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.datamodel.AlignmentI;
24 import jalview.datamodel.DBRefEntry;
25 import jalview.datamodel.DBRefSource;
26 import jalview.io.DataSourceType;
27 import jalview.io.FileFormat;
28 import jalview.io.FormatAdapter;
30 import com.stevesoft.pat.Regex;
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
51 * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
54 public String getAccessionSeparator()
56 // TODO Auto-generated method stub
63 * @see jalview.ws.DbSourceProxy#getAccessionValidator()
66 public Regex getAccessionValidator()
68 // TODO Auto-generated method stub
75 * @see jalview.ws.DbSourceProxy#getDbSource() public String getDbSource() { *
76 * this doesn't work - DbSource is key for the hash of DbSourceProxy instances
77 * - 1:many mapping for DbSource to proxy will be lost. * suggest : PFAM is an
78 * 'alignment' source - means proxy is higher level than a sequence source.
79 * return jalview.datamodel.DBRefSource.PFAM; }
85 * @see jalview.ws.DbSourceProxy#getDbSourceProperties() public Hashtable
86 * getDbSourceProperties() {
94 * @see jalview.ws.DbSourceProxy#getDbVersion()
97 public String getDbVersion()
99 // TODO Auto-generated method stub
104 * Returns base URL for selected Pfam alignment type
106 * @return PFAM URL stub for this DbSource
109 protected abstract String getXFAMURL();
114 * @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 FormatAdapter().readFile(getXFAMURL()
124 + queries.trim().toUpperCase(), DataSourceType.URL,
125 FileFormat.Stockholm);
126 for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++)
128 rcds.getSequenceAt(s).addDBRef(new DBRefEntry(DBRefSource.PFAM,
130 getDbVersion(), queries.trim().toUpperCase()));
131 if (!getDbSource().equals(DBRefSource.PFAM))
132 { // add the specific ref too
133 rcds.getSequenceAt(s).addDBRef(
134 new DBRefEntry(getDbSource(), getDbVersion(), queries
135 .trim().toUpperCase()));
145 * @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(); }
158 public String getXfamSource()
160 return DBRefSource.PFAM;