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;
29 public class EmblCdsSource extends EmblXmlSource
31 private Regex ACCESSION_REGEX = null;
33 public EmblCdsSource()
39 public String getAccessionSeparator()
45 public Regex getAccessionValidator()
47 if (ACCESSION_REGEX == null)
49 ACCESSION_REGEX = Platform.newRegex("^[A-Z]+[0-9]+");
51 return ACCESSION_REGEX;
56 public String getDbSource()
58 return DBRefSource.EMBLCDS;
62 public String getDbVersion()
64 return "0"; // TODO : this is dynamically set for a returned record - not
69 public AlignmentI getSequenceRecords(String queries) throws Exception
71 if (queries.indexOf(".") > -1)
73 queries = queries.substring(0, queries.indexOf("."));
75 return getEmblSequenceRecords(DBRefSource.EMBLCDS, queries);
79 public boolean isValidReference(String accession)
81 // most embl CDS refs look like ..
82 // TODO: improve EMBLCDS regex
83 return (accession == null || accession.length() < 2) ? false
84 : getAccessionValidator().search(accession);
88 * cDNA for LDHA_CHICK swissprot sequence
91 public String getTestQuery()
97 public String getDbName()