Merge branch 'develop' into features/JAL-2393customMatrices

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 27fc34c..a69cd59 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -372,7 +372,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        new TreeChooser(AlignFrame.this);
+        new CalculationChooser(AlignFrame.this);
       }
     });
     buildColourMenu();
@@ -2760,6 +2760,14 @@ 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);
@@ -3337,7 +3345,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
      */
     if (ResidueColourScheme.USER_DEFINED.equals(name))
     {
-      new UserDefinedColours(alignPanel, null);
+      new UserDefinedColours(alignPanel);
       return;
     }
 
@@ -3358,10 +3366,7 @@ 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);
 
@@ -3447,7 +3452,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
-            .getAlignment().getSequenceAt(0), null);
+            .getAlignment().getSequenceAt(0));
     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
             viewport.getAlignment()));
     alignPanel.paintAlignment(true);
@@ -5634,10 +5639,7 @@ 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);
+    ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
   }
 }