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;
26 import com.stevesoft.pat.Regex;
32 public class EmblSource extends EmblXmlSource
43 * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
46 public String getAccessionSeparator()
48 // TODO Auto-generated method stub
55 * @see jalview.ws.DbSourceProxy#getAccessionValidator()
58 public Regex getAccessionValidator()
60 return new Regex("^[A-Z]+[0-9]+");
66 * @see jalview.ws.DbSourceProxy#getDbSource()
69 public String getDbSource()
71 return DBRefSource.EMBL;
77 * @see jalview.ws.DbSourceProxy#getDbVersion()
80 public String getDbVersion()
82 // TODO Auto-generated method stub
89 * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
92 public AlignmentI getSequenceRecords(String queries) throws Exception
94 return getEmblSequenceRecords(DBRefSource.EMBL, queries);
100 * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
103 public boolean isValidReference(String accession)
105 // most embl refs look like ..
107 return (accession == null || accession.length() < 2) ? false
108 : getAccessionValidator().search(accession);
113 * return LHD_CHICK coding gene
116 public String getTestQuery()
122 public String getDbName()
124 return "EMBL"; // getDbSource();