JAL-3210 Improvements to eclipse detection. New src tree and SwingJS updated from...

[jalview.git] / src / jalview / controller / AlignViewController.java

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index a5a3591..33699cc 100644 (file)
--- 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;