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 java.util.Locale;
25 import jalview.bin.Cache;
26 import jalview.datamodel.DBRefSource;
27 import jalview.util.Platform;
29 import com.stevesoft.pat.Regex;
32 * TODO: later PFAM is a complex datasource - it could return a tree in addition
33 * to an alignment TODO: create interface to pass alignment properties and tree
34 * back to sequence fetcher
39 abstract public class Pfam extends Xfam
41 public static final String FULL="full",RP35="rp35",RP15="rp15",RP75="rp75",RP55="rp55",SEED="seed";
43 public String getPfamDownloadURL(String id,String alType) {
44 String url = Cache.getDefault(PFAM_BASEURL_KEY,DEFAULT_PFAM_BASEURL);
45 url = url.replace("$PFAMID$",id);
46 url = url.replace("$ALTYPE$",alType);
49 static final String PFAM_BASEURL_KEY = "PFAM_INTERPRO_URL_TEMPLATE";
51 protected String alignmentType;
52 private static final String DEFAULT_PFAM_BASEURL = "https://www.ebi.ac.uk/interpro/wwwapi/entry/pfam/$PFAMID$/?annotation=alignment:$ALTYPE$&download";
56 Platform.addJ2SDirectDatabaseCall(DEFAULT_PFAM_BASEURL);
65 String getURL(String queries)
67 return getPfamDownloadURL(
68 queries.trim().toUpperCase(Locale.ROOT), alignmentType);
74 * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
77 public String getAccessionSeparator()
85 * @see jalview.ws.DbSourceProxy#getAccessionValidator()
88 public Regex getAccessionValidator()
96 * @see jalview.ws.DbSourceProxy#getDbSource() public String getDbSource() { *
97 * this doesn't work - DbSource is key for the hash of DbSourceProxy instances
98 * - 1:many mapping for DbSource to proxy will be lost. * suggest : PFAM is an
99 * 'alignment' source - means proxy is higher level than a sequence source.
100 * return jalview.datamodel.DBRefSource.PFAM; }
106 * @see jalview.ws.DbSourceProxy#getDbSourceProperties() public Hashtable
107 * getDbSourceProperties() {
115 * @see jalview.ws.DbSourceProxy#getDbVersion()
118 public String getDbVersion()
124 protected String getURLPrefix()
126 return Cache.getDefault(PFAM_BASEURL_KEY, DEFAULT_PFAM_BASEURL);
132 * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
135 public boolean isValidReference(String accession)
137 return accession.indexOf("PF") == 0;
141 * public String getDbName() { return "PFAM"; // getDbSource(); }
145 public String getXfamSource()
147 return DBRefSource.PFAM;