2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
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 com.stevesoft.pat.Regex;
23 import jalview.ws.seqfetcher.DbSourceProxy;
26 * Contains methods for fetching sequences from Rfam database
28 * @author Lauren Michelle Lui
30 abstract public class Rfam extends Xfam implements DbSourceProxy
36 // all extensions of this RFAM source base class are DOMAINDB sources
37 addDbSourceProperty(jalview.datamodel.DBRefSource.DOMAINDB);
38 addDbSourceProperty(jalview.datamodel.DBRefSource.ALIGNMENTDB);
44 * @see jalview.ws.DbSourceProxy#getAccessionSeparator() Left here for
45 * consistency with Pfam class
47 public String getAccessionSeparator()
49 // TODO Auto-generated method stub
56 * @see jalview.ws.DbSourceProxy#getAccessionValidator() * Left here for
58 public Regex getAccessionValidator()
60 // TODO Auto-generated method stub
67 * Left here for consistency with Pfam class
69 * @see jalview.ws.DbSourceProxy#getDbSource() public String getDbSource() { *
70 * this doesn't work - DbSource is key for the hash of DbSourceProxy instances
71 * - 1:many mapping for DbSource to proxy will be lost. * suggest : RFAM is an
72 * 'alignment' source - means proxy is higher level than a sequence source.
73 * return jalview.datamodel.DBRefSource.RFAM; }
79 * @see jalview.ws.DbSourceProxy#getDbVersion()
82 public String getDbVersion()
84 // TODO Auto-generated method stub
89 * Returns base URL for selected Rfam alignment type
91 * @return RFAM URL stub for this DbSource
94 protected abstract String getXFAMURL();
99 * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
101 public boolean isValidReference(String accession)
103 return accession.indexOf("RF") == 0;
109 * @see jalview.ws.dbsources.Xfam#getXfamSource()
111 public String getXfamSource()
113 return jalview.datamodel.DBRefSource.RFAM;