X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=0d1dad38390a064bbf4c9d40e8a43f22d1b2b1d4;hb=a28c9340eeadfdaa551a21b9dea1d0f1530126e3;hp=858770a35ec187ca5849712d7b189fa046e988c6;hpb=29f89f52f3fc99e904a55e426c53a830290408cc;p=jalview.git

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 858770a..0d1dad3 100755
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -46,7 +46,7 @@ public class APopupMenu
   MenuItem noColourmenuItem = new MenuItem();
   protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
 
-  AlignmentPanel ap;
+  final AlignmentPanel ap;
   MenuItem unGroupMenuItem = new MenuItem();
   MenuItem nucleotideMenuItem = new MenuItem();
   Menu colourMenu = new Menu();
@@ -54,7 +54,7 @@ public class APopupMenu
   CheckboxMenuItem showText = new CheckboxMenuItem();
   CheckboxMenuItem showColourText = new CheckboxMenuItem();
 
-  public APopupMenu(AlignmentPanel ap, Sequence seq, Vector links)
+  public APopupMenu(AlignmentPanel apanel, Sequence seq, Vector links)
   {
     ///////////////////////////////////////////////////////////
     // If this is activated from the sequence panel, the user may want to
@@ -63,7 +63,7 @@ public class APopupMenu
     // If from the IDPanel, we must display the sequence menu
     //////////////////////////////////////////////////////////
 
-    this.ap = ap;
+    this.ap = apanel;
 
     try
     {
@@ -105,7 +105,7 @@ public class APopupMenu
            {
                public void actionPerformed(ActionEvent e)
                {
-                  jalview.bin.JalviewLite.showURL(url, target);
+                  ap.alignFrame.showURL(url, target);
                }
            });
           linkMenu.add(item);
@@ -319,6 +319,8 @@ public class APopupMenu
       }
         }
     ap.seqPanel.seqCanvas.repaint();
+    if(ap.overviewPanel!=null)
+      ap.overviewPanel.updateOverviewImage();
   }
 
   protected void clustalColour_actionPerformed(ActionEvent e)
@@ -379,29 +381,24 @@ public class APopupMenu
   protected void abovePIDColour_itemStateChanged(ItemEvent ie)
   {
     SequenceGroup sg = getGroup();
+    if(sg.cs==null)
+          return;
+
     if (abovePIDColour.getState())
     {
       sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
                                                ap.av.alignment.getWidth()));
       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
           getGroup().getName());
-      if (sg.cs instanceof ResidueColourScheme)
-      {
-        ( (ResidueColourScheme) sg.cs).setThreshold(threshold);
-      }
-      else if (sg.cs instanceof ScoreColourScheme)
-      {
-        ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
-      }
+
+      sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
 
       SliderPanel.showPIDSlider();
 
     }
     else // remove PIDColouring
     {
-      ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;
-      rcs.setThreshold(0);
-      sg.cs = rcs;
+      sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
     }
 
     refresh();
@@ -443,6 +440,8 @@ public class APopupMenu
   protected void conservationMenuItem_itemStateChanged(ItemEvent ie)
   {
     SequenceGroup sg = getGroup();
+    if(sg.cs==null)
+          return;
 
     if (conservationMenuItem.getState())
     {
@@ -454,17 +453,15 @@ public class APopupMenu
 
       c.calculate();
       c.verdict(false, ap.av.ConsPercGaps);
-      ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
 
-      sg.cs = ccs;
+      sg.cs.setConservation(c);
 
-      SliderPanel.setConservationSlider(ap, ccs, sg.getName());
+      SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
       SliderPanel.showConservationSlider();
     }
     else // remove ConservationColouring
     {
-      ConservationColourScheme ccs = (ConservationColourScheme) sg.cs;
-      sg.cs = ccs.cs;
+      sg.cs.setConservation(null);
     }
 
     refresh();
@@ -472,7 +469,7 @@ public class APopupMenu
 
   protected void analyze_actionPerformed(ActionEvent e)
   {
-    CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame.applet);
     Frame frame = new Frame();
     frame.add(cap);
     jalview.bin.JalviewLite.addFrame(frame, "Analyze this - ", 400, 300);