seqfeatdata.cpp

ncbi源码

    ADD_QUAL(usedin);
END_SUBTYPE

START_SUBTYPE(terminator)
    ADD_QUAL(allele);
    ADD_QUAL(citation);
    ADD_QUAL(db_xref);
    ADD_QUAL(evidence);
    ADD_QUAL(gene);
    ADD_QUAL(label);
    ADD_QUAL(locus_tag);
    ADD_QUAL(map);
    ADD_QUAL(note);
    ADD_QUAL(operon);
    ADD_QUAL(standard_name);
    ADD_QUAL(usedin);
END_SUBTYPE

START_SUBTYPE(transit_peptide)
    ADD_QUAL(allele);
    ADD_QUAL(citation);
    ADD_QUAL(db_xref);
    ADD_QUAL(evidence);
    ADD_QUAL(function);
    ADD_QUAL(gene);
    ADD_QUAL(label);
    ADD_QUAL(locus_tag);
    ADD_QUAL(map);
    ADD_QUAL(note);
    ADD_QUAL(product);
    ADD_QUAL(pseudo);
    ADD_QUAL(standard_name);
    ADD_QUAL(usedin);
END_SUBTYPE

START_SUBTYPE(unsure)
    ADD_QUAL(allele);
    ADD_QUAL(citation);
    ADD_QUAL(db_xref);
    ADD_QUAL(evidence);
    ADD_QUAL(gene);
    ADD_QUAL(label);
    ADD_QUAL(locus_tag);
    ADD_QUAL(map);
    ADD_QUAL(note);
    ADD_QUAL(replace);
    ADD_QUAL(usedin);
END_SUBTYPE

START_SUBTYPE(V_region)
    ADD_QUAL(allele);
    ADD_QUAL(citation);
    ADD_QUAL(db_xref);
    ADD_QUAL(evidence);
    ADD_QUAL(gene);
    ADD_QUAL(label);
    ADD_QUAL(locus_tag);
    ADD_QUAL(map);
    ADD_QUAL(note);
    ADD_QUAL(product);
    ADD_QUAL(pseudo);
    ADD_QUAL(standard_name);
    ADD_QUAL(usedin);
END_SUBTYPE

START_SUBTYPE(V_segment)
    ADD_QUAL(allele);
    ADD_QUAL(citation);
    ADD_QUAL(db_xref);
    ADD_QUAL(evidence);
    ADD_QUAL(gene);
    ADD_QUAL(label);
    ADD_QUAL(locus_tag);
    ADD_QUAL(map);
    ADD_QUAL(note);
    ADD_QUAL(product);
    ADD_QUAL(pseudo);
    ADD_QUAL(standard_name);
    ADD_QUAL(usedin);
END_SUBTYPE

START_SUBTYPE(variation)
    ADD_QUAL(allele);
    ADD_QUAL(citation);
    ADD_QUAL(db_xref);
    ADD_QUAL(evidence);
    ADD_QUAL(frequency);
    ADD_QUAL(gene);
    ADD_QUAL(label);
    ADD_QUAL(locus_tag);
    ADD_QUAL(map);
    ADD_QUAL(note);
    ADD_QUAL(phenotype);
    ADD_QUAL(product);
    ADD_QUAL(replace);
    ADD_QUAL(standard_name);
    ADD_QUAL(usedin);
END_SUBTYPE

//START_SUBTYPE(virion)

START_SUBTYPE(3clip)
    ADD_QUAL(allele);
    ADD_QUAL(citation);
    ADD_QUAL(db_xref);
    ADD_QUAL(evidence);
    ADD_QUAL(function);
    ADD_QUAL(gene);
    ADD_QUAL(label);
    ADD_QUAL(locus_tag);
    ADD_QUAL(map);
    ADD_QUAL(note);
    ADD_QUAL(standard_name);
    ADD_QUAL(usedin);
END_SUBTYPE

START_SUBTYPE(3UTR)
    ADD_QUAL(allele);
    ADD_QUAL(citation);
    ADD_QUAL(db_xref);
    ADD_QUAL(evidence);
    ADD_QUAL(function);
    ADD_QUAL(gene);
    ADD_QUAL(label);
    ADD_QUAL(locus_tag);
    ADD_QUAL(map);
    ADD_QUAL(note);
    ADD_QUAL(standard_name);
    ADD_QUAL(usedin);
END_SUBTYPE

START_SUBTYPE(5clip)
    ADD_QUAL(allele);
    ADD_QUAL(citation);
    ADD_QUAL(db_xref);
    ADD_QUAL(evidence);
    ADD_QUAL(function);
    ADD_QUAL(gene);
    ADD_QUAL(label);
    ADD_QUAL(locus_tag);
    ADD_QUAL(map);
    ADD_QUAL(note);
    ADD_QUAL(standard_name);
    ADD_QUAL(usedin);
END_SUBTYPE

START_SUBTYPE(5UTR)
    ADD_QUAL(allele);
    ADD_QUAL(citation);
    ADD_QUAL(db_xref);
    ADD_QUAL(evidence);
    ADD_QUAL(function);
    ADD_QUAL(gene);
    ADD_QUAL(label);
    ADD_QUAL(locus_tag);
    ADD_QUAL(map);
    ADD_QUAL(note);
    ADD_QUAL(standard_name);
    ADD_QUAL(usedin);
END_SUBTYPE

START_SUBTYPE(10_signal)
    ADD_QUAL(allele);
    ADD_QUAL(citation);
    ADD_QUAL(db_xref);
    ADD_QUAL(evidence);
    ADD_QUAL(gene);
    ADD_QUAL(label);
    ADD_QUAL(locus_tag);
    ADD_QUAL(map);
    ADD_QUAL(note);
    ADD_QUAL(operon);
    ADD_QUAL(standard_name);
    ADD_QUAL(usedin);
END_SUBTYPE

START_SUBTYPE(35_signal)
    ADD_QUAL(allele);
    ADD_QUAL(citation);
    ADD_QUAL(db_xref);
    ADD_QUAL(evidence);
    ADD_QUAL(gene);
    ADD_QUAL(label);
    ADD_QUAL(locus_tag);
    ADD_QUAL(map);
    ADD_QUAL(note);
    ADD_QUAL(operon);
    ADD_QUAL(standard_name);
    ADD_QUAL(usedin);
END_SUBTYPE

START_SUBTYPE(gap)
    ADD_QUAL(estimated_length);
END_SUBTYPE

START_SUBTYPE(operon)
    ADD_QUAL(allele);
    ADD_QUAL(citation);
    ADD_QUAL(db_xref);
    ADD_QUAL(evidence);
    ADD_QUAL(function);
    ADD_QUAL(label);
    ADD_QUAL(map);
    ADD_QUAL(note);
    ADD_QUAL(operon);
    ADD_QUAL(phenotype);
    ADD_QUAL(pseudo);
    ADD_QUAL(standard_name);
    ADD_QUAL(usedin);
END_SUBTYPE

START_SUBTYPE(oriT)
    ADD_QUAL(allele);
    ADD_QUAL(bound_moiety);
    ADD_QUAL(citation);
    ADD_QUAL(db_xref);
    ADD_QUAL(direction);
    ADD_QUAL(evidence);
    ADD_QUAL(gene);
    ADD_QUAL(label);
    ADD_QUAL(locus_tag);
    ADD_QUAL(map);
    ADD_QUAL(note);
    ADD_QUAL(rpt_family);
    ADD_QUAL(rpt_type);
    ADD_QUAL(rpt_unit);
    ADD_QUAL(standard_name);
    ADD_QUAL(usedin);
END_SUBTYPE

//START_SUBTYPE(site_ref)
//END_SUBTYPE

START_SUBTYPE(region)
    ADD_QUAL(allele);
    ADD_QUAL(citation);
    ADD_QUAL(db_xref);
    ADD_QUAL(evidence);
    ADD_QUAL(gene);
    ADD_QUAL(label);
    ADD_QUAL(locus_tag);
    ADD_QUAL(map);
    ADD_QUAL(note);
    ADD_QUAL(product);
    ADD_QUAL(pseudo);
    ADD_QUAL(standard_name);
    ADD_QUAL(usedin);
END_SUBTYPE

//START_SUBTYPE(comment)
//END_SUBTYPE

//START_SUBTYPE(bond)
//END_SUBTYPE

//START_SUBTYPE(site)
//END_SUBTYPE

//START_SUBTYPE(rsite)
//END_SUBTYPE

//START_SUBTYPE(user)
//END_SUBTYPE

//START_SUBTYPE(txinit)
//END_SUBTYPE

//START_SUBTYPE(num)
//END_SUBTYPE

//START_SUBTYPE(psec_str)
//END_SUBTYPE

//START_SUBTYPE(non_std_residue)
//END_SUBTYPE

//START_SUBTYPE(het)
//END_SUBTYPE

//START_SUBTYPE(biosrc)
//END_SUBTYPE

#undef START_SUBTYPE
#undef ADD_QUAL
#undef END_SYBTYPE
}


void CSeqFeatData::x_InitMandatoryQuals(void)
{
    sm_MandatoryQuals[eSubtype_conflict].push_back(eQual_citation);
    sm_MandatoryQuals[eSubtype_gap].push_back(eQual_estimated_length);
    sm_MandatoryQuals[eSubtype_misc_binding].push_back(eQual_bound_moiety);
    sm_MandatoryQuals[eSubtype_protein_bind].push_back(eQual_bound_moiety);
    sm_MandatoryQuals[eSubtype_modified_base].push_back(eQual_mod_base);
    sm_MandatoryQuals[eSubtype_old_sequence].push_back(eQual_citation);
    sm_MandatoryQuals[eSubtype_operon].push_back(eQual_operon);
}


void CSeqFeatData::x_InitQuals(void)
{
    static bool initialized = false;
    
    if ( initialized ) {
        return;
    }
    x_InitLegalQuals();
    x_InitMandatoryQuals();

    initialized = true;
}

typedef pair<CSeqFeatData::EQualifier, string> TQualPair;
static const TQualPair kQualPairs[] = {
    TQualPair(CSeqFeatData::eQual_bad, "bad"),
    TQualPair(CSeqFeatData::eQual_allele, "allele"),
    TQualPair(CSeqFeatData::eQual_anticodon, "anticodon"),
    TQualPair(CSeqFeatData::eQual_bound_moiety, "bound_moiety"),
    TQualPair(CSeqFeatData::eQual_cell_line, "cell_line"),
    TQualPair(CSeqFeatData::eQual_cell_type, "cell_type"),
    TQualPair(CSeqFeatData::eQual_chromosome, "chromosome"),
    TQualPair(CSeqFeatData::eQual_citation, "citation"),
    TQualPair(CSeqFeatData::eQual_clone, "clone"),
    TQualPair(CSeqFeatData::eQual_clone_lib, "clone_lib"),
    TQualPair(CSeqFeatData::eQual_codon, "codon"),
    TQualPair(CSeqFeatData::eQual_codon_start, "cons_splice"),
    TQualPair(CSeqFeatData::eQual_cons_splice, "cons_splice"),
    TQualPair(CSeqFeatData::eQual_country, "country"),
    TQualPair(CSeqFeatData::eQual_cultivar, "cultivar"),
    TQualPair(CSeqFeatData::eQual_db_xref, "db_xref"),
    TQualPair(CSeqFeatData::eQual_dev_stage, "dev_stage"),
    TQualPair(CSeqFeatData::eQual_direction, "direction"),
    TQualPair(CSeqFeatData::eQual_EC_number, "EC_number"),
    TQualPair(CSeqFeatData::eQual_ecotype, "ecotype"),
    TQualPair(CSeqFeatData::eQual_environmental_sample, "environmental_sample"),
    TQualPair(CSeqFeatData::eQual_estimated_length, "estimated_length"),
    TQualPair(CSeqFeatData::eQual_evidence, "evidence"),
    TQualPair(CSeqFeatData::eQual_exception, "exception"),
    TQualPair(CSeqFeatData::eQual_focus, "focus"),
    TQualPair(CSeqFeatData::eQual_frequency, "frequency"),
    TQualPair(CSeqFeatData::eQual_function, "function"),
    TQualPair(CSeqFeatData::eQual_gene, "gene"),
    TQualPair(CSeqFeatData::eQual_germline, "germline"),
    TQualPair(CSeqFeatData::eQual_haplotype, "haplotype"),
    TQualPair(CSeqFeatData::eQual_insertion_seq, "insertion_seq"),
    TQualPair(CSeqFeatData::eQual_isolate, "isolate"),
    TQualPair(CSeqFeatData::eQual_isolation_source, "isolation_source"),
    TQualPair(CSeqFeatData::eQual_label, "label"),
    TQualPair(CSeqFeatData::eQual_lab_host, "lab_host"),
    TQualPair(CSeqFeatData::eQual_locus_tag, "locus_tag"),
    TQualPair(CSeqFeatData::eQual_map, "map"),
    TQualPair(CSeqFeatData::eQual_macronuclear, "macronuclear"),
    TQualPair(CSeqFeatData::eQual_mod_base, "mod_base"),
    TQualPair(CSeqFeatData::eQual_mol_type, "mol_type"),
    TQualPair(CSeqFeatData::eQual_note, "note"),
    TQualPair(CSeqFeatData::eQual_number, "number"),
    TQualPair(CSeqFeatData::eQual_operon, "operon"),
    TQualPair(CSeqFeatData::eQual_organelle, "organelle"),
    TQualPair(CSeqFeatData::eQual_organism, "organism"),
    TQualPair(CSeqFeatData::eQual_partial, "partial"),
    TQualPair(CSeqFeatData::eQual_PCR_conditions, "PCR_conditions"),
    TQualPair(CSeqFeatData::eQual_phenotype, "phenotype"),
    TQualPair(CSeqFeatData::eQual_pop_variant, "pop_variant"),
    TQualPair(CSeqFeatData::eQual_plasmid, "plasmid"),
    TQualPair(CSeqFeatData::eQual_product, "product"),
    TQualPair(CSeqFeatData::eQual_protein_id, "protein_id"),
    TQualPair(CSeqFeatData::eQual_proviral, "proviral"),
    TQualPair(CSeqFeatData::eQual_pseudo, "pseudo"),
    TQualPair(CSeqFeatData::eQual_rearranged, "rearranged"),
    TQualPair(CSeqFeatData::eQual_replace, "replace"),
    TQualPair(CSeqFeatData::eQual_rpt_family, "rpt_family"),
    TQualPair(CSeqFeatData::eQual_rpt_type, "rpt_type"),
    TQualPair(CSeqFeatData::eQual_rpt_unit, "rpt_unit"),
    TQualPair(CSeqFeatData::eQual_segment, "segment"),
    TQualPair(CSeqFeatData::eQual_sequence_mol, "sequence_mol"),
    TQualPair(CSeqFeatData::eQual_serotype, "serotype"),
    TQualPair(CSeqFeatData::eQual_serovar, "serovar"),
    TQualPair(CSeqFeatData::eQual_sex, "sex"),
    TQualPair(CSeqFeatData::eQual_specific_host, "specific_host"),
    TQualPair(CSeqFeatData::eQual_specimen_voucher, "specimen_voucher"),
    TQualPair(CSeqFeatData::eQual_standard_name, "standard_name"),
    TQualPair(CSeqFeatData::eQual_strain, "strain"),
    TQualPair(CSeqFeatData::eQual_sub_clone, "sub_clone"),
    TQualPair(CSeqFeatData::eQual_sub_species, "sub_species"),
    TQualPair(CSeqFeatData::eQual_sub_strain, "sub_strain"),
    TQualPair(CSeqFeatData::eQual_tissue_lib, "tissue_lib"),
    TQualPair(CSeqFeatData::eQual_tissue_type, "tissue_type"),
    TQualPair(CSeqFeatData::eQual_transgenic, "transgenic"),
    TQualPair(CSeqFeatData::eQual_translation, "translation"),
    TQualPair(CSeqFeatData::eQual_transl_except, "transl_except"),
    TQualPair(CSeqFeatData::eQual_transl_table, "transl_table"),
    TQualPair(CSeqFeatData::eQual_transposon, "transposon"),
    TQualPair(CSeqFeatData::eQual_usedin, "usedin"),
    TQualPair(CSeqFeatData::eQual_variety, "variety"),
    TQualPair(CSeqFeatData::eQual_virion, "virion"),
};

typedef CStaticArrayMap<CSeqFeatData::EQualifier, string> TQualsMap;
static const TQualsMap sc_QualPairs(kQualPairs, sizeof(kQualPairs));

const string& CSeqFeatData::GetQulifierAsString(EQualifier qual)
{
    TQualsMap::const_iterator iter = sc_QualPairs.find(qual);
    return (iter != sc_QualPairs.end()) ? iter->second : kEmptyStr;
}


END_objects_SCOPE // namespace ncbi::objects::

END_NCBI_SCOPE

/*
* ===========================================================================
*
* $Log: SeqFeatData.cpp,v $
* Revision 1000.2  2004/06/01 19:34:09  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R6.13
*
* Revision 6.13  2004/05/19 17:26:04  gorelenk
* Added include of PCH - ncbi_pch.hpp
*
* Revision 6.12  2004/05/19 14:41:02  shomrat
* Added list of qualifiers
*
* Revision 6.11  2004/03/10 21:33:43  shomrat
* Fixed key for genbank vocabulary
*
* Revision 6.10  2003/10/24 17:14:28  shomrat
* added gap, operaon and oriT subtypes
*
* Revision 6.9  2003/06/02 18:06:10  ucko
* GetSubtype: handle imported features more efficiently.
*
* Revision 6.8  2003/05/20 01:29:39  ucko
* Added missing punctuation in imported keys' names.
*
* Revision 6.7  2003/05/19 18:21:32  ucko
* Add "break" statement accidentally dropped in last change.
*
* Revision 6.6  2003/05/19 17:35:56  ucko
* GetSubtype: properly honor Prot-ref.processed, and ignore bogus
* imports with corresponding names.
*
* Revision 6.5  2003/04/19 16:38:45  dicuccio
* Remove compiler warning about nested comments
*
* Revision 6.4  2003/04/18 21:21:25  kans
* added GetTypeFromSubtype, moved log to end of file
*
* Revision 6.3  2002/03/22 16:13:42  ucko
* CSeqFeatData::GetKey: return "Prot" rather than "Protein" in default
* vocabulary.  (Keep "Protein" for Genbank).
*
* Revision 6.2  2002/03/06 21:59:48  ucko
* CSeqFeatData::GetKey: return (misc_)RNA rather than extended name for
* RNA of type "other."
*
* Revision 6.1  2001/10/30 20:25:58  ucko
* Implement feature labels/keys, subtypes, and sorting
*
*
* ===========================================================================
*/
/* Original file checksum: lines: 61, chars: 1894, CRC32: 86fb976 */