maintain original threshold value

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

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index fc93fbc..162f978 100755 (executable)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -347,23 +347,29 @@ public class SeqPanel extends JPanel
   {\r
 \r
     if ( jalview.util.Comparison.isGap( av.alignment.getSequenceAt(seq).getSequence().charAt(j)))\r
-        av.alignment.getSequenceAt(seq).deleteCharAt(j);\r
+      av.alignment.getSequenceAt(seq).deleteCharAt(j);\r
 \r
     av.alignment.getWidth();\r
     repaint();\r
     seqEditOccurred=seq;\r
+\r
   }\r
 \r
 \r
   void updateConservation(int i)\r
   {\r
-    if(av.getGlobalColourScheme() instanceof jalview.schemes.ClustalxColourScheme)\r
-    {\r
-      av.setGlobalColourScheme(\r
-          new jalview.schemes.ClustalxColourScheme(av.alignment.getSequences(),av.alignment.getWidth() ));\r
-    }\r
     av.updateConservation();\r
     av.updateConsensus();\r
+\r
+    ColourSchemeI cs = av.getGlobalColourScheme();\r
+    if(cs instanceof ConservationColourScheme)\r
+      cs = ( (ConservationColourScheme) cs).cs;\r
+\r
+    if(cs instanceof ClustalxColourScheme)\r
+      cs = new ClustalxColourScheme(av.alignment.getSequences(), av.alignment.getWidth());\r
+\r
+    ap.alignFrame.changeColour(cs);\r
+\r
   }\r
 \r
 //////////////////////////////////////////\r