandleTrnaProductGBQual(CSeq_feat& feat, CRNA_ref& rna, const string& product);
    EAction x_HandleStandardNameRnaGBQual(CSeq_feat& feat, CRNA_ref& rna, const string& standard_name);
    EAction x_SeqFeatRnaGBQualBC(CSeq_feat& feat, CRNA_ref& rna, CGb_qual& gb_qual);
    EAction x_ProtGBQualBC(CProt_ref& prot, const CGb_qual& gb_qual, EGBQualOpt opt );
    void x_AddEnvSamplOrMetagenomic(CBioSource& biosrc);
    void x_CleanupOldName(COrg_ref& org);
    void x_CleanupOrgModNoteEC(COrg_ref& org);
    void x_AddToComment(CSeq_feat& feat, const string& comment);

    // publication-related cleanup
//    void x_FlattenPubEquiv(CPub_equiv& pe);

    // Date-related
    void x_DateStdBC( CDate_std& date );

    void x_AddReplaceQual(CSeq_feat& feat, const string& str);

    void x_SeqIntervalBC( CSeq_interval & seq_interval );
    void x_BothStrandBC( CSeq_loc &loc );
    void x_BothStrandBC( CSeq_interval & seq_interval );

    void x_SplitDbtag( CDbtag &dbt, vector< CRef< CDbtag > > & out_new_dbtags );

    void x_SeqFeatTRNABC( CSeq_feat& feat, CTrna_ext & tRNA );

    // modernize PCR Primer
    void x_ModernizePCRPrimers( CBioSource &biosrc );

    void x_CleanupOrgModAndSubSourceOther( COrgName &orgname, CBioSource &biosrc );

    void x_OrgnameModBC( COrgName &orgname, const string &org_ref_common );

    void x_SubSourceBC( CSubSource & subsrc );
    void x_OrgModBC( COrgMod & orgmod );

    void x_FixUnsetMolFromBiomol( CMolInfo& molinfo, CBioseq &bioseq );
    void FixUnsetMolFromBiomol(CMolInfo::TBiomol biomol, CBioseq& bioseq);

    void x_AddPartialToProteinTitle( CBioseq &bioseq );

    string x_ExtractSatelliteFromComment( string &comment );

    void x_RRNANameBC( string &name );

    void x_CleanupECNumber( string &ec_num );
    void x_CleanupECNumberList( CProt_ref::TEc & ec_num_list );
    void x_CleanupECNumberListEC( CProt_ref::TEc & ec_num_list );

    void x_CleanupAndRepairInference( string &inference );

    void x_MendSatelliteQualifier( string &val );

    // e.g. if ends with ",..", turn into "..."
    void x_FixUpEllipsis( string &str );

    void x_RemoveFlankingQuotes( string &val );

    void x_MoveCdregionXrefsToProt (CCdregion& cds, CSeq_feat& seqfeat);
    bool x_InGpsGenomic( const CSeq_feat& seqfeat );

    void x_AddNonCopiedQual(
        vector< CRef< CGb_qual > > &out_quals,
        const char *qual,
        const char *val );

    void x_GBQualToOrgRef( COrg_ref &org, CSeq_feat &seqfeat );
    void x_MoveSeqdescOrgToSourceOrg( CSeqdesc &seqdesc );
    void x_MoveSeqfeatOrgToSourceOrg( CSeq_feat &seqfeat );

    void x_MoveCDSFromNucAnnotToSetAnnot( CBioseq_set &set );

    // string cleanup funcs
    void x_CleanupStringMarkChanged( std::string &str );
    void x_CleanupStringJunkMarkChanged( std::string &str );
    void x_CleanupVisStringMarkChanged( std::string &str );
    void x_ConvertDoubleQuotesMarkChanged( std::string &str );
    bool x_CompressSpaces( string &str );
    void x_CompressStringSpacesMarkChanged( std::string &str );
    void x_StripSpacesMarkChanged( std::string& str );
    void x_RemoveSpacesBetweenTildesMarkChanged( std::string & str );
    void X_CommentTildeFixes( std::string & str );
    void x_TruncateSpacesMarkChanged( std::string & str );
    void x_TrimInternalSemicolonsMarkChanged( std::string & str );

    void x_PostSeqFeat( CSeq_feat& seq_feat );
    void x_PostOrgRef( COrg_ref& org );
    void x_PostBiosource( CBioSource& biosrc );

    void x_TranslateITSNameAndFlag( string &in_out_name ) ;

    void x_PCRPrimerSetBC( CPCRPrimerSet &primer_set );

    void x_CopyGBBlockDivToOrgnameDiv( CSeq_entry &seq_entry);

    void x_AuthListBCWithFixInitials( CAuth_list& al );

    // After we've traversed the hierarchy of objects, there may be some
    // processing that can only be done after the traversal is complete.
    // This function does that processing.
    void x_PostProcessing(void);

    // after cleaning bioseq and bioseq-set, need to clear empty descriptors
    void x_ClearEmptyDescr( CBioseq_set& bioseq_set );
    void x_ClearEmptyDescr( CBioseq& bioseq );

    // removes single-strandedness from non-viral nucleotide sequences
    void x_RemoveSingleStrand( CBioseq& bioseq );

    // functions that prepare for post-processing while traversing
    void x_NotePubdescOrAnnotPubs( const CPub_equiv &pub_equiv );
    void x_NotePubdescOrAnnotPubs_RecursionHelper(
        const CPub_equiv &pub_equiv, int &muid, int &pmid );
    void x_RememberPubOldLabel( CPub &pub );
    void x_RememberMuidThatMightBeConvertibleToPmid(CPub &pub );
    void x_RememberSeqFeatCitPubs( CPub &pub );

    void x_DecodeXMLMarkChanged( std::string & str );
    void AddMolInfo(CBioseq_set& set, const CMolInfo& mol);
    void AddMolInfo(CBioseq& seq, const CMolInfo& mol);

private:
    void x_SortSeqDescs( CSeq_entry & seq_entry );

    void x_FixStructuredCommentKeywords(CSeq_descr& descr);

    void x_RemoveDupBioSource( CBioseq_set & bioseq_set );
    void x_RemoveDupBioSource(CSeq_entry& se, const CBioSource& src);

    void x_RemoveDupPubs(CSeq_descr & descr);

    void x_RemoveProtDescThatDupsProtName( CProt_ref & prot );
    void x_RemoveRedundantComment( CGene_ref& gene, CSeq_feat& seq_feat );
    void x_ExceptTextEC(string& except_text);

    void x_tRNAEC(CSeq_feat& seq_feat);
    void x_tRNACodonEC(CSeq_feat& seq_feat);
    static bool x_IsCodonCorrect(int codon_index, int gcode, unsigned char aa);

    void x_RemoveEmptyUserObject( CSeq_descr & seq_descr );
    void x_SetMolInfoTechFromGenBankBlock(CSeq_descr& seq_descr, CGB_block& block);
    void x_SetMolInfoTechFromGenBankBlock(CSeq_descr& seq_descr);
    static bool x_CleanGenbankKeywords(CGB_block& blk, CMolInfo::TTech tech);
    void x_CleanupGenbankBlock(CBioseq& seq);
    void x_CleanupGenbankBlock(CBioseq_set& set);
    void x_CleanupGenbankBlock( CSeq_descr & seq_descr );
    void x_CleanupGenbankBlock(CGB_block& block, bool is_patent, CConstRef<CBioSource> biosrc, CMolInfo::TTech tech);
    static bool x_CanRemoveGenbankBlockSource(const string& src, const CBioSource& biosrc);
    void x_RescueMolInfo(CBioseq& seq);
    void x_RemoveOldDescriptors( CSeq_descr & seq_descr );
    void x_RemoveEmptyDescriptors(CSeq_descr& seq_descr);
    void x_RemoveEmptyFeatures( CSeq_annot & seq_annot );
    void x_RemoveEmptyFeatureTables( CBioseq & bioseq );
    void x_RemoveEmptyFeatureTables( CBioseq_set & bioseq_set );
    void x_MergeAdjacentFeatureTables( CBioseq & bioseq );
    void x_MergeAdjacentFeatureTables(list< CRef< CSeq_annot > > & annot_list);
    void x_MergeAdjacentFeatureTables(CBioseq_set & bioseq_set);
    bool x_CleanEmptyFeature(CSeq_feat& feat);
    bool x_ShouldRemoveEmptyFeature(const CSeq_feat& feat );
    bool x_CleanEmptyGene(CGene_ref& gene);
    bool x_ShouldRemoveEmptyGene(const CGene_ref& gene, const CSeq_feat& feat);
    bool x_CleanEmptyProt(CProt_ref& prot);
    bool x_ShouldRemoveEmptyProt(const CProt_ref& prot );
    void x_BondEC(CSeq_feat& feat);
    static bool x_IsPubContentBad(const CPubdesc& pub, bool strict);
    static bool x_IsPubContentBad(const CPub& pub);
    static bool x_IsPubContentBad(const CId_pat& pat);
    bool x_ShouldRemoveEmptyPub(const CPubdesc& pubdesc );
    static bool x_IsGenbankBlockEmpty(const CGB_block& gbk);
    void x_RemoveOldFeatures(CBioseq & bioseq);

    void x_BioseqSetEC( CBioseq_set & bioseq_set );
    void x_ChangePopToPhy(CBioseq_set& bioseq_set);
    void x_CollapseSet(CBioseq_set& set);
    void x_RemovePopPhyBioSource(CBioseq_set& set);
    void x_RemovePopPhyBioSource(CBioseq_set& set, const COrg_ref& org);
    void x_RemovePopPhyBioSource(CBioseq& seq, const COrg_ref& org);
    void x_RemovePopPhyMolInfo(CBioseq_set& set);
    void x_BioseqSetNucProtEC( CBioseq_set & bioseq_set );
    void x_BioseqSetGenBankEC(CBioseq_set & bioseq_set);
    void x_RemoveNestedGenBankSet(CBioseq_set & bioseq_set);
    void x_RemoveNestedNucProtSet(CBioseq_set & bioseq_set);
    void x_MoveNpDBlinks(CBioseq_set& bioseq_set);
    void x_MoveNpSrc(CBioseq_set& bioseq_set);
    void x_MoveNpSrc(CRef<CSeqdesc>& srcdesc, CSeq_descr& descr);
    void x_MoveNPTitle(CBioseq_set& set);

    void x_MoveNpPub(CBioseq_set& bioseq_set);
    void x_MoveNpPub(CBioseq_set& np_set, CSeq_descr& descr);
    void x_MovePopPhyMutPub(CBioseq_set& bioseq_set);
    void x_RemovePub(CSeq_entry& se, const CPubdesc& pub);

    bool x_IsDBLinkUserObj( const CSeqdesc & desc );

    bool x_FixMiscRNA(CSeq_feat& feat);
    void x_ModernizeRNAFeat(CSeq_feat& feat);

    void x_ExtendedCleanupExtra(CSeq_entry_Handle seh);

protected:

    // variables used for the whole cleaning process

    /// If set, holds all the cleanup changes that have occurred so far
    CRef<CCleanupChange>  m_Changes;
    /// See CCleanup::EValidOptions
    Uint4                 m_Options;
    /// For simplicity, the same object manager is used wherever possible
    CRef<CObjectManager>  m_Objmgr;
    /// For simplicity, the same CScope is used wherever possible
    CRef<CScope>          m_Scope;
    /// Set via m_Options when we're in gpipe cleanup mode
    bool                  m_IsGpipe      { false };
    /// Set via m_Options to synchronize Cdregion genetic codes with BioSource
    bool                  m_SyncGenCodes { false };

    void SetGlobalFlags(const CSeq_entry& se, bool reset = true);
    void SetGlobalFlags(const CSeq_submit& ss);
    void SetGlobalFlags(const CBioseq& bs, bool reset = true);
    void SetGlobalFlags(const CBioseq_set& set, bool reset = true);
    void ResetGlobalFlags() { m_StripSerial = true; m_IsEmblOrDdbj = false; }
    /// set if references should NOT have serial numbers
    /// under this entry.
    bool m_StripSerial     { true };
    /// tells if any Seq-id on any Bioseq in the blob being cleaned is embl or ddbj.
    bool m_IsEmblOrDdbj    { false };

    bool m_KeepTopNestedSet { false };
    bool m_KeepSingleSeqSet { false };

    friend class CAutogeneratedCleanup;
    friend class CAutogeneratedExtendedCleanup;
};


END_SCOPE(objects)
END_NCBI_SCOPE

#endif /* NEWCLEANUP__HPP */
