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.ext.ensembl.EnsemblGenomes;
25 import jalview.ws.dbsources.EmblCdsSource;
26 import jalview.ws.dbsources.EmblSource;
27 import jalview.ws.dbsources.Pdb;
28 import jalview.ws.dbsources.PfamFull;
29 import jalview.ws.dbsources.PfamSeed;
30 import jalview.ws.dbsources.RfamSeed;
31 import jalview.ws.dbsources.Uniprot;
32 import jalview.ws.dbsources.das.api.jalviewSourceI;
33 import jalview.ws.seqfetcher.ASequenceFetcher;
34 import jalview.ws.seqfetcher.DbSourceProxy;
36 import java.util.ArrayList;
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()
56 public SequenceFetcher(boolean addDas)
58 addDBRefSourceImpl(EnsemblGene.class);
59 addDBRefSourceImpl(EnsemblGenomes.class);
60 addDBRefSourceImpl(EmblSource.class);
61 addDBRefSourceImpl(EmblCdsSource.class);
62 addDBRefSourceImpl(Uniprot.class);
63 addDBRefSourceImpl(Pdb.class);
64 addDBRefSourceImpl(PfamFull.class);
65 addDBRefSourceImpl(PfamSeed.class);
66 addDBRefSourceImpl(RfamSeed.class);
70 registerDasSequenceSources();
75 * return an ordered list of database sources where non-das database classes
76 * appear before das database classes
78 public String[] getOrderedSupportedSources()
80 String[] srcs = this.getSupportedDb();
81 ArrayList<String> dassrc = new ArrayList<String>(),
82 nondas = new ArrayList<String>();
83 for (int i = 0; i < srcs.length; i++)
85 boolean das = false, skip = false;
87 for (DbSourceProxy dbs : getSourceProxy(srcs[i]))
89 // Skip the alignment databases for the moment - they're not useful for
90 // verifying a single sequence against its reference source
91 if (dbs.isAlignmentSource())
99 srcs[i]) instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
101 if (nm.startsWith("das:"))
103 nm = nm.substring(4);
123 String[] tosort = nondas.toArray(new String[0]),
124 sorted = nondas.toArray(new String[0]);
125 for (int j = 0, jSize = sorted.length; j < jSize; j++)
127 tosort[j] = tosort[j].toLowerCase();
129 jalview.util.QuickSort.sort(tosort, sorted);
130 // construct array with all sources listed
132 srcs = new String[sorted.length + dassrc.size()];
134 for (int j = sorted.length - 1; j >= 0; j--, i++)
140 sorted = dassrc.toArray(new String[0]);
141 tosort = dassrc.toArray(new String[0]);
142 for (int j = 0, jSize = sorted.length; j < jSize; j++)
144 tosort[j] = tosort[j].toLowerCase();
146 jalview.util.QuickSort.sort(tosort, sorted);
147 for (int j = sorted.length - 1; j >= 0; j--, i++)
155 * query the currently defined DAS source registry for sequence sources and
156 * add a DasSequenceSource instance for each source to the SequenceFetcher
159 public void registerDasSequenceSources()
161 // TODO: define a context as a registry provider (either desktop,
162 // jalview.bin.cache, or something else).
163 for (jalviewSourceI source : jalview.bin.Cache.getDasSourceRegistry()
166 if (source.isSequenceSource())
168 List<DbSourceProxy> dassources = source.getSequenceSourceProxies();
169 for (DbSourceProxy seqsrc : dassources)
171 addDbRefSourceImpl(seqsrc);