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.DBRefSource;
26 import jalview.ws.seqfetcher.DbSourceProxy;
29 * Test class for accessing GeneDB - not yet finished.
34 public class GeneDbSource extends EmblXmlSource implements DbSourceProxy
39 addDbSourceProperty(DBRefSource.DNASEQDB);
40 addDbSourceProperty(DBRefSource.CODINGSEQDB);
46 * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
48 public String getAccessionSeparator()
50 // TODO Auto-generated method stub
57 * @see jalview.ws.DbSourceProxy#getAccessionValidator()
59 public Regex getAccessionValidator()
61 // TODO Auto-generated method stub
68 * @see jalview.ws.DbSourceProxy#getDbSource()
70 public String getDbSource()
72 return DBRefSource.GENEDB;
78 * @see jalview.ws.DbSourceProxy#getDbVersion()
80 public String getDbVersion()
82 // TODO Auto-generated method stub
89 * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
91 public AlignmentI getSequenceRecords(String queries) throws Exception
94 // http://www.genedb.org/genedb/ArtemisFormHandler?id=&dest=EMBL
96 return getEmblSequenceRecords(DBRefSource.GENEDB, queries);
102 * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
104 public boolean isValidReference(String accession)
106 // TODO Auto-generated method stub
111 * return T.Brucei Mannosyl-Transferase TbPIG-M
113 public String getTestQuery()
115 return "Tb927.6.3300";
118 public String getDbName()
120 return "GeneDB"; // getDbSource();