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[jalview.git] / src / jalview / appletgui / APopupMenu.java

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 858770a..68960f4 100755 (executable)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -379,29 +379,24 @@ public class APopupMenu
   protected void abovePIDColour_itemStateChanged(ItemEvent ie)\r
   {\r
     SequenceGroup sg = getGroup();\r
+    if(sg.cs==null)\r
+          return;\r
+\r
     if (abovePIDColour.getState())\r
     {\r
       sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
                                                ap.av.alignment.getWidth()));\r
       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
           getGroup().getName());\r
-      if (sg.cs instanceof ResidueColourScheme)\r
-      {\r
-        ( (ResidueColourScheme) sg.cs).setThreshold(threshold);\r
-      }\r
-      else if (sg.cs instanceof ScoreColourScheme)\r
-      {\r
-        ( (ScoreColourScheme) sg.cs).setThreshold(threshold);\r
-      }\r
+\r
+      sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());\r
 \r
       SliderPanel.showPIDSlider();\r
 \r
     }\r
     else // remove PIDColouring\r
     {\r
-      ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;\r
-      rcs.setThreshold(0);\r
-      sg.cs = rcs;\r
+      sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
     }\r
 \r
     refresh();\r
@@ -443,6 +438,8 @@ public class APopupMenu
   protected void conservationMenuItem_itemStateChanged(ItemEvent ie)\r
   {\r
     SequenceGroup sg = getGroup();\r
+    if(sg.cs==null)\r
+          return;\r
 \r
     if (conservationMenuItem.getState())\r
     {\r
@@ -454,17 +451,15 @@ public class APopupMenu
 \r
       c.calculate();\r
       c.verdict(false, ap.av.ConsPercGaps);\r
-      ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
 \r
-      sg.cs = ccs;\r
+      sg.cs.setConservation(c);\r
 \r
-      SliderPanel.setConservationSlider(ap, ccs, sg.getName());\r
+      SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());\r
       SliderPanel.showConservationSlider();\r
     }\r
     else // remove ConservationColouring\r
     {\r
-      ConservationColourScheme ccs = (ConservationColourScheme) sg.cs;\r
-      sg.cs = ccs.cs;\r
+      sg.cs.setConservation(null);\r
     }\r
 \r
     refresh();\r
@@ -472,7 +467,7 @@ public class APopupMenu
 \r
   protected void analyze_actionPerformed(ActionEvent e)\r
   {\r
-    CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame.applet);\r
     Frame frame = new Frame();\r
     frame.add(cap);\r
     jalview.bin.JalviewLite.addFrame(frame, "Analyze this - ", 400, 300);\r