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;
21 import com.stevesoft.pat.Regex;
23 import jalview.datamodel.AlignmentI;
24 import jalview.datamodel.DBRefSource;
25 import jalview.ws.seqfetcher.DbSourceProxy;
28 * Test class for accessing GeneDB - not yet finished.
33 public class GeneDbSource extends EmblXmlSource implements DbSourceProxy
38 addDbSourceProperty(DBRefSource.DNASEQDB);
39 addDbSourceProperty(DBRefSource.CODINGSEQDB);
45 * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
47 public String getAccessionSeparator()
49 // TODO Auto-generated method stub
56 * @see jalview.ws.DbSourceProxy#getAccessionValidator()
58 public Regex getAccessionValidator()
60 // TODO Auto-generated method stub
67 * @see jalview.ws.DbSourceProxy#getDbSource()
69 public String getDbSource()
71 return DBRefSource.GENEDB;
77 * @see jalview.ws.DbSourceProxy#getDbVersion()
79 public String getDbVersion()
81 // TODO Auto-generated method stub
88 * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
90 public AlignmentI getSequenceRecords(String queries) throws Exception
93 // http://www.genedb.org/genedb/ArtemisFormHandler?id=&dest=EMBL
95 return getEmblSequenceRecords(DBRefSource.GENEDB, queries);
101 * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
103 public boolean isValidReference(String accession)
105 // TODO Auto-generated method stub
110 * return T.Brucei Mannosyl-Transferase TbPIG-M
112 public String getTestQuery()
114 return "Tb927.6.3300";
117 public String getDbName()
119 return "GeneDB"; // getDbSource();