2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
3 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
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/>.
18 package jalview.ws.dbsources;
20 import com.stevesoft.pat.Regex;
22 import jalview.ws.seqfetcher.DbSourceProxy;
25 * Contains methods for fetching sequences from Rfam database
27 * @author Lauren Michelle Lui
29 abstract public class Rfam extends Xfam implements DbSourceProxy
35 // all extensions of this RFAM source base class are DOMAINDB sources
36 addDbSourceProperty(jalview.datamodel.DBRefSource.DOMAINDB);
42 * @see jalview.ws.DbSourceProxy#getAccessionSeparator() Left here for
43 * consistency with Pfam class
45 public String getAccessionSeparator()
47 // TODO Auto-generated method stub
54 * @see jalview.ws.DbSourceProxy#getAccessionValidator() * Left here for
56 public Regex getAccessionValidator()
58 // TODO Auto-generated method stub
65 * Left here for consistency with Pfam class
67 * @see jalview.ws.DbSourceProxy#getDbSource() public String getDbSource() { *
68 * this doesn't work - DbSource is key for the hash of DbSourceProxy instances
69 * - 1:many mapping for DbSource to proxy will be lost. * suggest : RFAM is an
70 * 'alignment' source - means proxy is higher level than a sequence source.
71 * return jalview.datamodel.DBRefSource.RFAM; }
77 * @see jalview.ws.DbSourceProxy#getDbVersion()
80 public String getDbVersion()
82 // TODO Auto-generated method stub
86 /**Returns base URL for selected Rfam alignment type
88 * @return RFAM URL stub for this DbSource
91 protected abstract String getXFAMURL();
96 * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
98 public boolean isValidReference(String accession)
100 return accession.indexOf("RF") == 0;
104 * @see jalview.ws.dbsources.Xfam#getXfamSource()
106 public String getXfamSource()
108 return jalview.datamodel.DBRefSource.RFAM;