Merge branch 'Release_2_9_0b1_Branch' of https://source.jalview.org/git/jalview.git...

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

diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index 95a134a..c2efee7 100644 (file)
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,7 +20,6 @@
  */
 package jalview.ws.dbsources;
 
-import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
@@ -156,7 +155,7 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
     {
       queries = queries.toUpperCase().replaceAll(
               "(UNIPROT\\|?|UNIPROT_|UNIREF\\d+_|UNIREF\\d+\\|?)", "");
-      Alignment al = null;
+      AlignmentI al = null;
       EBIFetchClient ebi = new EBIFetchClient();
       // uniprotxml parameter required since december 2007
       // uniprotkb dbname changed introduced december 2008
@@ -226,8 +225,7 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
       name.append(n);
     }
 
-    if (entry.getProtein() != null
-            && entry.getProtein().getName() != null)
+    if (entry.getProtein() != null && entry.getProtein().getName() != null)
     {
       for (String nm : entry.getProtein().getName())
       {
@@ -245,7 +243,7 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
    * @param entries
    *          a list of n uniprot entries to be analysed.
    */
-  public void addUniprotXrefs(Alignment al, Vector<UniprotEntry> entries)
+  public void addUniprotXrefs(AlignmentI al, Vector<UniprotEntry> entries)
   {
     final String dbVersion = getDbVersion();