JAL-2089 patch broken merge to master for Release 2.10.0b1

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

diff --git a/src/jalview/ws/dbsources/GeneDbSource.java b/src/jalview/ws/dbsources/GeneDbSource.java
index 07677d8..ce21ad0 100644 (file)
--- a/src/jalview/ws/dbsources/GeneDbSource.java
+++ b/src/jalview/ws/dbsources/GeneDbSource.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.
  * 
@@ -20,12 +20,10 @@
  */
 package jalview.ws.dbsources;
 
-
-import com.stevesoft.pat.Regex;
-
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefSource;
-import jalview.ws.seqfetcher.DbSourceProxy;
+
+import com.stevesoft.pat.Regex;
 
 /**
  * Test class for accessing GeneDB - not yet finished.
@@ -33,13 +31,12 @@ import jalview.ws.seqfetcher.DbSourceProxy;
  * @author JimP
  * 
  */
-public class GeneDbSource extends EmblXmlSource implements DbSourceProxy
+public class GeneDbSource extends EmblXmlSource
 {
 
   public GeneDbSource()
   {
-    addDbSourceProperty(DBRefSource.DNASEQDB);
-    addDbSourceProperty(DBRefSource.CODINGSEQDB);
+    super();
   }
 
   /*
@@ -47,6 +44,7 @@ public class GeneDbSource extends EmblXmlSource implements DbSourceProxy
    * 
    * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
    */
+  @Override
   public String getAccessionSeparator()
   {
     // TODO Auto-generated method stub
@@ -58,6 +56,7 @@ public class GeneDbSource extends EmblXmlSource implements DbSourceProxy
    * 
    * @see jalview.ws.DbSourceProxy#getAccessionValidator()
    */
+  @Override
   public Regex getAccessionValidator()
   {
     // TODO Auto-generated method stub
@@ -69,6 +68,7 @@ public class GeneDbSource extends EmblXmlSource implements DbSourceProxy
    * 
    * @see jalview.ws.DbSourceProxy#getDbSource()
    */
+  @Override
   public String getDbSource()
   {
     return DBRefSource.GENEDB;
@@ -79,6 +79,7 @@ public class GeneDbSource extends EmblXmlSource implements DbSourceProxy
    * 
    * @see jalview.ws.DbSourceProxy#getDbVersion()
    */
+  @Override
   public String getDbVersion()
   {
     // TODO Auto-generated method stub
@@ -90,6 +91,7 @@ public class GeneDbSource extends EmblXmlSource implements DbSourceProxy
    * 
    * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
    */
+  @Override
   public AlignmentI getSequenceRecords(String queries) throws Exception
   {
     // query of form
@@ -103,6 +105,7 @@ public class GeneDbSource extends EmblXmlSource implements DbSourceProxy
    * 
    * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
    */
+  @Override
   public boolean isValidReference(String accession)
   {
     // TODO Auto-generated method stub
@@ -112,15 +115,18 @@ public class GeneDbSource extends EmblXmlSource implements DbSourceProxy
   /**
    * return T.Brucei Mannosyl-Transferase TbPIG-M
    */
+  @Override
   public String getTestQuery()
   {
     return "Tb927.6.3300";
   }
 
+  @Override
   public String getDbName()
   {
     return "GeneDB"; // getDbSource();
   }
+
   @Override
   public int getTier()
   {