-/**\r
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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 jalview.ws.seqfetcher.DbSourceProxyImpl;\r
\r
/**\r
+ * Test class for accessing GeneDB - not yet finished.\r
+ * \r
* @author JimP\r
- *\r
+ * \r
*/\r
public class GeneDbSource extends EmblXmlSource implements DbSourceProxy\r
{\r
\r
- public GeneDbSource() {\r
+ public GeneDbSource()\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
return null;\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.GENEDB;\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
- // query of form http://www.genedb.org/genedb/ArtemisFormHandler?id=&dest=EMBL\r
- // \r
+ // query of form\r
+ // http://www.genedb.org/genedb/ArtemisFormHandler?id=&dest=EMBL\r
+ //\r
return getEmblSequenceRecords(DBRefSource.GENEDB, 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
\r
/**\r
- * return T.Brucei Mannosyl-Transferase TbPIG-M \r
+ * return T.Brucei Mannosyl-Transferase TbPIG-M\r
*/\r
public String getTestQuery()\r
{\r
\r
public String getDbName()\r
{\r
- return getDbSource();\r
+ return "GeneDB"; // getDbSource();\r
}\r
}\r