2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
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/>.
18 package jalview.ws.dbsources;
20 import java.util.Hashtable;
22 import com.stevesoft.pat.Regex;
24 import jalview.datamodel.AlignmentI;
25 import jalview.datamodel.DBRefEntry;
26 import jalview.io.AppletFormatAdapter;
27 import jalview.io.FastaFile;
28 import jalview.io.StockholmFile;
29 import jalview.ws.seqfetcher.DbSourceProxy;
30 import jalview.ws.seqfetcher.DbSourceProxyImpl;
33 * TODO: later PFAM is a complex datasource - it could return a tree in addition
34 * to an alignment TODO: create interface to pass alignment properties and tree
35 * back to sequence fetcher
40 abstract public class Pfam extends Xfam implements DbSourceProxy
46 // all extensions of this PFAM source base class are DOMAINDB sources
47 addDbSourceProperty(jalview.datamodel.DBRefSource.DOMAINDB);
48 addDbSourceProperty(jalview.datamodel.DBRefSource.ALIGNMENTDB);
54 * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
56 public String getAccessionSeparator()
58 // TODO Auto-generated method stub
65 * @see jalview.ws.DbSourceProxy#getAccessionValidator()
67 public Regex getAccessionValidator()
69 // TODO Auto-generated method stub
76 * @see jalview.ws.DbSourceProxy#getDbSource() public String getDbSource() { *
77 * this doesn't work - DbSource is key for the hash of DbSourceProxy instances
78 * - 1:many mapping for DbSource to proxy will be lost. * suggest : PFAM is an
79 * 'alignment' source - means proxy is higher level than a sequence source.
80 * return jalview.datamodel.DBRefSource.PFAM; }
86 * @see jalview.ws.DbSourceProxy#getDbSourceProperties() public Hashtable
87 * getDbSourceProperties() {
95 * @see jalview.ws.DbSourceProxy#getDbVersion()
98 public String getDbVersion()
100 // TODO Auto-generated method stub
105 * Returns base URL for selected Pfam alignment type
107 * @return PFAM URL stub for this DbSource
110 protected abstract String getXFAMURL();
115 * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
117 public AlignmentI getSequenceRecords(String queries) throws Exception
119 // TODO: this is not a perfect implementation. We need to be able to add
120 // individual references to each sequence in each family alignment that's
123 AlignmentI rcds = new jalview.io.FormatAdapter().readFile(getXFAMURL()
124 + queries.trim().toUpperCase(), jalview.io.FormatAdapter.URL,
126 for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++)
128 rcds.getSequenceAt(s).addDBRef(
129 new DBRefEntry(jalview.datamodel.DBRefSource.PFAM,
131 getDbVersion(), queries.trim().toUpperCase()));
132 if (!getDbSource().equals(jalview.datamodel.DBRefSource.PFAM))
133 { // add the specific ref too
134 rcds.getSequenceAt(s).addDBRef(
135 new DBRefEntry(getDbSource(), getDbVersion(), queries
136 .trim().toUpperCase()));
146 * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
148 public boolean isValidReference(String accession)
150 return accession.indexOf("PF") == 0;
154 * public String getDbName() { return "PFAM"; // getDbSource(); }
157 public String getXfamSource()
159 return jalview.datamodel.DBRefSource.PFAM;