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.
23 import jalview.datamodel.DBRefSource;
24 import jalview.ext.ensembl.EnsemblGene;
25 import jalview.ws.dbsources.Uniprot;
26 import jalview.ws.seqfetcher.ASequenceFetcher;
27 import jalview.ws.seqfetcher.DbSourceProxy;
29 import java.util.ArrayList;
30 import java.util.Collections;
31 import java.util.List;
34 * This implements the run-time discovery of sequence database clients.
37 public class SequenceFetcher extends ASequenceFetcher
40 * Thread safe construction of database proxies TODO: extend to a configurable
41 * database plugin mechanism where classes are instantiated by reflection and
42 * queried for their DbRefSource and version association.
45 public SequenceFetcher()
50 public void addAllDatabases()
52 addDBRefSourceImpl(EnsemblGene.class); // includes EnsemblGenomes.class
53 addDBRefSourceImpl(Uniprot.class); // includes UniprotName.class
54 // addDBRefSourceImpl(EmblSource.class);
55 // addDBRefSourceImpl(EmblCdsSource.class);
56 // addDBRefSourceImpl(Pdb.class);
57 // addDBRefSourceImpl(PfamFull.class);
58 // addDBRefSourceImpl(PfamSeed.class);
59 // addDBRefSourceImpl(RfamSeed.class);
60 addDBRefSourceImpl(DBRefSource.EMBL,
61 "jalview.ws.dbsources.EmblSource");
62 addDBRefSourceImpl(DBRefSource.EMBLCDS,
63 "jalview.ws.dbsources.EmblCdsSource");
64 addDBRefSourceImpl(DBRefSource.PDB, "jalview.ws.dbsources.Pdb");
65 addDBRefSourceImpl(DBRefSource.PFAM_FULL,
66 "jalview.ws.dbsources.PfamFull");
67 addDBRefSourceImpl(DBRefSource.PFAM_SEED,
68 "jalview.ws.dbsources.PfamSeed");
69 addDBRefSourceImpl(DBRefSource.RFAM_SEED,
70 "jalview.ws.dbsources.RfamSeed");
74 * return an ordered list of database sources excluding alignment only
77 public String[] getNonAlignmentSources()
79 String[] srcs = this.getSupportedDb();
80 List<String> src = new ArrayList<>();
81 outer: for (int i = 0; i < srcs.length; i++)
83 for (DbSourceProxy dbs : getSourceProxy(srcs[i]))
85 // Skip the alignment databases for the moment - they're not useful for
86 // verifying a single sequence against its reference source
87 if (dbs.isAlignmentSource())
94 Collections.sort(src, String.CASE_INSENSITIVE_ORDER);
95 return src.toArray(new String[src.size()]);