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.bin.ApplicationSingletonProvider;
24 import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
25 import jalview.ext.ensembl.EnsemblGene;
26 import jalview.ws.dbsources.EmblCdsSource;
27 import jalview.ws.dbsources.EmblSource;
28 import jalview.ws.dbsources.Pdb;
29 import jalview.ws.dbsources.PfamFull;
30 import jalview.ws.dbsources.PfamSeed;
31 import jalview.ws.dbsources.RfamSeed;
32 import jalview.ws.dbsources.Uniprot;
33 import jalview.ws.seqfetcher.ASequenceFetcher;
34 import jalview.ws.seqfetcher.DbSourceProxy;
36 import java.util.ArrayList;
37 import java.util.Collections;
38 import java.util.List;
41 * This implements the run-time discovery of sequence database clients.
44 public class SequenceFetcher extends ASequenceFetcher implements ApplicationSingletonI
47 * set a mock fetcher here for testing only - reset to null afterwards
49 private static SequenceFetcher mockFetcher;
52 * Set the instance object to use (intended for unit testing with mock
55 * Be sure to reset to null in the tearDown method of any tests!
59 public static void setMockFetcher(SequenceFetcher sf)
65 * Returns a new SequenceFetcher singleton, or a mock object if one has been
70 public static SequenceFetcher getInstance()
72 return mockFetcher != null ? mockFetcher
73 : (SequenceFetcher) ApplicationSingletonProvider
74 .getInstance(SequenceFetcher.class);
78 * Thread safe construction of database proxies TODO: extend to a configurable
79 * database plugin mechanism where classes are instantiated by reflection and
80 * queried for their DbRefSource and version association.
83 public SequenceFetcher()
85 addDBRefSourceImpl(EnsemblGene.class);
86 // addDBRefSourceImpl(EnsemblGenomes.class);
87 addDBRefSourceImpl(EmblSource.class);
88 addDBRefSourceImpl(EmblCdsSource.class);
89 addDBRefSourceImpl(Uniprot.class);
90 addDBRefSourceImpl(Pdb.class);
91 addDBRefSourceImpl(PfamFull.class);
92 addDBRefSourceImpl(PfamSeed.class);
93 addDBRefSourceImpl(RfamSeed.class);
97 * return an ordered list of database sources excluding alignment only databases
99 public String[] getNonAlignmentSources()
101 String[] srcs = this.getSupportedDb();
102 List<String> src = new ArrayList<>();
104 for (int i = 0; i < srcs.length; i++)
106 boolean accept = true;
107 for (DbSourceProxy dbs : getSourceProxy(srcs[i]))
109 // Skip the alignment databases for the moment - they're not useful for
110 // verifying a single sequence against its reference source
111 if (dbs.isAlignmentSource())
123 Collections.sort(src, String.CASE_INSENSITIVE_ORDER);
124 return src.toArray(new String[src.size()]);