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 e5f0c62..4cff4a0 100644 (file)
--- a/src/jalview/ws/dbsources/EmblSource.java
+++ b/src/jalview/ws/dbsources/EmblSource.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,44 +20,19 @@
  */
 package jalview.ws.dbsources;
 
-import com.stevesoft.pat.Regex;
-
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefSource;
-import jalview.ws.seqfetcher.DbSourceProxy;
 
 /**
  * @author JimP
  * 
  */
-public class EmblSource extends EmblXmlSource implements DbSourceProxy
+public class EmblSource extends /* EmblXmlSource */ EmblFlatfileSource
 {
 
   public EmblSource()
   {
-    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()
-  {
-    return new com.stevesoft.pat.Regex("^[A-Z]+[0-9]+");
+    super();
   }
 
   /*
@@ -65,6 +40,7 @@ public class EmblSource extends EmblXmlSource implements DbSourceProxy
    * 
    * @see jalview.ws.DbSourceProxy#getDbSource()
    */
+  @Override
   public String getDbSource()
   {
     return DBRefSource.EMBL;
@@ -73,54 +49,26 @@ public class EmblSource extends EmblXmlSource implements DbSourceProxy
   /*
    * (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[])
    */
+  @Override
   public AlignmentI getSequenceRecords(String queries) throws Exception
   {
     return getEmblSequenceRecords(DBRefSource.EMBL, queries);
   }
 
-  /*
-   * (non-Javadoc)
-   * 
-   * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
-   */
-  public boolean isValidReference(String accession)
-  {
-    // most embl refs look like ..
-
-    return (accession == null || accession.length() < 2) ? false
-            : getAccessionValidator().search(accession);
-
-  }
-
   /**
    * return LHD_CHICK coding gene
    */
+  @Override
   public String getTestQuery()
   {
     return "X53828";
   }
 
+  @Override
   public String getDbName()
   {
     return "EMBL"; // getDbSource();
   }
-
-  @Override
-  public int getTier()
-  {
-    return 0;
-  }
 }