From d9ad2fe9891df2dcba7713f888f57bc3c79ee1c0 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 1 Feb 2005 19:03:04 +0000
Subject: [PATCH] Conservation and PID colouring methods updated, also remove
 group added

---
 src/jalview/gui/PopupMenu.java |   71 ++++++++++++++++++++++++----------------
 1 file changed, 43 insertions(+), 28 deletions(-)

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 722bad1..4ad7090 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -40,6 +40,7 @@ public class PopupMenu extends JPopupMenu
   JMenuItem annotateResidue = new JMenuItem();
 
   SequenceI sequence;
+  JMenuItem unGroupMenuItem = new JMenuItem();
 
   public PopupMenu(AlignmentPanel ap, SequenceI seq)
   {
@@ -104,9 +105,9 @@ public class PopupMenu extends JPopupMenu
 
       if (sg.cs instanceof ConservationColourScheme)
         conservationMenuItem.setSelected(true);
-
     }
 
+
     if(seq!=null)
     {
       residueMenu.setVisible(false);
@@ -180,10 +181,19 @@ public class PopupMenu extends JPopupMenu
     residueMenu.setText("Residue");
     annotateResidue.setText("annotate residue???");
     PIDColour.setFocusPainted(false);
+    unGroupMenuItem.setText("Remove Group");
+    unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        unGroupMenuItem_actionPerformed(e);
+      }
+    });
     add(groupMenu);
     this.add(sequenceMenu);
     this.add(residueMenu);
     groupMenu.add(defineMenu);
+    groupMenu.add(unGroupMenuItem);
     groupMenu.addSeparator();
     groupMenu.add(copyGroup);
     groupMenu.add(moveGroup);
@@ -343,7 +353,8 @@ public class PopupMenu extends JPopupMenu
 
   protected void clustalColour_actionPerformed(ActionEvent e)
   {
-    getGroup().cs = new ClustalxColourScheme();
+    SequenceGroup sg = getGroup();
+    sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());
     refresh();
   }
 
@@ -391,26 +402,9 @@ public class PopupMenu extends JPopupMenu
   }
 
 
-/*
-public void conservationColourIncMenuItem_actionPerformed(ActionEvent e)
-{
-ConservationIncrementPanel cip = new ConservationIncrementPanel(viewport, alignPanel);
-JInternalFrame frame = new JInternalFrame();
-frame.setContentPane(cip);
-Desktop.addInternalFrame(frame, "Conservation Colour Increment", 400,90);
-frame.setMaximizable(false);
-
- }*/
-
-
   protected void abovePIDColour_actionPerformed(ActionEvent e)
   {
-    SliderPanel sp = new SliderPanel(ap, 70, false, getGroup().cs );
-    JInternalFrame frame = new JInternalFrame();
-    frame.setContentPane(sp);
-    Desktop.addInternalFrame(frame, "Percentage Identity Threshold ("+getGroup().getName()+")" , 400,90);
-    frame.setMaximizable(false);
-
+    Desktop.setPIDSliderSource(ap, getGroup().cs, getGroup().getName());
   }
 
 
@@ -448,15 +442,28 @@ frame.setMaximizable(false);
   {
     SequenceGroup sg = getGroup();
 
-    Conservation c = new Conservation("Group",
-                          ResidueProperties.propHash, 3, sg.sequences, sg.getStartRes(),
-                          sg.getEndRes() );
+    if(conservationMenuItem.isSelected())
+    {
+
+        Conservation c = new Conservation("Group",
+                                          ResidueProperties.propHash, 3,
+                                          sg.sequences, 0,
+                                          ap.av.alignment.getWidth());
 
-     c.calculate();
-     c.verdict(false, 100);
-     ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
+        c.calculate();
+        c.verdict(false, 100);
+        ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
 
-     sg.cs = ccs;
+
+      sg.cs = ccs;
+
+      Desktop.setConservationSliderSource(ap, ccs, sg.getName());
+    }
+    else // remove ConservationColouring
+    {
+        ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
+        sg.cs = ccs.cs;
+    }
 
      refresh();
   }
@@ -528,7 +535,7 @@ frame.setMaximizable(false);
 
     ap.av.alignment.deleteGroup(sg);
     ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());
-    ap.seqPanel.parent.RefreshPanels();
+    ap.RefreshPanels();
 
   }
 
@@ -582,4 +589,12 @@ frame.setMaximizable(false);
     }
 
   }
+
+  void unGroupMenuItem_actionPerformed(ActionEvent e)
+  {
+     SequenceGroup sg = ap.av.getRubberbandGroup();
+     ap.av.alignment.deleteGroup(sg);
+     ap.av.setRubberbandGroup(null);
+     ap.RefreshPanels();
+  }
 }
-- 
1.7.10.2