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;
27 public class EmblCdsSouce extends EmblXmlSource implements DbSourceProxy
33 addDbSourceProperty(DBRefSource.CODINGSEQDB);
36 public String getAccessionSeparator()
41 public Regex getAccessionValidator()
43 return new com.stevesoft.pat.Regex("^[A-Z]+[0-9]+");
46 public String getDbSource()
48 return DBRefSource.EMBLCDS;
51 public String getDbVersion()
53 return "0"; // TODO : this is dynamically set for a returned record - not
57 public AlignmentI getSequenceRecords(String queries) throws Exception
59 if (queries.indexOf(".") > -1)
61 queries = queries.substring(0, queries.indexOf("."));
63 return getEmblSequenceRecords(DBRefSource.EMBLCDS, queries);
66 public boolean isValidReference(String accession)
68 // most embl CDS refs look like ..
69 // TODO: improve EMBLCDS regex
70 return (accession == null || accession.length() < 2) ? false
71 : getAccessionValidator().search(accession);
75 * cDNA for LDHA_CHICK swissprot sequence
77 public String getTestQuery()
82 public String getDbName()