JAL-3692 EMBL flatfile fetcher / parser (todo: CDS dbrefs and mappings)

[jalview.git] / src / jalview / ws / dbsources / EmblSource.java

diff --git a/src/jalview/ws/dbsources/EmblSource.java b/src/jalview/ws/dbsources/EmblSource.java
index 08c020e..4cff4a0 100644 (file)
--- a/src/jalview/ws/dbsources/EmblSource.java
+++ b/src/jalview/ws/dbsources/EmblSource.java
@@ -1,127 +1,74 @@
-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)\r
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- * \r
- * This program 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 2\r
- * of the License, or (at your option) any later version.\r
- * \r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
- * GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\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 : 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 /* EmblXmlSource */ EmblFlatfileSource
+{
+
+  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();
+  }
+}