2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
3 * Copyright (C) 2014 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 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
17 * The Jalview Authors are detailed in the 'AUTHORS' file.
19 package jalview.ws.dbsources;
21 import jalview.datamodel.AlignmentI;
22 import jalview.datamodel.DBRefEntry;
23 import jalview.ws.seqfetcher.DbSourceProxyImpl;
26 * Acts as a superclass for the Rfam and Pfam classes
28 * @author Lauren Michelle Lui
31 public abstract class Xfam extends DbSourceProxyImpl
39 protected abstract String getXFAMURL();
41 public abstract String getDbVersion();
43 abstract String getXfamSource();
45 public AlignmentI getSequenceRecords(String queries) throws Exception
47 // TODO: this is not a perfect implementation. We need to be able to add
48 // individual references to each sequence in each family alignment that's
51 // TODO: trap HTTP 404 exceptions and return null
52 AlignmentI rcds = new jalview.io.FormatAdapter().readFile(getXFAMURL()
53 + queries.trim().toUpperCase(), jalview.io.FormatAdapter.URL,
55 for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++)
57 rcds.getSequenceAt(s).addDBRef(new DBRefEntry(getXfamSource(),
59 getDbVersion(), queries.trim().toUpperCase()));
60 if (!getDbSource().equals(getXfamSource()))
61 { // add the specific ref too
62 rcds.getSequenceAt(s).addDBRef(
63 new DBRefEntry(getDbSource(), getDbVersion(), queries
64 .trim().toUpperCase()));