2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
3 * Copyright (C) 2014 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 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/>.
17 * The Jalview Authors are detailed in the 'AUTHORS' file.
19 package jalview.ws.dbsources;
22 import com.stevesoft.pat.Regex;
24 import jalview.datamodel.AlignmentI;
25 import jalview.datamodel.DBRefEntry;
26 import jalview.ws.seqfetcher.DbSourceProxy;
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 implements DbSourceProxy
42 // all extensions of this PFAM source base class are DOMAINDB sources
43 addDbSourceProperty(jalview.datamodel.DBRefSource.DOMAINDB);
44 addDbSourceProperty(jalview.datamodel.DBRefSource.ALIGNMENTDB);
50 * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
52 public String getAccessionSeparator()
54 // TODO Auto-generated method stub
61 * @see jalview.ws.DbSourceProxy#getAccessionValidator()
63 public Regex getAccessionValidator()
65 // TODO Auto-generated method stub
72 * @see jalview.ws.DbSourceProxy#getDbSource() public String getDbSource() { *
73 * this doesn't work - DbSource is key for the hash of DbSourceProxy instances
74 * - 1:many mapping for DbSource to proxy will be lost. * suggest : PFAM is an
75 * 'alignment' source - means proxy is higher level than a sequence source.
76 * return jalview.datamodel.DBRefSource.PFAM; }
82 * @see jalview.ws.DbSourceProxy#getDbSourceProperties() public Hashtable
83 * getDbSourceProperties() {
91 * @see jalview.ws.DbSourceProxy#getDbVersion()
94 public String getDbVersion()
96 // TODO Auto-generated method stub
101 * Returns base URL for selected Pfam alignment type
103 * @return PFAM URL stub for this DbSource
106 protected abstract String getXFAMURL();
111 * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
113 public AlignmentI getSequenceRecords(String queries) throws Exception
115 // TODO: this is not a perfect implementation. We need to be able to add
116 // individual references to each sequence in each family alignment that's
119 AlignmentI rcds = new jalview.io.FormatAdapter().readFile(getXFAMURL()
120 + queries.trim().toUpperCase(), jalview.io.FormatAdapter.URL,
122 for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++)
124 rcds.getSequenceAt(s).addDBRef(
125 new DBRefEntry(jalview.datamodel.DBRefSource.PFAM,
127 getDbVersion(), queries.trim().toUpperCase()));
128 if (!getDbSource().equals(jalview.datamodel.DBRefSource.PFAM))
129 { // add the specific ref too
130 rcds.getSequenceAt(s).addDBRef(
131 new DBRefEntry(getDbSource(), getDbVersion(), queries
132 .trim().toUpperCase()));
142 * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
144 public boolean isValidReference(String accession)
146 return accession.indexOf("PF") == 0;
150 * public String getDbName() { return "PFAM"; // getDbSource(); }
153 public String getXfamSource()
155 return jalview.datamodel.DBRefSource.PFAM;