From 2bfdb1bb7faa5724a86d7e6c3531c0713736c47e Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 19 Nov 2004 17:24:11 +0000
Subject: [PATCH] set display boxes must be applied to groups

---
 src/jalview/gui/AlignFrame.java |   47 +++++++++++++++++++++++++++++++++------
 1 file changed, 40 insertions(+), 7 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 76c483e..4707f3a 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -86,6 +86,7 @@ public class AlignFrame extends GAlignFrame
     public void run()
     {
       PrinterJob printJob = PrinterJob.getPrinterJob();
+    //  printJob.
       PageFormat pf = printJob.pageDialog(printJob.defaultPage());
       printJob.setPrintable(alignPanel, pf);
       if (printJob.printDialog())
@@ -395,8 +396,7 @@ public class AlignFrame extends GAlignFrame
 
   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
   {
-    viewport.setColourText( colourTextMenuItem.isSelected() );
-    alignPanel.RefreshPanels();
+      updateResidueView();
   }
 
   void SetFont()
@@ -416,20 +416,53 @@ public class AlignFrame extends GAlignFrame
 
   protected void wrapMenuItem_actionPerformed(ActionEvent e)
   {
-    viewport.setWrapAlignment( wrapMenuItem.isSelected() );
-    alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );
+     updateResidueView();
   }
 
 
   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
   {
-    viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );
-    alignPanel.RefreshPanels();
+     updateResidueView();
   }
 
   public void viewTextMenuItem_actionPerformed(ActionEvent e)
   {
-    viewport.setShowText( viewTextMenuItem.isSelected() );
+     updateResidueView();
+  }
+
+  void updateResidueView()
+  {
+    if (viewport.getSelection().size() == 0)
+     {
+       for (int i = 0; i < viewport.alignment.getGroups().size(); i++)
+       {
+         SequenceGroup sg = (SequenceGroup) viewport.alignment.getGroups().elementAt(i);
+         sg.setDisplayBoxes( viewBoxesMenuItem.isSelected() );
+         sg.setDisplayText( viewTextMenuItem.isSelected() );
+         sg.setColourText( colourTextMenuItem.isSelected() );
+       }
+     }
+     else
+     {
+       SequenceGroup sg = viewport.alignment.findGroup( (Sequence) viewport.sel.sequenceAt(0));
+       if (alignPanel.seqPanel.isNewSelection(sg))
+       {
+         sg = viewport.getAlignment().addGroup();
+         for (int i = 0; i < viewport.getSelection().size(); i++)
+         {
+           viewport.alignment.removeFromGroup(viewport.alignment.findGroup( (
+               Sequence) viewport.sel.sequenceAt(i)),
+                                              (Sequence) viewport.sel.sequenceAt(
+               i));
+           viewport.alignment.addToGroup(sg,
+                                         (Sequence) viewport.sel.sequenceAt(i));
+         }
+       }
+
+       sg.setDisplayBoxes(viewBoxesMenuItem.isSelected());
+       sg.setDisplayText(viewTextMenuItem.isSelected());
+       sg.setColourText(colourTextMenuItem.isSelected());
+     }
     alignPanel.RefreshPanels();
   }
 
-- 
1.7.10.2