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)
31 public class DBRefSource
34 * UNIPROT Accession Number
36 public static String UNIPROT = "UNIPROT";
41 public static String UP_NAME = "UNIPROT_NAME".toUpperCase();
44 * Uniprot Knowledgebase/TrEMBL as served from EMBL protein products.
46 public static final String UNIPROTKB = "UniProtKB/TrEMBL".toUpperCase();
48 public static final String EMBLCDSProduct = "EMBLCDSProtein"
54 public static String PDB = "PDB";
59 public static String EMBL = "EMBL";
64 public static String EMBLCDS = "EMBLCDS";
69 public static String PFAM = "PFAM";
74 public static String RFAM = "RFAM";
79 public static final String GENEDB = "GeneDB".toUpperCase();
82 * List of databases whose sequences might have coding regions annotated
84 public static final String[] DNACODINGDBS = { EMBL, EMBLCDS, GENEDB };
86 public static final String[] CODINGDBS = { EMBLCDS, GENEDB };
88 public static final String[] PROTEINDBS = { UNIPROT, PDB, UNIPROTKB,
91 public static final String[] PROTEINSEQ = { UNIPROT, UNIPROTKB,
94 public static final String[] PROTEINSTR = { PDB };
96 public static final String[] DOMAINDBS = { PFAM, RFAM };