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 com.stevesoft.pat.Regex;
27 import jalview.bin.Cache;
28 import jalview.datamodel.DBRefSource;
29 import jalview.util.Platform;
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",
42 RP75 = "rp75", RP55 = "rp55", SEED = "seed", UNIPROT = "uniprot";
44 public String getPfamDownloadURL(String id, String alType)
46 String url = Cache.getDefault(PFAM_BASEURL_KEY, DEFAULT_PFAM_BASEURL);
47 url = url.replace("$PFAMID$", id);
48 url = url.replace("$ALTYPE$", alType);
52 static final String PFAM_BASEURL_KEY = "PFAM_INTERPRO_URL_TEMPLATE";
54 protected String alignmentType;
57 * docs are http://www.ebi.ac.uk/interpro/api/
59 private static final String DEFAULT_PFAM_BASEURL = "https://www.ebi.ac.uk/interpro/api/entry/pfam/$PFAMID$/?annotation=alignment:$ALTYPE$";
63 Platform.addJ2SDirectDatabaseCall(DEFAULT_PFAM_BASEURL);
72 String getURL(String queries)
74 return getPfamDownloadURL(queries.trim().toUpperCase(Locale.ROOT),
81 * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
84 public String getAccessionSeparator()
92 * @see jalview.ws.DbSourceProxy#getAccessionValidator()
95 public Regex getAccessionValidator()
103 * @see jalview.ws.DbSourceProxy#getDbSource() public String getDbSource() { *
104 * this doesn't work - DbSource is key for the hash of DbSourceProxy instances
105 * - 1:many mapping for DbSource to proxy will be lost. * suggest : PFAM is an
106 * 'alignment' source - means proxy is higher level than a sequence source.
107 * return jalview.datamodel.DBRefSource.PFAM; }
113 * @see jalview.ws.DbSourceProxy#getDbSourceProperties() public Hashtable
114 * getDbSourceProperties() {
122 * @see jalview.ws.DbSourceProxy#getDbVersion()
125 public String getDbVersion()
131 protected String getURLPrefix()
133 return Cache.getDefault(PFAM_BASEURL_KEY, DEFAULT_PFAM_BASEURL);
139 * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
142 public boolean isValidReference(String accession)
144 return accession.indexOf("PF") == 0;
148 * public String getDbName() { return "PFAM"; // getDbSource(); }
152 public String getXfamSource()
154 return DBRefSource.PFAM;