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.DBRefSource;
25 import jalview.ws.seqfetcher.DbSourceProxy;
27 import com.stevesoft.pat.Regex;
30 * Test class for accessing GeneDB - not yet finished.
35 public class GeneDbSource extends EmblXmlSource implements DbSourceProxy
40 addDbSourceProperty(DBRefSource.DNASEQDB);
41 addDbSourceProperty(DBRefSource.CODINGSEQDB);
47 * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
49 public String getAccessionSeparator()
51 // TODO Auto-generated method stub
58 * @see jalview.ws.DbSourceProxy#getAccessionValidator()
60 public Regex getAccessionValidator()
62 // TODO Auto-generated method stub
69 * @see jalview.ws.DbSourceProxy#getDbSource()
71 public String getDbSource()
73 return DBRefSource.GENEDB;
79 * @see jalview.ws.DbSourceProxy#getDbVersion()
81 public String getDbVersion()
83 // TODO Auto-generated method stub
90 * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
92 public AlignmentI getSequenceRecords(String queries) throws Exception
95 // http://www.genedb.org/genedb/ArtemisFormHandler?id=&dest=EMBL
97 return getEmblSequenceRecords(DBRefSource.GENEDB, queries);
103 * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
105 public boolean isValidReference(String accession)
107 // TODO Auto-generated method stub
112 * return T.Brucei Mannosyl-Transferase TbPIG-M
114 public String getTestQuery()
116 return "Tb927.6.3300";
119 public String getDbName()
121 return "GeneDB"; // getDbSource();