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;
23 import java.lang.reflect.Field;
24 import java.util.ArrayList;
25 import java.util.List;
28 * BH 2018 SwingJS note: If additional final static Strings are added to this
29 * file, they should be added to public static final String[] allTypes.
31 * Defines internal constants for unambiguous annotation of DbRefEntry source
32 * strings and describing the data retrieved from external database sources (see
33 * jalview.ws.DbSourcProxy) <br/>
34 * TODO: replace with ontology to allow recognition of particular attributes
35 * (e.g. protein coding, alignment (ortholog db, paralog db, domain db),
36 * genomic, transcriptomic, 3D structure providing (PDB, MODBASE, etc) ..).
43 public class DBRefSource
49 * UNIPROT Accession Number
51 public static final String UNIPROT = "UNIPROT";
56 public static final String UP_NAME = "UNIPROT_NAME".toUpperCase();
59 * Uniprot Knowledgebase/TrEMBL as served from EMBL protein products.
61 public static final String UNIPROTKB = "UniProtKB/TrEMBL".toUpperCase();
63 public static final String EMBLCDSProduct = "EMBLCDSProtein".toUpperCase();
69 public static final String PDB = "PDB";
74 public static final String EMBL = "EMBL";
79 public static final String EMBLCDS = "EMBLCDS";
85 public static final String PFAM = "PFAM";
90 public static final String RFAM = "RFAM";
95 public static final String GENEDB = "GeneDB".toUpperCase();
101 public static final String ENSEMBL = "ENSEMBL";
103 public static final String ENSEMBLGENOMES = "ENSEMBLGENOMES";
107 * List of databases whose sequences might have coding regions annotated
109 public static final String[] DNACODINGDBS = { EMBL, EMBLCDS, GENEDB,
110 ENSEMBL, ENSEMBLGENOMES };
112 public static final String[] CODINGDBS = { EMBLCDS, GENEDB, ENSEMBL };
114 public static final String[] PROTEINDBS = { UNIPROT, UNIPROTKB,
115 EMBLCDSProduct, ENSEMBL }; // Ensembl ENSP* entries are protein
118 public static final String[] allTypes = new String[] {
119 UNIPROT, UP_NAME, UNIPROTKB,
120 EMBLCDSProduct, PDB, EMBL,
122 GENEDB, ENSEMBL, ENSEMBLGENOMES
126 public static String[] allSourcesFromReflection;
128 public static String[] allSources()
134 * return C$.allTypes;
139 if (allSourcesFromReflection == null)
141 List<String> src = new ArrayList<>();
142 for (Field f : DBRefSource.class.getFields())
144 if (String.class.equals(f.getType()))
148 src.add((String) f.get(null));
149 } catch (Exception x)
155 allSourcesFromReflection = src.toArray(new String[0]);
157 return allSourcesFromReflection;