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.ext.ensembl.EnsemblGene;
24 import jalview.ws.dbsources.EmblCdsSource;
25 import jalview.ws.dbsources.EmblSource;
26 import jalview.ws.dbsources.Pdb;
27 import jalview.ws.dbsources.PfamFull;
28 import jalview.ws.dbsources.PfamSeed;
29 import jalview.ws.dbsources.RfamSeed;
30 import jalview.ws.dbsources.TDBeacons;
31 import jalview.ws.dbsources.Uniprot;
32 import jalview.ws.seqfetcher.ASequenceFetcher;
33 import jalview.ws.seqfetcher.DbSourceProxy;
35 import java.util.ArrayList;
36 import java.util.Collections;
37 import java.util.List;
40 * This implements the run-time discovery of sequence database clients.
43 public class SequenceFetcher extends ASequenceFetcher
46 * Thread safe construction of database proxies TODO: extend to a configurable
47 * database plugin mechanism where classes are instantiated by reflection and
48 * queried for their DbRefSource and version association.
51 public SequenceFetcher()
53 addDBRefSourceImpl(EnsemblGene.class);
54 // addDBRefSourceImpl(EnsemblGenomes.class);
55 addDBRefSourceImpl(EmblSource.class);
56 addDBRefSourceImpl(EmblCdsSource.class);
57 addDBRefSourceImpl(Uniprot.class);
58 // not a sequence source yet
59 // addDBRefSourceImpl(TDBeacons.class);
60 addDBRefSourceImpl(Pdb.class);
61 addDBRefSourceImpl(PfamFull.class);
62 addDBRefSourceImpl(PfamSeed.class);
63 addDBRefSourceImpl(RfamSeed.class);
67 * return an ordered list of database sources excluding alignment only
70 public String[] getNonAlignmentSources()
72 String[] srcs = this.getSupportedDb();
73 List<String> src = new ArrayList<>();
75 for (int i = 0; i < srcs.length; i++)
77 boolean accept = true;
78 for (DbSourceProxy dbs : getSourceProxy(srcs[i]))
80 // Skip the alignment databases for the moment - they're not useful for
81 // verifying a single sequence against its reference source
82 if (dbs.isAlignmentSource())
94 Collections.sort(src, String.CASE_INSENSITIVE_ORDER);
95 return src.toArray(new String[src.size()]);