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;
26 import com.stevesoft.pat.Regex;
29 * TODO: later PFAM is a complex datasource - it could return a tree in addition
30 * to an alignment TODO: create interface to pass alignment properties and tree
31 * back to sequence fetcher
36 abstract public class Pfam extends Xfam
39 * append to URLs to retrieve as a gzipped file
41 protected static final String GZIPPED = "/gzipped";
43 static final String PFAM_BASEURL_KEY = "PFAM_BASEURL";
45 private static final String DEFAULT_PFAM_BASEURL = "https://pfam.xfam.org";
55 * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
58 public String getAccessionSeparator()
66 * @see jalview.ws.DbSourceProxy#getAccessionValidator()
69 public Regex getAccessionValidator()
77 * @see jalview.ws.DbSourceProxy#getDbSource() public String getDbSource() { *
78 * this doesn't work - DbSource is key for the hash of DbSourceProxy instances
79 * - 1:many mapping for DbSource to proxy will be lost. * suggest : PFAM is an
80 * 'alignment' source - means proxy is higher level than a sequence source.
81 * return jalview.datamodel.DBRefSource.PFAM; }
87 * @see jalview.ws.DbSourceProxy#getDbSourceProperties() public Hashtable
88 * getDbSourceProperties() {
96 * @see jalview.ws.DbSourceProxy#getDbVersion()
99 public String getDbVersion()
105 protected String getURLPrefix()
107 return Cache.getDefault(PFAM_BASEURL_KEY, DEFAULT_PFAM_BASEURL);
113 * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
116 public boolean isValidReference(String accession)
118 return accession.indexOf("PF") == 0;
122 * public String getDbName() { return "PFAM"; // getDbSource(); }
126 public String getXfamSource()
128 return DBRefSource.PFAM;