feat_config_list.cpp

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/*
 * ===========================================================================
 * PRODUCTION $Log: feat_config_list.cpp,v $
 * PRODUCTION Revision 1000.1  2004/06/01 20:43:13  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.6
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: feat_config_list.cpp,v 1000.1 2004/06/01 20:43:13 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.
 *
 * ===========================================================================
 *
 * Authors:  Robert Smith
 *
 */

/// @file feat_config_list.cpp
/// 
/// List of feature types to configure preferences for viewing SeqFeats.


#include <ncbi_pch.hpp>
#include <gui/config/feat_config_list.hpp>


BEGIN_NCBI_SCOPE

const CFeatConfigList* GetFeatConfigList()
{
    static CFeatConfigList* theFeatConfigList = 0;
    
    if (theFeatConfigList == 0) {
        theFeatConfigList = new CFeatConfigList();
        
    }
    return theFeatConfigList;
}

#define kMasterDescString "All"
static string   s_MasterDesc(kMasterDescString);

string  ChangeMasterFeatDescription(const string& oldDesc, const string& newMasterDesc)
{
    string newDesc = oldDesc;
    SIZE_TYPE mast_pos = newDesc.find(s_MasterDesc);
    while (mast_pos != NPOS) {
        newDesc.replace(mast_pos, s_MasterDesc.size(), newMasterDesc);
        mast_pos = newDesc.find(s_MasterDesc, mast_pos + newMasterDesc.size());
    }
    return newDesc;
}

USING_SCOPE(objects);

namespace {

CFeatConfigItem config_item_init[] = {
    CFeatConfigItem( CSeqFeatData::e_not_set,   CSeqFeatData::eSubtype_any,   kMasterDescString,  "Master" ),
    CFeatConfigItem( CSeqFeatData::e_Gene,      CSeqFeatData::eSubtype_gene,  "Gene", "Gene" ),
    CFeatConfigItem( CSeqFeatData::e_Org,      CSeqFeatData::eSubtype_org,   "Org",  "Org" ),
    CFeatConfigItem( CSeqFeatData::e_Cdregion, CSeqFeatData::eSubtype_cdregion,  "CDS",  "CDS" ),

    CFeatConfigItem( CSeqFeatData::e_Prot,     CSeqFeatData::eSubtype_any,   "Protein, " kMasterDescString,  "Prot Master" ),
    CFeatConfigItem( CSeqFeatData::e_Prot,     CSeqFeatData::eSubtype_prot,  "Protein", "Prot" ),
    CFeatConfigItem( CSeqFeatData::e_Prot,     CSeqFeatData::eSubtype_preprotein,    "PreProtein", "PreProtein" ),
    CFeatConfigItem( CSeqFeatData::e_Prot,     CSeqFeatData::eSubtype_mat_peptide_aa,    "Mature Peptide AA", "Mat-Peptide AA" ),
    CFeatConfigItem( CSeqFeatData::e_Prot,     CSeqFeatData::eSubtype_sig_peptide_aa,    "Signal Peptide AA", "Sig-Peptide AA" ), 
    CFeatConfigItem( CSeqFeatData::e_Prot,     CSeqFeatData::eSubtype_transit_peptide_aa,    "Transit Peptide AA", "Transit-Peptide AA" ), 

    CFeatConfigItem( CSeqFeatData::e_Rna,     CSeqFeatData::eSubtype_any,   "RNA, " kMasterDescString, "RNA Master" ),
    CFeatConfigItem( CSeqFeatData::e_Rna,     CSeqFeatData::eSubtype_preRNA,  "precursor_RNA",   "precursor_RNA" ),   
    CFeatConfigItem( CSeqFeatData::e_Rna,     CSeqFeatData::eSubtype_mRNA,  "mRNA", "mRNA" ), 
    CFeatConfigItem( CSeqFeatData::e_Rna,     CSeqFeatData::eSubtype_tRNA,  "tRNA", "tRNA" ), 
    CFeatConfigItem( CSeqFeatData::e_Rna,     CSeqFeatData::eSubtype_rRNA,  "rRNA", "rRNA" ), 
    CFeatConfigItem( CSeqFeatData::e_Rna,     CSeqFeatData::eSubtype_snRNA,  "snRNA", "snRNA" ), 
    CFeatConfigItem( CSeqFeatData::e_Rna,     CSeqFeatData::eSubtype_scRNA,  "scRNA", "scRNA" ), 
    CFeatConfigItem( CSeqFeatData::e_Rna,     CSeqFeatData::eSubtype_snoRNA,  "sno_RNA", "sno_RNA" ), 
    CFeatConfigItem( CSeqFeatData::e_Rna,     CSeqFeatData::eSubtype_otherRNA,  "misc_RNA",  "misc_RNA" ),

    CFeatConfigItem( CSeqFeatData::e_Pub,     CSeqFeatData::eSubtype_pub,   "Pub", "Pub" ),
    CFeatConfigItem( CSeqFeatData::e_Seq,     CSeqFeatData::eSubtype_seq,   "Seq", "Seq" ),

    CFeatConfigItem( CSeqFeatData::e_Imp,      CSeqFeatData::eSubtype_any,       "Import, " kMasterDescString,  "Import Master" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,      CSeqFeatData::eSubtype_imp,       "import",       "import" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_allele,     "allele",       "allele" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_attenuator, "attenuator",   "attenuator"),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_C_region,   "C_region",     "C_region" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_CAAT_signal,"CAAT_signal",  "CAAT_signal" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_Imp_CDS,    "Imp_CDS",      "Imp_CDS"), 
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_conflict,   "conflict",     "conflict"), 
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_D_loop,     "D_loop",       "D_loop"),  
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_D_segment,  "D_segment",    "D_segment"), 
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_enhancer,   "enhancer",     "enhancer" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_exon,       "exon",         "exon" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_GC_signal,  "GC_signal",    "GC_signal" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_iDNA,       "iDNA",         "iDNA" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_intron,     "intron",       "intron" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_J_segment,  "J_segment",    "J_segment" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_LTR,        "LTR",          "LTR" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_mat_peptide,"mat_peptide",  "mat_peptide" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_misc_binding,       "misc_binding",     "misc_binding" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_misc_difference,    "misc_difference",  "misc_difference" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_misc_feature,       "misc_feature",     "misc_feature" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_misc_recomb,        "misc_recomb",      "misc_recomb" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_misc_RNA,           "misc_RNA",         "misc_RNA" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_misc_signal,        "misc_signal",      "misc_signal" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_misc_structure,     "misc_structure",   "misc_structure" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_modified_base,  "modified_base",    "modified_base" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_mutation,       "mutation",     "mutation" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_N_region,       "N_region",     "N_region" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_old_sequence,   "old_sequence", "old_sequence" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_polyA_signal,   "polyA_signal", "polyA_signal" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_polyA_site,     "polyA_site",   "polyA_site" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_precursor_RNA,  "precursor_RNA",    "precursor_RNA" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_prim_transcript,"prim_transcript",     "prim_transcript" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_primer_bind,    "primer_bind",     "primer_bind" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_promoter,    "promoter",     "promoter" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_protein_bind,    "protein_bind",     "protein_bind" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_RBS,    "RBS",     "RBS" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_repeat_region,    "repeat_region",     "repeat_region" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_repeat_unit,    "repeat_unit",     "repeat_unit" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_rep_origin,    "rep_origin",     "rep_origin" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_S_region,    "S_region",     "S_region" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_satellite,    "satellite",     "satellite" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_sig_peptide,    "sig_peptide",     "sig_peptide" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_source,    "source",     "source" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_stem_loop,    "stem_loop",     "stem_loop" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_STS,    "STS",     "STS" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_TATA_signal,    "TATA_signal",     "TATA_signal" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_terminator,    "terminator",     "terminator" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_transit_peptide,    "transit_peptide",     "transit_peptide" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_unsure,    "unsure",     "unsure" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_V_region,    "V_region",     "V_region" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_V_segment,    "V_segment",     "V_segment" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_variation,    "variation",     "variation" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_virion,    "virion",     "virion" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_3clip,    "3'clip",     "3'clip" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_3UTR,    "3'UTR",     "3'UTR" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_5clip,    "5'clip",     "5'clip" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_5UTR,    "5'UTR",     "5'UTR" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_10_signal,    "-10_signal",     "-10_signal" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_35_signal,    "-35_signal",     "-35_signal" ),
    CFeatConfigItem( CSeqFeatData::e_Imp,     CSeqFeatData::eSubtype_site_ref,    "site_ref",     "site_ref" ),

    CFeatConfigItem( CSeqFeatData::e_Region,   CSeqFeatData::eSubtype_region,    "region",     "region" ),
    CFeatConfigItem( CSeqFeatData::e_Comment,  CSeqFeatData::eSubtype_comment,    "comment",     "comment" ),
    CFeatConfigItem( CSeqFeatData::e_Bond,     CSeqFeatData::eSubtype_bond,    "bond",     "bond" ),
    CFeatConfigItem( CSeqFeatData::e_Site,     CSeqFeatData::eSubtype_site,    "site",     "site" ),
    CFeatConfigItem( CSeqFeatData::e_Rsite,    CSeqFeatData::eSubtype_rsite,    "rsite",     "rsite" ),
    CFeatConfigItem( CSeqFeatData::e_User,     CSeqFeatData::eSubtype_user,    "user",     "user" ),
    CFeatConfigItem( CSeqFeatData::e_Txinit,   CSeqFeatData::eSubtype_txinit,    "txinit",     "txinit" ),
    CFeatConfigItem( CSeqFeatData::e_Num,      CSeqFeatData::eSubtype_num,    "num",     "num" ),
    CFeatConfigItem( CSeqFeatData::e_Psec_str, CSeqFeatData::eSubtype_psec_str,    "psec_str",     "psec_str" ),
    CFeatConfigItem( CSeqFeatData::e_Non_std_residue,     CSeqFeatData::eSubtype_non_std_residue,    "non_std_residue",     "non_std_residue" ),
    CFeatConfigItem( CSeqFeatData::e_Het,      CSeqFeatData::eSubtype_het,    "het",     "het" ),
    CFeatConfigItem( CSeqFeatData::e_Biosrc,   CSeqFeatData::eSubtype_biosrc,    "biosrc",     "biosrc" ),
};
} // unnamed namespace


/**
    CFeatConfigItem comparator 
    to sort the set properly.
*/
bool CFeatConfigItem::operator<(const CFeatConfigItem& rhs) const {
    if (m_Type == rhs.m_Type) {
        // the 'Any' subtype should sort lower than anything else in that type.