2 * Jalview - A Sequence Alignment Editor and Viewer
3 * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
19 package jalview.datamodel;
21 * Defines internal constants for unambiguous annotation
22 * of DbRefEntry source strings and describing the data
23 * retrieved from external database sources (see jalview.ws.DbSourcProxy)
27 public class DBRefSource
30 * UNIPROT Accession Number
32 public static String UNIPROT = "UNIPROT";
36 public static String UP_NAME = "UNIPROT_NAME";
38 * Uniprot Knowledgebase/TrEMBL
39 * as served from EMBL protein products.
41 public static final String UNIPROTKB = "UniProtKB/TrEMBL";
45 public static String PDB = "PDB";
49 public static String EMBL = "EMBL";
53 public static String EMBLCDS = "EMBLCDS";
57 public static String PFAM = "PFAM";
61 public static final String GENEDB = "GeneDB";
64 * List of databases whose sequences might have coding regions annotated
66 public static final String[] DNACODINGDBS = { EMBL, EMBLCDS, GENEDB};
67 public static final String[] CODINGDBS = { EMBLCDS, GENEDB};
68 public static final String[] PROTEINDBS = { UNIPROT, PDB, UNIPROTKB};
69 public static final String[] PROTEINSEQ = { UNIPROT, UNIPROTKB};
70 public static final String[] PROTEINSTR = { PDB };
71 public static final String[] DOMAINDBS = { PFAM };
73 * set of unique DBRefSource property constants.
74 * These could be used to reconstruct the above groupings
76 public static final Object SEQDB = "SQ";
78 * database of nucleic acid sequences
80 public static final Object DNASEQDB = "NASQ";
82 * database of amino acid sequences
84 public static final Object PROTSEQDB = "PROTSQ";
86 * database of cDNA sequences
88 public static final Object CODINGSEQDB = "CODING";
90 * database of na sequences with exon annotation
92 public static final Object DNACODINGSEQDB = "XONCODING";
94 * DB returns several sequences associated with a protein domain
96 public static final Object DOMAINDB = "DOMAIN";
98 * DB query can take multiple accession codes concatenated
99 * by a separator. Value of property indicates maximum number of accession codes to send at a time.
101 public static final Object MULTIACC = "MULTIACC";