X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=722bad1d4e5b74d8eee4b537507efa4de970d218;hb=b7c522b6eba60889fb1078f75e83e8e6c97ef7f8;hp=62d69d00aa38ecb2e5ec035bb4741478894afd08;hpb=714aae012ecf6cb27e602eaafdb6458b885dc80c;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 62d69d0..722bad1 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -25,7 +25,7 @@ public class PopupMenu extends JPopupMenu
   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
-  protected JRadioButtonMenuItem abovePIDColour = new JRadioButtonMenuItem();
+  protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
@@ -75,7 +75,37 @@ public class PopupMenu extends JPopupMenu
 
     SequenceGroup sg = ap.av.getRubberbandGroup();
     if(sg!=null)
-      groupName.setText( sg.getName() );
+    {
+      groupName.setText(sg.getName());
+      if(sg.cs instanceof ZappoColourScheme)
+        zappoColour.setSelected(true);
+      else if(sg.cs instanceof TaylorColourScheme)
+        taylorColour.setSelected(true);
+      else if (sg.cs instanceof PIDColourScheme)
+        PIDColour.setSelected(true);
+      else if (sg.cs instanceof Blosum62ColourScheme)
+        BLOSUM62Colour.setSelected(true);
+      else if (sg.cs instanceof UserColourScheme)
+        userDefinedColour.setSelected(true);
+      else if (sg.cs instanceof HydrophobicColourScheme)
+        hydrophobicityColour.setSelected(true);
+      else if (sg.cs instanceof HelixColourScheme)
+        helixColour.setSelected(true);
+      else if (sg.cs instanceof StrandColourScheme)
+        strandColour.setSelected(true);
+      else if (sg.cs instanceof TurnColourScheme)
+        turnColour.setSelected(true);
+      else if (sg.cs instanceof BuriedColourScheme)
+        buriedColour.setSelected(true);
+      else if (sg.cs instanceof ClustalxColourScheme)
+        clustalColour.setSelected(true);
+      else
+        noColourmenuItem.setSelected(true);
+
+      if (sg.cs instanceof ConservationColourScheme)
+        conservationMenuItem.setSelected(true);
+
+    }
 
     if(seq!=null)
     {
@@ -183,7 +213,6 @@ public class PopupMenu extends JPopupMenu
     residueMenu.add(annotateResidue);
 
     noColourmenuItem.setText("None");
-    noColourmenuItem.setSelected(true);
     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -192,7 +221,6 @@ public class PopupMenu extends JPopupMenu
       }
     });
 
-    clustalColour.setSelected(false);
     clustalColour.setText("Clustalx colours");
     clustalColour.addActionListener(new java.awt.event.ActionListener()
     {
@@ -304,6 +332,11 @@ public class PopupMenu extends JPopupMenu
 
   void refresh()
   {
+    SequenceGroup sg = getGroup();
+    SuperGroup superG = ap.av.alignment.getSuperGroup( sg );
+    if( superG !=null)
+      superG.setSuperGroupProperties( sg );
+
     ap.seqPanel.seqCanvas.paintFlag=true;
     ap.seqPanel.repaint();
   }
@@ -375,7 +408,7 @@ frame.setMaximizable(false);
     SliderPanel sp = new SliderPanel(ap, 70, false, getGroup().cs );
     JInternalFrame frame = new JInternalFrame();
     frame.setContentPane(sp);
-    Desktop.addInternalFrame(frame, "Percentage Identity Threshold", 400,90);
+    Desktop.addInternalFrame(frame, "Percentage Identity Threshold ("+getGroup().getName()+")" , 400,90);
     frame.setMaximizable(false);
 
   }
@@ -386,7 +419,7 @@ frame.setMaximizable(false);
     JInternalFrame frame = new JInternalFrame();
     UserDefinedColours chooser = new UserDefinedColours( frame, ap, getGroup());
     frame.setContentPane(chooser);
-    Desktop.addInternalFrame(frame,"User defined colours", 450,540 );
+    Desktop.addInternalFrame(frame,"User defined colours ("+getGroup().getName()+")", 450,540 );
     frame.setResizable(false);
     frame.setIconifiable(false);
     frame.setMaximizable(false);