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 jalview.bin.Cache;
24 import jalview.datamodel.DBRefSource;
25 import jalview.util.Platform;
27 import com.stevesoft.pat.Regex;
30 * Contains methods for fetching sequences from Rfam database
32 * @author Lauren Michelle Lui
34 abstract public class Rfam extends Xfam
36 static final String RFAM_BASEURL_KEY = "RFAM_BASEURL";
38 private static final String DEFAULT_RFAM_BASEURL = "https://rfam.org";
42 Platform.addJ2SDirectDatabaseCall(DEFAULT_RFAM_BASEURL);
46 * append to URLs to retrieve as a gzipped file
48 protected static final String GZIPPED = "?gzip=1&download=1";
51 protected String getURLPrefix()
53 return Cache.getDefault(RFAM_BASEURL_KEY, DEFAULT_RFAM_BASEURL);
64 * @see jalview.ws.DbSourceProxy#getAccessionSeparator() Left here for
65 * consistency with Pfam class
68 public String getAccessionSeparator()
76 * @see jalview.ws.DbSourceProxy#getAccessionValidator() * Left here for
79 public Regex getAccessionValidator()
87 * Left here for consistency with Pfam class
89 * @see jalview.ws.DbSourceProxy#getDbSource() public String getDbSource() { *
90 * this doesn't work - DbSource is key for the hash of DbSourceProxy instances
91 * - 1:many mapping for DbSource to proxy will be lost. * suggest : RFAM is an
92 * 'alignment' source - means proxy is higher level than a sequence source.
93 * return jalview.datamodel.DBRefSource.RFAM; }
99 * @see jalview.ws.DbSourceProxy#getDbVersion()
102 public String getDbVersion()
110 * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
113 public boolean isValidReference(String accession)
115 return accession.indexOf("RF") == 0;
121 * @see jalview.ws.dbsources.Xfam#getXfamSource()
124 public String getXfamSource()
126 return DBRefSource.RFAM;