Merge branch 'Release_2_9_0b1_Branch'

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 8f9e49e..a83438c 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -2370,26 +2370,26 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     /*
      * If the cut affects all sequences, warn, remove highlighted columns
      */
-
-    boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
-            .getAlignment().getWidth()) ? true : false;
-    if (sg.getSize() == viewport.getAlignment().getHeight()
-            && isEntireAlignWidth)
+    if (sg.getSize() == viewport.getAlignment().getHeight())
     {
-      int confirm = JOptionPane.showConfirmDialog(this,
-              MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
-              MessageManager.getString("label.delete_all"), // $NON-NLS-1$
-              JOptionPane.OK_CANCEL_OPTION);
-
-      if (confirm == JOptionPane.CANCEL_OPTION
-              || confirm == JOptionPane.CLOSED_OPTION)
+      boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
+              .getAlignment().getWidth()) ? true : false;
+      if (isEntireAlignWidth)
       {
-        return;
+        int confirm = JOptionPane.showConfirmDialog(this,
+                MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
+                MessageManager.getString("label.delete_all"), // $NON-NLS-1$
+                JOptionPane.OK_CANCEL_OPTION);
+
+        if (confirm == JOptionPane.CANCEL_OPTION
+                || confirm == JOptionPane.CLOSED_OPTION)
+        {
+          return;
+        }
       }
+      viewport.getColumnSelection().removeElements(sg.getStartRes(),
+              sg.getEndRes() + 1);
     }
-
-    viewport.getColumnSelection().removeElements(sg.getStartRes(),
-            sg.getEndRes() + 1);
     SequenceI[] cut = sg.getSequences()
             .toArray(new SequenceI[sg.getSize()]);
 
@@ -2415,7 +2415,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
   }
 
-
   /**
    * DOCUMENT ME!
    * 
@@ -3517,6 +3516,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
                 cs, "Background"));
       }
+      if (cs instanceof TCoffeeColourScheme)
+      {
+        tcoffeeColour.setEnabled(true);
+        tcoffeeColour.setSelected(true);
+      }
     }
 
     viewport.setGlobalColourScheme(cs);