Commented out code removed

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

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