Works out exisiting colur of a group

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 62d69d0..19698b7 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
@@ -375,7 +403,7 @@ 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 +414,7 @@ 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
@@ -428,6 +456,219 @@ frame.setMaximizable(false);
      refresh();\r
   }\r
 \r
+/*\r
+  protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
+  {\r
+    viewport.setGlobalColourScheme( null );\r
+    changeColour();\r
+  }\r
+\r
+\r
+  public void clustalColour_actionPerformed(ActionEvent e)\r
+  {\r
+    viewport.setGlobalColourScheme(new ClustalxColourScheme( ));\r
+    conservationMenuItem.setSelected(false);\r
+    abovePIDThreshold.setSelected(false);\r
+    changeColour();\r
+  }\r
+\r
+  public void zappoColour_actionPerformed(ActionEvent e)\r
+  {\r
+    viewport.setGlobalColourScheme(new ZappoColourScheme() );\r
+    changeColour();\r
+  }\r
+\r
+  public void taylorColour_actionPerformed(ActionEvent e)\r
+  {\r
+    viewport.setGlobalColourScheme(new TaylorColourScheme() );\r
+    changeColour();\r
+  }\r
+\r
+\r
+  public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
+  {\r
+    viewport.setGlobalColourScheme( new HydrophobicColourScheme() );\r
+    changeColour();\r
+  }\r
+\r
+  public void helixColour_actionPerformed(ActionEvent e)\r
+  {\r
+    viewport.setGlobalColourScheme( new HelixColourScheme()  );\r
+    changeColour();\r
+  }\r
+\r
+\r
+  public void strandColour_actionPerformed(ActionEvent e)\r
+  {\r
+    viewport.setGlobalColourScheme(new StrandColourScheme() );\r
+    changeColour();\r
+  }\r
+\r
+\r
+  public void turnColour_actionPerformed(ActionEvent e)\r
+  {\r
+    viewport.setGlobalColourScheme(new TurnColourScheme() );\r
+    changeColour();\r
+  }\r
+\r
+\r
+  public void buriedColour_actionPerformed(ActionEvent e)\r
+  {\r
+    viewport.setGlobalColourScheme( new BuriedColourScheme() );\r
+    changeColour();\r
+  }\r
+\r
+  void changeColour()\r
+  {\r
+    if(abovePIDThreshold.isSelected())\r
+      abovePIDThreshold_actionPerformed(null);\r
+    else if(conservationMenuItem.isSelected())\r
+      conservationMenuItem_actionPerformed(null);\r
+\r
+     alignPanel.seqPanel.seqCanvas.paintFlag = true;\r
+     alignPanel.repaint();\r
+  }\r
+\r
+  void addConservationOrPIDColour()\r
+  {\r
+    int x=0, y=0, threshold = 70;\r
+\r
+    if(sliderFrame!=null)\r
+       try\r
+       {\r
+         x = sliderFrame.getX();\r
+         y = sliderFrame.getY();\r
+         SliderPanel sp = (SliderPanel) sliderFrame.getContentPane();\r
+         threshold = sp.getValue();\r
+         sliderFrame.setClosed(true);\r
+       }\r
+       catch (Exception ex)\r
+       {    ex.printStackTrace();   }\r
+\r
+     ColourSchemeI oldCs = viewport.getGlobalColourScheme();\r
+\r
+     ConservationColourScheme ccs = null;\r
+     if (oldCs instanceof ConservationColourScheme)\r
+       ccs = (ConservationColourScheme) oldCs;\r
+\r
+     if(conservationMenuItem.isSelected())\r
+     {\r
+       Alignment al = (Alignment)viewport.alignment;\r
+       Conservation c = new Conservation("All",\r
+                            ResidueProperties.propHash, 3, al.getSequences(), 0,\r
+                            al.getWidth() );\r
+\r
+       c.calculate();\r
+       c.verdict(false, 100);\r
+\r
+       if(ccs!=null)\r
+         ccs = new ConservationColourScheme(c, ccs.cs);\r
+       else\r
+         ccs = new ConservationColourScheme(c, oldCs);\r
+\r
+        viewport.setGlobalColourScheme( ccs );\r
+\r
+     }\r
+     else if(oldCs instanceof ConservationColourScheme)\r
+     {\r
+       oldCs = ccs.cs;\r
+       viewport.setGlobalColourScheme( oldCs );\r
+     }\r
+\r
+\r
+     if( conservationMenuItem.isSelected() || abovePIDThreshold.isSelected() )\r
+     {\r
+       sliderFrame = new JInternalFrame();\r
+       sliderFrame.setMaximizable(false);\r
+       sliderFrame.setResizable(false);\r
+\r
+       SliderPanel sp = null;\r
+       if (conservationMenuItem.isSelected())\r
+       {\r
+        if(threshold > 50)\r
+          threshold = 30;\r
+        sp = new SliderPanel(alignPanel, threshold, true,ccs);\r
+        Desktop.addInternalFrame(sliderFrame, "Conservation Colour Increment  (Global colour)", 400, 90);\r
+        threshold = 0;\r
+       }\r
+       else if (abovePIDThreshold.isSelected())\r
+       {\r
+         sp = new SliderPanel(alignPanel, threshold, false, oldCs);\r
+         sp.cs = oldCs;\r
+         Desktop.addInternalFrame(sliderFrame, "Percentage Identity Threshold (Global colour)", 400, 90);\r
+       }\r
+\r
+       sliderFrame.setContentPane(sp);\r
+       if(x!=0 && y!=0)\r
+               sliderFrame.setLocation(x,y);\r
+\r
+     }\r
+     else\r
+       threshold = 0;\r
+\r
+\r
+     if (oldCs instanceof ResidueColourScheme)\r
+     {\r
+       ResidueColourScheme rcs = (ResidueColourScheme) oldCs;\r
+       rcs.setThreshold(threshold);\r
+     }\r
+     else if (oldCs instanceof ScoreColourScheme)\r
+     {\r
+       ScoreColourScheme scs = (ScoreColourScheme) oldCs;\r
+       scs.setThreshold(threshold);\r
+     }\r
+\r
+     alignPanel.seqPanel.seqCanvas.paintFlag = true;\r
+     alignPanel.repaint();\r
+\r
+  }\r
+\r
+  protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
+  {\r
+   if(abovePIDThreshold.isSelected())\r
+    abovePIDThreshold.setSelected(false);\r
+\r
+   viewport.setConservationSelected(conservationMenuItem.isSelected());\r
+\r
+   addConservationOrPIDColour();\r
+  }\r
+\r
+  JInternalFrame sliderFrame;\r
+  public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
+  {\r
+      if(conservationMenuItem.isSelected())\r
+        conservationMenuItem.setSelected(false);\r
+\r
+      addConservationOrPIDColour();\r
+  }\r
+\r
+\r
+\r
+  public void userDefinedColour_actionPerformed(ActionEvent e)\r
+  {\r
+    JInternalFrame frame = new JInternalFrame();\r
+    UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);\r
+    frame.setContentPane(chooser);\r
+    Desktop.addInternalFrame(frame,"User defined colours", 450,540 );\r
+    frame.setResizable(false);\r
+    frame.setIconifiable(false);\r
+    frame.setMaximizable(false);\r
+  }\r
+\r
+  public void PIDColour_actionPerformed(ActionEvent e)\r
+  {\r
+    viewport.setGlobalColourScheme( new PIDColourScheme() );\r
+    alignPanel.setColourScheme( );\r
+  }\r
+\r
+\r
+  public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
+  {\r
+    viewport.setGlobalColourScheme( new Blosum62ColourScheme(viewport)  );\r
+    alignPanel.setColourScheme();\r
+  }\r
+*/\r
+//////////////////////////////////////\r
   protected void groupAnnotation_actionPerformed(ActionEvent e)\r
   {\r
 \r