validatorp.hpp

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    void ValidateProt(const CProt_ref& prot, const CSerialObject& obj);

    void ValidateRna(const CRNA_ref& rna, const CSeq_feat& feat);
    void ValidateTrnaCodons(const CTrna_ext& trna, const CSeq_feat& feat);
    void ValidateMrnaTrans(const CSeq_feat& feat);
    void ValidateCommonMRNAProduct(const CSeq_feat& feat);
    void ValidateRnaProductType(const CRNA_ref& rna, const CSeq_feat& feat);

    void ValidateImp(const CImp_feat& imp, const CSeq_feat& feat);
    void ValidateImpGbquals(const CImp_feat& imp, const CSeq_feat& feat);
    void ValidatePeptideOnCodonBoundry(const CSeq_feat& feat, 
        const string& key);

    void ValidateFeatPartialness(const CSeq_feat& feat);
    void ValidateExcept(const CSeq_feat& feat);
    void ValidateExceptText(const string& text, const CSeq_feat& feat);

    void ValidateFeatCit(const CPub_set& cit, const CSeq_feat& feat);
    void ValidateFeatComment(const string& comment, const CSeq_feat& feat);
    void ValidateFeatBioSource(const CBioSource& bsrc, const CSeq_feat& feat);

    bool IsPlastid(int genome);
    bool IsOverlappingGenePseudo(const CSeq_feat& feat);
    unsigned char Residue(unsigned char res);
    int  CheckForRaggedEnd(const CSeq_loc&, const CCdregion& cdr);
    bool SuppressCheck(const string& except_text);
    string MapToNTCoords(const CSeq_feat& feat, const CSeq_loc& product,
        TSeqPos pos);

    bool IsPartialAtSpliceSite(const CSeq_loc& loc, unsigned int errtype);
    bool IsTransgenic(const CBioSource& bsrc);
    bool IsSameAsCDS(const CSeq_feat& feat);
    bool IsCDDFeat(const CSeq_feat& feat) const;

    // data
    size_t m_NumGenes;
    size_t m_NumGeneXrefs;
};


// =============================  Validate SeqDesc  ============================


class CValidError_desc : private CValidError_base
{
public:
    CValidError_desc(CValidError_imp& imp);
    virtual ~CValidError_desc(void);

    void ValidateSeqDesc(const CSeqdesc& desc);

private:

    void ValidateComment(const string& comment, const CSeqdesc& desc);
    void ValidateUser(const CUser_object& usr, const CSeqdesc& desc);
    void ValidateMolInfo(const CMolInfo& minfo, const CSeqdesc& desc);
};


// ============================  Validate SeqAlign  ============================


class CValidError_align : private CValidError_base
{
public:
    CValidError_align(CValidError_imp& imp);
    virtual ~CValidError_align(void);

    void ValidateSeqAlign(const CSeq_align& align);

private:
    typedef CSeq_align::C_Segs::TDendiag    TDendiag;
    typedef CSeq_align::C_Segs::TDenseg     TDenseg;
    typedef CSeq_align::C_Segs::TPacked     TPacked;
    typedef CSeq_align::C_Segs::TStd        TStd;
    typedef CSeq_align::C_Segs::TDisc       TDisc;

    void x_ValidateDendiag(const TDendiag& dendiags, const CSeq_align& align);
    void x_ValidateDenseg(const TDenseg& denseg, const CSeq_align& align);
    void x_ValidateStd(const TStd& stdsegs, const CSeq_align& align);
    void x_ValidatePacked(const TPacked& packed, const CSeq_align& align);
    size_t x_CountBits(const CPacked_seg::TPresent& present);

    // Check if dimension is valid
    template <typename T>
    bool x_ValidateDim(T& obj, const CSeq_align& align, size_t part = 0);

    // Check if the  strand is consistent in SeqAlignment of global 
    // or partial type
    void x_ValidateStrand(const TDenseg& denseg, const CSeq_align& align);
    void x_ValidateStrand(const TPacked& packed, const CSeq_align& align);
    void x_ValidateStrand(const TStd& std_segs, const CSeq_align& align);

    // Check if an alignment is FASTA-like. 
    // Alignment is FASTA-like if all gaps are at the end with dimensions > 2.
    void x_ValidateFastaLike(const TDenseg& denseg, const CSeq_align& align);
    void x_ValidateFastaLike(const TPacked& packed, const CSeq_align& align);
    void x_ValidateFastaLike(const TStd& std_segs, const CSeq_align& align);

    // Check if there is a gap for all sequences in a segment.
    void x_ValidateSegmentGap(const TDenseg& denseg, const CSeq_align& align);
    void x_ValidateSegmentGap(const TPacked& packed, const CSeq_align& align);
    void x_ValidateSegmentGap(const TStd& std_segs, const CSeq_align& align);

    // Validate SeqId in sequence alignment.
    void x_ValidateSeqId(const CSeq_align& align);
    void x_GetIds(const CSeq_align& align, vector< CRef< CSeq_id > >& ids);

    // Check segment length, start and end point in Dense_seg, Dense_diag 
    // and Std_seg
    void x_ValidateSeqLength(const TDenseg& denseg, const CSeq_align& align);
    void x_ValidateSeqLength(const TPacked& packed, const CSeq_align& align);
    void x_ValidateSeqLength(const TStd& std_segs, const CSeq_align& align);
    void x_ValidateSeqLength(const CDense_diag& dendiag, size_t dendiag_num,
        const CSeq_align& align);
};


// ============================  Validate SeqGraph  ============================


class CValidError_graph : private CValidError_base
{
public:
    CValidError_graph(CValidError_imp& imp);
    virtual ~CValidError_graph(void);

    void ValidateSeqGraph(const CSeq_graph& graph);

    SIZE_TYPE GetNumMisplacedGraphs(void) const { return m_NumMisplaced; }

private:
    bool x_IsMisplaced(const CSeq_graph& graph);

    SIZE_TYPE   m_NumMisplaced;
};


// ============================  Validate SeqAnnot  ============================


class CValidError_annot : private CValidError_base
{
public:
    CValidError_annot(CValidError_imp& imp);
    virtual ~CValidError_annot(void);

    void ValidateSeqAnnot(const CSeq_annot& annot);
private:
};


// ============================  Validate SeqDescr  ============================


class CValidError_descr : private CValidError_base
{
public:
    CValidError_descr(CValidError_imp& imp);
    virtual ~CValidError_descr(void);

    void ValidateSeqDescr(const CSeq_descr& descr);
private:
};


END_SCOPE(validator)
END_SCOPE(objects)
END_NCBI_SCOPE


/*
* ===========================================================================
*
* $Log: validatorp.hpp,v $
* Revision 1000.3  2004/06/01 19:47:42  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.64
*
* Revision 1.64  2004/05/10 13:56:22  shomrat
* Use CSeq_feat_Handle instead of FeatAnnotMap
*
* Revision 1.63  2004/05/10 13:20:11  shomrat
* + methods for validation of abutting UTRs
*
* Revision 1.62  2004/04/27 18:40:50  shomrat
* ProtWithoutFullRef report CDS feature instead of protein bioseq
*
* Revision 1.61  2004/04/23 16:26:35  shomrat
* Use sequence::GetNucleotideParent() instead of GetNucGivenProt()
*
* Revision 1.60  2004/03/25 18:32:26  shomrat
* + ValidatemRNABioseqContext()
*
* Revision 1.59  2004/03/19 14:48:14  shomrat
* + SEQ_FEAT_PartialsInconsistent
*
* Revision 1.58  2004/03/10 21:23:09  shomrat
* + SEQ_DESCR_UnwantedCompleteFlag
*
* Revision 1.57  2004/03/01 18:39:21  shomrat
* Added alternative start codon error
*
* Revision 1.56  2004/02/25 15:52:51  shomrat
* Added CollidingLocusTags error
*
* Revision 1.55  2004/01/16 20:08:14  shomrat
* Added LocusTagProblem error
*
* Revision 1.54  2004/01/12 20:24:42  shomrat
* Added ValidateCitSub
*
* Revision 1.53  2003/12/17 19:15:19  shomrat
* declarations for graph packaging problem test
*
* Revision 1.52  2003/12/16 17:34:48  shomrat
* Added SEQ_INST_SeqLocLength
*
* Revision 1.51  2003/12/16 16:18:40  shomrat
* Added ValidateCdConflict
*
* Revision 1.50  2003/11/14 15:55:48  shomrat
* added TPA history check
*
* Revision 1.49  2003/11/12 20:30:24  shomrat
* added error code for multiple cds on mRNA bioseq
*
* Revision 1.48  2003/10/27 17:00:37  shomrat
* changed signature of ValidatePubArticle
*
* Revision 1.47  2003/10/27 14:53:57  shomrat
* added eErr_SEQ_FEAT_UTRdoesNotAbutCDS
*
* Revision 1.46  2003/10/27 14:14:11  shomrat
* added eErr_SEQ_INST_SeqLitGapLength0
*
* Revision 1.45  2003/10/24 17:56:07  shomrat
* added ValidateOperon
*
* Revision 1.44  2003/10/20 18:30:43  shomrat
* added x_IsArtificial
*
* Revision 1.43  2003/10/20 16:08:55  shomrat
* genes and gene xrefs counters
*
* Revision 1.42  2003/10/13 18:44:02  shomrat
* Added error code for bad tRNA amino acid
*
* Revision 1.41  2003/10/01 22:42:45  ucko
* Actually declare CValidError_feat::IsCDDFeat....
*
* Revision 1.40  2003/09/23 13:25:55  shomrat
* Added IsDeltaSeqOnly test
*
* Revision 1.39  2003/09/22 20:23:33  shomrat
* Added x_IsMicroRNA
*
* Revision 1.38  2003/09/03 18:25:09  shomrat
* added SEQ_DESCR_RefGeneTrackingWithoutStatus
*
* Revision 1.37  2003/08/06 15:05:42  shomrat
* Added test for adjacent Ns in Seq-literal
*
* Revision 1.36  2003/07/24 20:16:18  vasilche
* Fixed typedefs for dbxref: list<CRef<CDbtag>> -> vector<CRef<CDbtag>>
*
* Revision 1.35  2003/07/21 21:18:19  shomrat
* Added eErr_SEQ_FEAT_MissingLocation
*
* Revision 1.34  2003/07/15 18:26:43  shomrat
* Added x_IsActiveFin
*
* Revision 1.33  2003/07/02 21:03:38  shomrat
* Added ValidateCDSPartial
*
* Revision 1.32  2003/06/27 18:53:20  shomrat
* Changed ValidateDbxref definition
*
* Revision 1.31  2003/06/19 15:34:09  shomrat
* Added IsOtherDNA and IsSynthetic
*
* Revision 1.30  2003/06/02 16:06:43  dicuccio
* Rearranged src/objects/ subtree.  This includes the following shifts:
*     - src/objects/asn2asn --> arc/app/asn2asn
*     - src/objects/testmedline --> src/objects/ncbimime/test
*     - src/objects/objmgr --> src/objmgr
*     - src/objects/util --> src/objmgr/util
*     - src/objects/alnmgr --> src/objtools/alnmgr
*     - src/objects/flat --> src/objtools/flat
*     - src/objects/validator --> src/objtools/validator
*     - src/objects/cddalignview --> src/objtools/cddalignview
* In addition, libseq now includes six of the objects/seq... libs, and libmmdb
* replaces the three libmmdb? libs.
*
* Revision 1.29  2003/05/28 16:23:45  shomrat
* Minor corrections.
*
* Revision 1.28  2003/05/05 15:35:45  shomrat
* Added ValidateCdsProductId
*
* Revision 1.27  2003/04/29 14:55:09  shomrat
* Added SeqAlign validation
*
* Revision 1.26  2003/04/24 16:16:00  vasilche
* Added missing includes and forward class declarations.
*
* Revision 1.25  2003/04/15 14:53:32  shomrat
* Added a progress callback mechanism
*
* Revision 1.24  2003/04/10 19:25:07  shomrat
* Added ValidateMolTypeContext
*
* Revision 1.23  2003/04/07 14:56:09  shomrat
* Added Seq-loc ids validation
*
* Revision 1.22  2003/04/04 18:39:17  shomrat
* Added Internal Exception error and tests for the availabilty of the sequence
*
* Revision 1.21  2003/03/31 14:41:21  shomrat
* $id: -> $id$
*
* Revision 1.20  2003/03/28 16:28:53  shomrat
* Added Seq-graph tests related methods
*
* Revision 1.19  2003/03/21 21:12:17  shomrat
* Added eErr_SEQ_DESCR_UnnecessaryBioSourceFocus; Change to signature of ValidateOrgContext
*
* Revision 1.18  2003/03/21 19:37:04  shomrat
* Added IsNucAcc and IsFlybaseDbxrefs
*
* Revision 1.17  2003/03/21 16:21:46  shomrat
* Added ValidateIDSetAgainstDb
*
* Revision 1.16  2003/03/20 18:55:28  shomrat
* Added validation of standalone Seq-annot objects
*
* Revision 1.15  2003/02/24 20:16:41  shomrat
* Holds refernce to the CValidError object, and not the internal TErrs
*
* Revision 1.14  2003/02/14 21:46:20  shomrat
* Added methods to check Bioseqs with no MolInfo
*
* Revision 1.13  2003/02/12 17:40:35  shomrat
* Added function for SEQ_DESCR checks
*
* Revision 1.12  2003/02/07 21:09:43  shomrat
* Added eErr_SEQ_INST_TerminalNs; Added helper methods
*
* Revision 1.11  2003/02/03 20:18:14  shomrat
* Added flag to skip performance bottlenecks (for testing)
*
* Revision 1.10  2003/02/03 17:08:48  shomrat
* Changed return value for GetCDSGivenProduct
*
* Revision 1.9  2003/01/29 21:55:19  shomrat
* Added check for et al
*
* Revision 1.8  2003/01/24 20:39:40  shomrat
* Added history validation for bioseq
*
* Revision 1.7  2003/01/21 20:20:43  shomrat
* Added private methods to facilitate the PubDesc Validation
*
* Revision 1.6  2003/01/10 16:31:23  shomrat
* Added private functions to CValidError_feat
*
* Revision 1.5  2003/01/08 18:35:31  shomrat
* Added mapping features to their enclosing annotation
*
* Revision 1.4  2003/01/02 21:57:21  shomrat
* Add eErr_SEQ_FEAT_BadProductSeqId error; Chenges in (mostly private) interfaces of validation classes
*
* Revision 1.3  2002/12/24 16:52:15  shomrat
* Changes to include directives
*
* Revision 1.2  2002/12/23 20:09:02  shomrat
* Added static functions as private members; Added base class for specific validation classes
*
*
* ===========================================================================
*/

#endif  /* VALIDATOR___VALIDATORP__HPP */