2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.datamodel;
24 * Defines internal constants for unambiguous annotation of DbRefEntry source
25 * strings and describing the data retrieved from external database sources (see
26 * jalview.ws.DbSourcProxy) <br/>
27 * TODO: replace with ontology to allow recognition of particular attributes
28 * (e.g. protein coding, alignment (ortholog db, paralog db, domain db),
29 * genomic, transcriptomic, 3D structure providing (PDB, MODBASE, etc) ..).
34 public class DBRefSource
37 * UNIPROT Accession Number
39 public static String UNIPROT = "UNIPROT";
44 public static String UP_NAME = "UNIPROT_NAME".toUpperCase();
47 * Uniprot Knowledgebase/TrEMBL as served from EMBL protein products.
49 public static final String UNIPROTKB = "UniProtKB/TrEMBL".toUpperCase();
51 public static final String EMBLCDSProduct = "EMBLCDSProtein"
57 public static String PDB = "PDB";
62 public static String MMCIF = "mmCIF";
67 public static String EMBL = "EMBL";
72 public static String EMBLCDS = "EMBLCDS";
77 public static String PFAM = "PFAM";
82 public static String RFAM = "RFAM";
87 public static final String GENEDB = "GeneDB".toUpperCase();
92 public static final String ENSEMBL = "ENSEMBL";
94 public static final String ENSEMBLGENOMES = "ENSEMBLGENOMES";
97 * List of databases whose sequences might have coding regions annotated
99 public static final String[] DNACODINGDBS = { EMBL, EMBLCDS, GENEDB,
102 public static final String[] CODINGDBS = { EMBLCDS, GENEDB, ENSEMBL };
104 public static final String[] PROTEINDBS = { UNIPROT, PDB, UNIPROTKB,
105 EMBLCDSProduct, ENSEMBL }; // Ensembl ENSP* entries are protein