seqfeatdata.hpp

ncbi源码

/*
 * ===========================================================================
 * PRODUCTION $Log: SeqFeatData.hpp,v $
 * PRODUCTION Revision 1000.1  2004/06/01 19:30:46  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.6
 * PRODUCTION
 * ===========================================================================
 */

/* $Id: SeqFeatData.hpp,v 1000.1 2004/06/01 19:30:46 gouriano Exp $
 * ===========================================================================
 *
 *                            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:  .......
 *
 * File Description:
 *   .......
 *
 * Remark:
 *   This code was originally generated by application DATATOOL
 *   using specifications from the ASN data definition file
 *   'seqfeat.asn'.
 */

#ifndef OBJECTS_SEQFEAT_SEQFEATDATA_HPP
#define OBJECTS_SEQFEAT_SEQFEATDATA_HPP


// generated includes
#include <objects/seqfeat/SeqFeatData_.hpp>

// generated classes

BEGIN_NCBI_SCOPE

BEGIN_objects_SCOPE // namespace ncbi::objects::

class NCBI_SEQFEAT_EXPORT CSeqFeatData : public CSeqFeatData_Base
{
    typedef CSeqFeatData_Base Tparent;
public:
    // constructor
    CSeqFeatData(void);
    // destructor
    ~CSeqFeatData(void);

    // ASCII representation of subtype (GenBank feature key, e.g.)
    enum EVocabulary {
        eVocabulary_full,
        eVocabulary_genbank
    };
    string GetKey(EVocabulary vocab = eVocabulary_full) const;

    enum ESubtype {
        // These no longer need to match the FEATDEF values in the
        // C toolkit's objfdef.h
        eSubtype_bad = 0,
        eSubtype_gene,
        eSubtype_org,
        eSubtype_cdregion,
        eSubtype_prot,
        eSubtype_preprotein,
        eSubtype_mat_peptide_aa,
        eSubtype_sig_peptide_aa,
        eSubtype_transit_peptide_aa,
        eSubtype_preRNA,
        eSubtype_mRNA,
        eSubtype_tRNA,
        eSubtype_rRNA,
        eSubtype_snRNA,
        eSubtype_scRNA,
        eSubtype_snoRNA,
        eSubtype_otherRNA,
        eSubtype_pub,
        eSubtype_seq,
        eSubtype_imp,
        eSubtype_allele,
        eSubtype_attenuator,
        eSubtype_C_region,
        eSubtype_CAAT_signal,
        eSubtype_Imp_CDS,
        eSubtype_conflict,
        eSubtype_D_loop,
        eSubtype_D_segment,
        eSubtype_enhancer,
        eSubtype_exon,
        eSubtype_GC_signal,
        eSubtype_iDNA,
        eSubtype_intron,
        eSubtype_J_segment,
        eSubtype_LTR,
        eSubtype_mat_peptide,
        eSubtype_misc_binding,
        eSubtype_misc_difference,
        eSubtype_misc_feature,
        eSubtype_misc_recomb,
        eSubtype_misc_RNA,
        eSubtype_misc_signal,
        eSubtype_misc_structure,
        eSubtype_modified_base,
        eSubtype_mutation,
        eSubtype_N_region,
        eSubtype_old_sequence,
        eSubtype_polyA_signal,
        eSubtype_polyA_site,
        eSubtype_precursor_RNA,
        eSubtype_prim_transcript,
        eSubtype_primer_bind,
        eSubtype_promoter,
        eSubtype_protein_bind,
        eSubtype_RBS,
        eSubtype_repeat_region,
        eSubtype_repeat_unit,
        eSubtype_rep_origin,
        eSubtype_S_region,
        eSubtype_satellite,
        eSubtype_sig_peptide,
        eSubtype_source,
        eSubtype_stem_loop,
        eSubtype_STS,
        eSubtype_TATA_signal,
        eSubtype_terminator,
        eSubtype_transit_peptide,
        eSubtype_unsure,
        eSubtype_V_region,
        eSubtype_V_segment,
        eSubtype_variation,
        eSubtype_virion,
        eSubtype_3clip,
        eSubtype_3UTR,
        eSubtype_5clip,
        eSubtype_5UTR,
        eSubtype_10_signal,
        eSubtype_35_signal,
        eSubtype_gap,
        eSubtype_operon,
        eSubtype_oriT,
        eSubtype_site_ref,
        eSubtype_region,
        eSubtype_comment,
        eSubtype_bond,
        eSubtype_site,
        eSubtype_rsite,
        eSubtype_user,
        eSubtype_txinit,
        eSubtype_num,
        eSubtype_psec_str,
        eSubtype_non_std_residue,
        eSubtype_het,
        eSubtype_biosrc,
        eSubtype_max,
        eSubtype_any = 255
    };
    ESubtype GetSubtype(void) const;
    
    // Call after changes that could affect the subtype
    void InvalidateSubtype(void);

    static E_Choice GetTypeFromSubtype (ESubtype subtype);

    // List of available qualifiers for feature keys.
    // For more information see: 
    //   The DDBJ/EMBL/GenBank Feature Table: Definition
    //   (http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html)
    enum EQualifier
    {
        eQual_bad = 0,
        eQual_allele,
        eQual_anticodon,
        eQual_bound_moiety,
        eQual_cell_line,
        eQual_cell_type,
        eQual_chromosome,
        eQual_citation,
        eQual_clone,
        eQual_clone_lib,
        eQual_codon,
        eQual_codon_start,
        eQual_cons_splice,
        eQual_country,
        eQual_cultivar,
        eQual_db_xref,
        eQual_dev_stage,
        eQual_direction,
        eQual_EC_number,
        eQual_ecotype,
        eQual_environmental_sample,
        eQual_estimated_length,
        eQual_evidence,
        eQual_exception,
        eQual_focus,
        eQual_frequency,
        eQual_function,
        eQual_gene,
        eQual_germline,
        eQual_haplotype,
        eQual_insertion_seq,
        eQual_isolate,
        eQual_isolation_source,
        eQual_label,
        eQual_lab_host,
        eQual_locus_tag,
        eQual_map,
        eQual_macronuclear,
        eQual_mod_base,
        eQual_mol_type,
        eQual_note,
        eQual_number,
        eQual_operon,
        eQual_organelle,
        eQual_organism,
        eQual_partial,
        eQual_PCR_conditions,
        eQual_phenotype,
        eQual_pop_variant,
        eQual_plasmid,
        eQual_product,
        eQual_protein_id,
        eQual_proviral,
        eQual_pseudo,
        eQual_rearranged,
        eQual_replace,
        eQual_rpt_family,
        eQual_rpt_type,
        eQual_rpt_unit,
        eQual_segment,
        eQual_sequence_mol,
        eQual_serotype,
        eQual_serovar,
        eQual_sex,
        eQual_specific_host,
        eQual_specimen_voucher,
        eQual_standard_name,
        eQual_strain,
        eQual_sub_clone,
        eQual_sub_species,
        eQual_sub_strain,
        eQual_tissue_lib,
        eQual_tissue_type,
        eQual_transgenic,
        eQual_translation,
        eQual_transl_except,
        eQual_transl_table,
        eQual_transposon,
        eQual_usedin,
        eQual_variety,
        eQual_virion
    };
    typedef vector<EQualifier> TQualifiers;

    // Test wheather a certain qualifier is legal for the feature
    bool IsLegalQualifier(EQualifier qual) const;
    static bool IsLegalQualifier(ESubtype subtype, EQualifier qual);

    // Get a list of all the legal qualifiers for the feature.
    const TQualifiers& GetLegalQualifiers(void) const;
    static const TQualifiers& GetLegalQualifiers(ESubtype subtype);

    // Get the list of all mandatory qualifiers for the feature.
    const TQualifiers& GetMandatoryQualifiers(void) const;
    static const TQualifiers& GetMandatoryQualifiers(ESubtype subtype);
    
    // Convert a qualifier from an enumerated value to a string representation.
    static const string& GetQulifierAsString(EQualifier qual);

private:
    mutable ESubtype m_Subtype; // cached

    // Prohibit copy constructor and assignment operator
    CSeqFeatData(const CSeqFeatData& value);
    CSeqFeatData& operator=(const CSeqFeatData& value);

    typedef map<ESubtype, TQualifiers> TFeatQuals;
    static void x_InitQuals(void);
    static void x_InitLegalQuals(void);
    static void x_InitMandatoryQuals(void);

    static TFeatQuals sm_LegalQuals;
    static TFeatQuals sm_MandatoryQuals;
};



/////////////////// CSeqFeatData inline methods

// constructor
inline
CSeqFeatData::CSeqFeatData(void) : m_Subtype(eSubtype_any)
{
}


inline
void CSeqFeatData::InvalidateSubtype(void)
{
    m_Subtype = eSubtype_any;
}


inline
bool CSeqFeatData::IsLegalQualifier(EQualifier qual) const
{
    x_InitQuals();  // does nothing if already intialized
    return IsLegalQualifier(GetSubtype(), qual);
}


inline
const CSeqFeatData::TQualifiers& CSeqFeatData::GetLegalQualifiers(void) const
{
    x_InitQuals();  // does nothing if already intialized
    return GetLegalQualifiers(GetSubtype());
}


inline
const CSeqFeatData::TQualifiers& CSeqFeatData::GetMandatoryQualifiers(void) const
{
    x_InitQuals();  // does nothing if already intialized
    return GetMandatoryQualifiers(GetSubtype());
}

/////////////////// end of CSeqFeatData inline methods


END_objects_SCOPE // namespace ncbi::objects::

END_NCBI_SCOPE


#endif // OBJECTS_SEQFEAT_SEQFEATDATA_HPP

/*
* ===========================================================================
*
* $Log: SeqFeatData.hpp,v $
* Revision 1000.1  2004/06/01 19:30:46  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.6
*
* Revision 1.6  2004/05/19 14:39:42  shomrat
* Added list of qualifiers
*
* Revision 1.5  2003/10/24 17:13:49  shomrat
* added gap, operaon and oriT subtypes
*
* Revision 1.4  2003/04/19 16:38:06  dicuccio
* Remove compiler warning about nested c-style comments
*
* Revision 1.3  2003/04/18 21:20:44  kans
* regrouped ESubtype, removing most explicit numbers, added GetTypeFromSubtype, moved log to end of file
*
* Revision 1.2  2002/12/26 12:43:27  dicuccio
* Added Win32 export specifiers
*
* Revision 1.1  2001/10/30 20:25:56  ucko
* Implement feature labels/keys, subtypes, and sorting
*
*
* ===========================================================================
*/
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