X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcontroller%2FAlignViewController.java;h=33699ccf9b646f1792838fd6a587aea84e52753b;hb=22751aff02dc52ad529a85962a8ebc7733176d7e;hp=a5a35910c1b5d9ac7139d4c228d2cb5354a87835;hpb=6c2b68627777b6731f3e1081fb7437b9678c9670;p=jalview.git

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index a5a3591..33699cc 100644
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -107,8 +107,7 @@ public class AlignViewController implements AlignViewControllerI
         viewport.getAlignment().addGroup(gps[g]);
         if (colours != null)
         {
-          gps[g].setColourScheme(colours.getInstance(viewport, gps[g],
-                  viewport.getHiddenRepSequences()));
+          gps[g].setColourScheme(colours.getInstance(viewport, gps[g]));
         }
         Color col = new Color((int) (Math.random() * 255),
                 (int) (Math.random() * 255), (int) (Math.random() * 255));
@@ -354,7 +353,7 @@ public class AlignViewController implements AlignViewControllerI
   }
 
   @Override
-  public boolean parseFeaturesFile(String file, DataSourceType protocol,
+  public boolean parseFeaturesFile(Object file, DataSourceType protocol,
           boolean relaxedIdMatching)
   {
     boolean featuresAdded = false;