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;
26 import com.stevesoft.pat.Regex;
28 public class EmblCdsSource extends EmblXmlSource
31 public EmblCdsSource()
37 public String getAccessionSeparator()
43 public Regex getAccessionValidator()
45 return new Regex("^[A-Z]+[0-9]+");
49 public String getDbSource()
51 return DBRefSource.EMBLCDS;
55 public String getDbVersion()
57 return "0"; // TODO : this is dynamically set for a returned record - not
62 public AlignmentI getSequenceRecords(String queries) throws Exception
64 if (queries.indexOf(".") > -1)
66 queries = queries.substring(0, queries.indexOf("."));
68 return getEmblSequenceRecords(DBRefSource.EMBLCDS, queries);
72 public boolean isValidReference(String accession)
74 // most embl CDS refs look like ..
75 // TODO: improve EMBLCDS regex
76 return (accession == null || accession.length() < 2) ? false
77 : getAccessionValidator().search(accession);
81 * cDNA for LDHA_CHICK swissprot sequence
84 public String getTestQuery()
90 public String getDbName()