-/**\r
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)\r
+ * Copyright (C) 2010 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
\r
/**\r
* @author JimP\r
- *\r
+ * \r
*/\r
public class EmblSource extends EmblXmlSource implements DbSourceProxy\r
{\r
\r
- public EmblSource() {\r
+ public EmblSource()\r
+ {\r
addDbSourceProperty(DBRefSource.DNASEQDB);\r
addDbSourceProperty(DBRefSource.CODINGSEQDB);\r
}\r
- \r
- /* (non-Javadoc)\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
* @see jalview.ws.DbSourceProxy#getAccessionSeparator()\r
*/\r
public String getAccessionSeparator()\r
return null;\r
}\r
\r
- /* (non-Javadoc)\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
* @see jalview.ws.DbSourceProxy#getAccessionValidator()\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
- /* (non-Javadoc)\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
* @see jalview.ws.DbSourceProxy#getDbSource()\r
*/\r
public String getDbSource()\r
{\r
return DBRefSource.EMBL;\r
}\r
- /* (non-Javadoc)\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
* @see jalview.ws.DbSourceProxy#getDbVersion()\r
*/\r
public String getDbVersion()\r
return "0";\r
}\r
\r
- /* (non-Javadoc)\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
* @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])\r
*/\r
public AlignmentI getSequenceRecords(String queries) throws Exception\r
{\r
return getEmblSequenceRecords(DBRefSource.EMBL, queries);\r
}\r
- /* (non-Javadoc)\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
* @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)\r
*/\r
public boolean isValidReference(String accession)\r
{\r
- // TODO Auto-generated method stub\r
- return false;\r
+ // most embl refs look like ..\r
+\r
+ return (accession == null || accession.length() < 2) ? false\r
+ : getAccessionValidator().search(accession);\r
+\r
}\r
\r
/**\r
- * return LHD_CHICK coding gene \r
+ * return LHD_CHICK coding gene\r
*/\r
public String getTestQuery()\r
{\r
\r
public String getDbName()\r
{\r
- return getDbSource();\r
+ return "EMBL"; // getDbSource();\r
}\r
}\r