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 6bbe2e1..4cff4a0 100644 (file)
--- a/src/jalview/ws/dbsources/EmblSource.java
+++ b/src/jalview/ws/dbsources/EmblSource.java
@@ -23,13 +23,11 @@ package jalview.ws.dbsources;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefSource;
 
-import com.stevesoft.pat.Regex;
-
 /**
  * @author JimP
  * 
  */
-public class EmblSource extends EmblXmlSource
+public class EmblSource extends /* EmblXmlSource */ EmblFlatfileSource
 {
 
   public EmblSource()
@@ -40,29 +38,6 @@ public class EmblSource extends EmblXmlSource
   /*
    * (non-Javadoc)
    * 
-   * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
-   */
-  @Override
-  public String getAccessionSeparator()
-  {
-    // TODO Auto-generated method stub
-    return null;
-  }
-
-  /*
-   * (non-Javadoc)
-   * 
-   * @see jalview.ws.DbSourceProxy#getAccessionValidator()
-   */
-  @Override
-  public Regex getAccessionValidator()
-  {
-    return new Regex("^[A-Z]+[0-9]+");
-  }
-
-  /*
-   * (non-Javadoc)
-   * 
    * @see jalview.ws.DbSourceProxy#getDbSource()
    */
   @Override
@@ -74,18 +49,6 @@ public class EmblSource extends EmblXmlSource
   /*
    * (non-Javadoc)
    * 
-   * @see jalview.ws.DbSourceProxy#getDbVersion()
-   */
-  @Override
-  public String getDbVersion()
-  {
-    // TODO Auto-generated method stub
-    return "0";
-  }
-
-  /*
-   * (non-Javadoc)
-   * 
    * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
    */
   @Override
@@ -94,21 +57,6 @@ public class EmblSource extends EmblXmlSource
     return getEmblSequenceRecords(DBRefSource.EMBL, queries);
   }
 
-  /*
-   * (non-Javadoc)
-   * 
-   * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
-   */
-  @Override
-  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
    */
@@ -123,10 +71,4 @@ public class EmblSource extends EmblXmlSource
   {
     return "EMBL"; // getDbSource();
   }
-
-  @Override
-  public int getTier()
-  {
-    return 0;
-  }
 }