2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
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/>.
18 package jalview.ws.dbsources;
20 import com.stevesoft.pat.Regex;
22 import jalview.datamodel.AlignmentI;
23 import jalview.datamodel.DBRefSource;
24 import jalview.ws.seqfetcher.DbSourceProxy;
26 public class EmblCdsSouce extends EmblXmlSource implements DbSourceProxy
32 addDbSourceProperty(DBRefSource.CODINGSEQDB);
35 public String getAccessionSeparator()
40 public Regex getAccessionValidator()
42 return new com.stevesoft.pat.Regex("^[A-Z]+[0-9]+");
45 public String getDbSource()
47 return DBRefSource.EMBLCDS;
50 public String getDbVersion()
52 return "0"; // TODO : this is dynamically set for a returned record - not
56 public AlignmentI getSequenceRecords(String queries) throws Exception
58 if (queries.indexOf(".") > -1)
60 queries = queries.substring(0, queries.indexOf("."));
62 return getEmblSequenceRecords(DBRefSource.EMBLCDS, queries);
65 public boolean isValidReference(String accession)
67 // most embl CDS refs look like ..
68 // TODO: improve EMBLCDS regex
69 return (accession == null || accession.length() < 2) ? false
70 : getAccessionValidator().search(accession);
74 * cDNA for LDHA_CHICK swissprot sequence
76 public String getTestQuery()
81 public String getDbName()