-/*\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.io.File;\r
-import java.util.Hashtable;\r
-import java.util.Iterator;\r
-import java.util.StringTokenizer;\r
-\r
-import com.stevesoft.pat.Regex;\r
-\r
-import jalview.datamodel.Alignment;\r
-import jalview.datamodel.AlignmentI;\r
-import jalview.datamodel.DBRefSource;\r
-import jalview.datamodel.SequenceI;\r
-import jalview.datamodel.xdb.embl.EmblEntry;\r
-import jalview.ws.ebi.EBIFetchClient;\r
-import jalview.ws.seqfetcher.DbSourceProxy;\r
-import jalview.ws.seqfetcher.DbSourceProxyImpl;\r
-\r
-/**\r
- * Test class for accessing GeneDB - not yet finished.\r
- * \r
- * @author JimP\r
- * \r
- */\r
-public class GeneDbSource extends EmblXmlSource implements DbSourceProxy\r
-{\r
-\r
- public GeneDbSource()\r
- {\r
- addDbSourceProperty(DBRefSource.DNASEQDB);\r
- addDbSourceProperty(DBRefSource.CODINGSEQDB);\r
- }\r
-\r
- /*\r
- * (non-Javadoc)\r
- * \r
- * @see jalview.ws.DbSourceProxy#getAccessionSeparator()\r
- */\r
- public String getAccessionSeparator()\r
- {\r
- // TODO Auto-generated method stub\r
- return null;\r
- }\r
-\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
- }\r
-\r
- /*\r
- * (non-Javadoc)\r
- * \r
- * @see jalview.ws.DbSourceProxy#getDbSource()\r
- */\r
- public String getDbSource()\r
- {\r
- return DBRefSource.GENEDB;\r
- }\r
-\r
- /*\r
- * (non-Javadoc)\r
- * \r
- * @see jalview.ws.DbSourceProxy#getDbVersion()\r
- */\r
- public String getDbVersion()\r
- {\r
- // TODO Auto-generated method stub\r
- return "0";\r
- }\r
-\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\r
- // http://www.genedb.org/genedb/ArtemisFormHandler?id=&dest=EMBL\r
- //\r
- return getEmblSequenceRecords(DBRefSource.GENEDB, queries);\r
- }\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
- }\r
-\r
- /**\r
- * return T.Brucei Mannosyl-Transferase TbPIG-M\r
- */\r
- public String getTestQuery()\r
- {\r
- return "Tb927.6.3300";\r
- }\r
-\r
- public String getDbName()\r
- {\r
- return "GeneDB"; // getDbSource();\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.ws.dbsources;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefSource;
+import jalview.ws.seqfetcher.DbSourceProxy;
+
+import com.stevesoft.pat.Regex;
+
+/**
+ * Test class for accessing GeneDB - not yet finished.
+ *
+ * @author JimP
+ *
+ */
+public class GeneDbSource extends EmblXmlSource implements DbSourceProxy
+{
+
+ public GeneDbSource()
+ {
+ addDbSourceProperty(DBRefSource.DNASEQDB);
+ addDbSourceProperty(DBRefSource.CODINGSEQDB);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
+ */
+ public String getAccessionSeparator()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getAccessionValidator()
+ */
+ public Regex getAccessionValidator()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getDbSource()
+ */
+ public String getDbSource()
+ {
+ return DBRefSource.GENEDB;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getDbVersion()
+ */
+ public String getDbVersion()
+ {
+ // TODO Auto-generated method stub
+ return "0";
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
+ */
+ public AlignmentI getSequenceRecords(String queries) throws Exception
+ {
+ // query of form
+ // http://www.genedb.org/genedb/ArtemisFormHandler?id=&dest=EMBL
+ //
+ return getEmblSequenceRecords(DBRefSource.GENEDB, queries);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
+ */
+ public boolean isValidReference(String accession)
+ {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ /**
+ * return T.Brucei Mannosyl-Transferase TbPIG-M
+ */
+ public String getTestQuery()
+ {
+ return "Tb927.6.3300";
+ }
+
+ public String getDbName()
+ {
+ return "GeneDB"; // getDbSource();
+ }
+
+ @Override
+ public int getTier()
+ {
+ return 0;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff