X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=a49470889096237447a92dfbe732ad676246dd65;hb=63a18b71aa3ed6503b6fbb8ec3543b5d66ed3f70;hp=353a1397e45c6aa15fb247a34ce1759440b96ae6;hpb=915ef58a91b8aa971abc3ee6ec68fcf85c872d25;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 353a139..a494708 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -3235,10 +3235,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
         threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
                 "Background");
-
         cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
-
-        viewport.setGlobalColourScheme(cs);
       }
       else
       {
@@ -5547,6 +5544,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       alignPanel.paintAlignment(true);
     }
   }
+  public void clearAlignmentSeqRep()
+  {
+    // TODO refactor alignmentseqrep to controller
+    if (viewport.getAlignment().hasSeqrep()) {
+      viewport.getAlignment().setSeqrep(null);
+      PaintRefresher.Refresh(this, viewport.getSequenceSetId());
+      alignPanel.updateAnnotation();
+      alignPanel.paintAlignment(true);
+    }
+  }
 
   @Override
   protected void createGroup_actionPerformed(ActionEvent e)