-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)\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
-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
- * @author JimP\r
- * \r
- */\r
-public class EmblSource extends EmblXmlSource implements DbSourceProxy\r
-{\r
-\r
- public EmblSource()\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
- return new com.stevesoft.pat.Regex("^[A-Z]+[0-9]+");\r
- }\r
-\r
- /*\r
- * (non-Javadoc)\r
- * \r
- * @see jalview.ws.DbSourceProxy#getDbSource()\r
- */\r
- public String getDbSource()\r
- {\r
- return DBRefSource.EMBL;\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
- return getEmblSequenceRecords(DBRefSource.EMBL, 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
- // 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
- */\r
- public String getTestQuery()\r
- {\r
- return "X53828";\r
- }\r
-\r
- public String getDbName()\r
- {\r
- return "EMBL"; // getDbSource();\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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;
+
+/**
+ * @author JimP
+ *
+ */
+public class EmblSource extends EmblFlatfileSource // was EmblXmlSource
+{
+
+ public EmblSource()
+ {
+ super();
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getDbSource()
+ */
+ @Override
+ public String getDbSource()
+ {
+ return DBRefSource.EMBL;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
+ */
+ @Override
+ public AlignmentI getSequenceRecords(String queries) throws Exception
+ {
+ return getEmblSequenceRecords(DBRefSource.EMBL, queries);
+ }
+
+ /**
+ * return LHD_CHICK coding gene
+ */
+ @Override
+ public String getTestQuery()
+ {
+ return "X53828";
+ }
+
+ @Override
+ public String getDbName()
+ {
+ return "EMBL"; // getDbSource();
+ }
+}