JAL-2439 Fix to hidden column marker being one row too short

[jalview.git] / src / jalview / gui / AlignFrame.java

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 445e967..d4c87d8 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -2750,6 +2750,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
      */
     newap.av.replaceMappings(viewport.getAlignment());
 
+    /*
+     * start up cDNA consensus (if applicable) now mappings are in place
+     */
+    if (newap.av.initComplementConsensus())
+    {
+      newap.refresh(true); // adjust layout of annotations
+    }
+
     newap.av.viewName = getNewViewName(viewTitle);
 
     addAlignmentPanel(newap, true);
@@ -3327,7 +3335,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
      */
     if (ResidueColourScheme.USER_DEFINED.equals(name))
     {
-      new UserDefinedColours(alignPanel, null);
+      new UserDefinedColours(alignPanel);
       return;
     }
 
@@ -3348,10 +3356,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void changeColour(ColourSchemeI cs)
   {
     // TODO: pull up to controller method
-    if (cs != null)
-    {
-      ColourMenuHelper.setColourSelected(colourMenu, cs.getSchemeName());
-    }
+    ColourMenuHelper.setColourSelected(colourMenu, cs);
 
     viewport.setGlobalColourScheme(cs);
 
@@ -5700,27 +5705,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     colourMenu.add(annotationColour);
 
     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
-    String schemeName = colourScheme == null ? null : colourScheme
-            .getSchemeName();
-
-    ColourMenuHelper.setColourSelected(colourMenu, schemeName);
-  }
-
-  /**
-   * Disable inapplicable items in the Select menu when it is clicked
-   */
-  @Override
-  protected void configureSelectMenu()
-  {
-    createGroup.setEnabled(false);
-    unGroup.setEnabled(false);
-    SequenceGroup sg = viewport.getSelectionGroup();
-    if (sg != null)
-    {
-      List<SequenceGroup> groups = viewport.getAlignment().getGroups();
-      createGroup.setEnabled(groups == null || !groups.contains(sg));
-      unGroup.setEnabled(groups != null && groups.contains(sg));
-    }
+    ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
   }
 }