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;
33 public class EmblSource 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 return new com.stevesoft.pat.Regex("^[A-Z]+[0-9]+");
66 * @see jalview.ws.DbSourceProxy#getDbSource()
68 public String getDbSource()
70 return DBRefSource.EMBL;
76 * @see jalview.ws.DbSourceProxy#getDbVersion()
78 public String getDbVersion()
80 // TODO Auto-generated method stub
87 * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
89 public AlignmentI getSequenceRecords(String queries) throws Exception
91 return getEmblSequenceRecords(DBRefSource.EMBL, queries);
97 * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
99 public boolean isValidReference(String accession)
101 // most embl refs look like ..
103 return (accession == null || accession.length() < 2) ? false
104 : getAccessionValidator().search(accession);
109 * return LHD_CHICK coding gene
111 public String getTestQuery()
116 public String getDbName()
118 return "EMBL"; // getDbSource();