X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FEmblCdsSource.java;h=d02910cf24d52c29d25d4f9e2e2016137eeb9de3;hb=6ca8a32d88328b8f2162512f41c657c87e131045;hp=03f0d169602c4b8bc4d2aaf0cdd75c6cbaed7f04;hpb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;p=jalview.git

diff --git a/src/jalview/ws/dbsources/EmblCdsSource.java b/src/jalview/ws/dbsources/EmblCdsSource.java
index 03f0d16..d02910c 100644
--- a/src/jalview/ws/dbsources/EmblCdsSource.java
+++ b/src/jalview/ws/dbsources/EmblCdsSource.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 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.
  * 
@@ -23,9 +23,7 @@ package jalview.ws.dbsources;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefSource;
 
-import com.stevesoft.pat.Regex;
-
-public class EmblCdsSource extends EmblXmlSource
+public class EmblCdsSource extends EmblFlatfileSource // was EmblXmlSource
 {
 
   public EmblCdsSource()
@@ -34,31 +32,12 @@ public class EmblCdsSource extends EmblXmlSource
   }
 
   @Override
-  public String getAccessionSeparator()
-  {
-    return null;
-  }
-
-  @Override
-  public Regex getAccessionValidator()
-  {
-    return new Regex("^[A-Z]+[0-9]+");
-  }
-
-  @Override
   public String getDbSource()
   {
     return DBRefSource.EMBLCDS;
   }
 
   @Override
-  public String getDbVersion()
-  {
-    return "0"; // TODO : this is dynamically set for a returned record - not
-    // tied to proxy
-  }
-
-  @Override
   public AlignmentI getSequenceRecords(String queries) throws Exception
   {
     if (queries.indexOf(".") > -1)
@@ -68,15 +47,6 @@ public class EmblCdsSource extends EmblXmlSource
     return getEmblSequenceRecords(DBRefSource.EMBLCDS, queries);
   }
 
-  @Override
-  public boolean isValidReference(String accession)
-  {
-    // most embl CDS refs look like ..
-    // TODO: improve EMBLCDS regex
-    return (accession == null || accession.length() < 2) ? false
-            : getAccessionValidator().search(accession);
-  }
-
   /**
    * cDNA for LDHA_CHICK swissprot sequence
    */
@@ -92,10 +62,4 @@ public class EmblCdsSource extends EmblXmlSource
     return "EMBL (CDS)";
   }
 
-  @Override
-  public int getTier()
-  {
-    return 0;
-  }
-
 }