001/**
002 * Copyright (C) 2010-2015 The Roslin Institute <contact andy.law@roslin.ed.ac.uk>
003 *
004 * This file is part of JEnsembl: a Java API to Ensembl data sources developed by the
005 * Bioinformatics Group at The Roslin Institute, The Royal (Dick) School of
006 * Veterinary Studies, University of Edinburgh.
007 *
008 * Project hosted at: http://jensembl.sourceforge.net
009 *
010 * This is free software: you can redistribute it and/or modify
011 * it under the terms of the GNU General Public License (version 3) as published by
012 * the Free Software Foundation.
013 *
014 * This software is distributed in the hope that it will be useful,
015 * but WITHOUT ANY WARRANTY; without even the implied warranty of
016 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
017 * GNU General Public License for more details.
018 *
019 * You should have received a copy of the GNU General Public License
020 * in this software distribution. If not, see: http://opensource.org/licenses/gpl-3.0.html
021 */
022package uk.ac.roslin.ensembl.config;
023
024public class ExternalDBType extends EnsemblType {
025
026    /*
027     * In the external_db for human, we have {Vega genes, Havana Genes,
028     * clone-based vega genes...} presumably these represent different stages on
029     * the pipeline??
030     *
031        * db_name : db_display_name [priority]
032        *
033        * OTTG : Havana gene [1] 
034        * Vega_gene : Vega gene [5] 
035        * Vega_gene_like : Vega gene like [5] 
036        * Clone_based_vega_gene : Clone-based (Vega) [5]
037     *
038     * my understanding is that Vega is the datasource for Havana anotations
039     *
040     */
041    public static ExternalDBType VegaGene = new ExternalDBType("OTTG");
042    public static ExternalDBType VegaTranscript = new ExternalDBType("OTTT");
043    //public static ExternalDBType VegaProtein = new ExternalDBType("OTTP");
044    public static ExternalDBType VegaProtein = new ExternalDBType("Vega_translation");
045    
046    public static ExternalDBType DisplayID = new ExternalDBType("DisplayID");
047   
048    /*
049     * The Consensus CDS (CCDS) project is a collaborative effort to identify a 
050     * core set of human and mouse protein coding regions that are consistently 
051     * annotated and of high quality. The long term goal is to support convergence 
052     * towards a standard set of gene annotations. 
053     */
054    public static ExternalDBType CCDS = new ExternalDBType("CCDS");
055
056    private ExternalDBType(String value) {
057        this.label = value;
058    }
059}