+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
+ */\r
package jalview.ws.dbsources;\r
\r
import java.util.Hashtable;\r
public class EmblCdsSouce extends EmblXmlSource implements DbSourceProxy\r
{\r
\r
- public EmblCdsSouce() {\r
+ public EmblCdsSouce()\r
+ {\r
super();\r
- addDbSourceProperty(DBRefSource.CODINGSEQDB); \r
+ addDbSourceProperty(DBRefSource.CODINGSEQDB);\r
}\r
- \r
+\r
public String getAccessionSeparator()\r
{\r
- return null;\r
+ return null;\r
}\r
\r
public Regex getAccessionValidator()\r
{\r
- // TODO Auto-generated method stub\r
- return null;\r
+ return new com.stevesoft.pat.Regex("^[A-Z]+[0-9]+");\r
}\r
\r
public String getDbSource()\r
\r
public String getDbVersion()\r
{\r
- return "0"; // TODO : this is dynamically set for a returned record - not tied to proxy\r
+ return "0"; // TODO : this is dynamically set for a returned record - not\r
+ // tied to proxy\r
}\r
\r
public AlignmentI getSequenceRecords(String queries) throws Exception\r
- { \r
- if (queries.indexOf(".")>-1)\r
+ {\r
+ if (queries.indexOf(".") > -1)\r
{\r
queries = queries.substring(0, queries.indexOf("."));\r
}\r
\r
public boolean isValidReference(String accession)\r
{\r
- // TODO Auto-generated method stub\r
- return true;\r
+ // most embl CDS refs look like ..\r
+ // TODO: improve EMBLCDS regex\r
+ return (accession == null || accession.length() < 2) ? false\r
+ : getAccessionValidator().search(accession);\r
}\r
+\r
/**\r
* cDNA for LDHA_CHICK swissprot sequence\r
*/\r
return "CAA37824";\r
}\r
\r
+ public String getDbName()\r
+ {\r
+ return "EMBL (CDS)";\r
+ }\r
+\r
}\r