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;
21 import com.stevesoft.pat.Regex;
23 import jalview.datamodel.AlignmentI;
24 import jalview.datamodel.DBRefSource;
25 import jalview.ws.seqfetcher.DbSourceProxy;
31 public class EmblSource extends EmblXmlSource implements DbSourceProxy
36 addDbSourceProperty(DBRefSource.DNASEQDB);
37 addDbSourceProperty(DBRefSource.CODINGSEQDB);
43 * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
45 public String getAccessionSeparator()
47 // TODO Auto-generated method stub
54 * @see jalview.ws.DbSourceProxy#getAccessionValidator()
56 public Regex getAccessionValidator()
58 return new com.stevesoft.pat.Regex("^[A-Z]+[0-9]+");
64 * @see jalview.ws.DbSourceProxy#getDbSource()
66 public String getDbSource()
68 return DBRefSource.EMBL;
74 * @see jalview.ws.DbSourceProxy#getDbVersion()
76 public String getDbVersion()
78 // TODO Auto-generated method stub
85 * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
87 public AlignmentI getSequenceRecords(String queries) throws Exception
89 return getEmblSequenceRecords(DBRefSource.EMBL, queries);
95 * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
97 public boolean isValidReference(String accession)
99 // most embl refs look like ..
101 return (accession == null || accession.length() < 2) ? false
102 : getAccessionValidator().search(accession);
107 * return LHD_CHICK coding gene
109 public String getTestQuery()
114 public String getDbName()
116 return "EMBL"; // getDbSource();