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.util.Platform;
27 import com.stevesoft.pat.Regex;
33 public class EmblSource extends EmblXmlSource
36 private static Regex ACCESSION_REGEX;
46 * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
49 public String getAccessionSeparator()
51 // TODO Auto-generated method stub
58 * @see jalview.ws.DbSourceProxy#getAccessionValidator()
61 public Regex getAccessionValidator()
63 if (ACCESSION_REGEX == null)
65 ACCESSION_REGEX = Platform.newRegex("^[A-Z]+[0-9]+");
67 return ACCESSION_REGEX;
73 * @see jalview.ws.DbSourceProxy#getDbSource()
76 public String getDbSource()
78 return DBRefSource.EMBL;
84 * @see jalview.ws.DbSourceProxy#getDbVersion()
87 public String getDbVersion()
89 // TODO Auto-generated method stub
96 * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
99 public AlignmentI getSequenceRecords(String queries) throws Exception
101 return getEmblSequenceRecords(DBRefSource.EMBL, queries);
107 * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
110 public boolean isValidReference(String accession)
112 // most embl refs look like ..
114 return (accession == null || accession.length() < 2) ? false
115 : getAccessionValidator().search(accession);
120 * return LHD_CHICK coding gene
123 public String getTestQuery()
129 public String getDbName()
131 return "EMBL"; // getDbSource();