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.
21 package jalview.ws.dbsources;
23 import com.stevesoft.pat.Regex;
25 import jalview.ws.seqfetcher.DbSourceProxy;
28 * Contains methods for fetching sequences from Rfam database
30 * @author Lauren Michelle Lui
32 abstract public class Rfam extends Xfam implements DbSourceProxy
38 // all extensions of this RFAM source base class are DOMAINDB sources
39 addDbSourceProperty(jalview.datamodel.DBRefSource.DOMAINDB);
40 addDbSourceProperty(jalview.datamodel.DBRefSource.ALIGNMENTDB);
46 * @see jalview.ws.DbSourceProxy#getAccessionSeparator() Left here for
47 * consistency with Pfam class
49 public String getAccessionSeparator()
51 // TODO Auto-generated method stub
58 * @see jalview.ws.DbSourceProxy#getAccessionValidator() * Left here for
60 public Regex getAccessionValidator()
62 // TODO Auto-generated method stub
69 * Left here for consistency with Pfam class
71 * @see jalview.ws.DbSourceProxy#getDbSource() public String getDbSource() { *
72 * this doesn't work - DbSource is key for the hash of DbSourceProxy instances
73 * - 1:many mapping for DbSource to proxy will be lost. * suggest : RFAM is an
74 * 'alignment' source - means proxy is higher level than a sequence source.
75 * return jalview.datamodel.DBRefSource.RFAM; }
81 * @see jalview.ws.DbSourceProxy#getDbVersion()
84 public String getDbVersion()
86 // TODO Auto-generated method stub
91 * Returns base URL for selected Rfam alignment type
93 * @return RFAM URL stub for this DbSource
96 protected abstract String getXFAMURL();
101 * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
103 public boolean isValidReference(String accession)
105 return accession.indexOf("RF") == 0;
111 * @see jalview.ws.dbsources.Xfam#getXfamSource()
113 public String getXfamSource()
115 return jalview.datamodel.DBRefSource.RFAM;