PaintRefresh changed

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 25b74b6..b314854 100755 (executable)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -749,10 +749,6 @@ public class AlignFrame
       {\r
         ( (ResidueColourScheme) cs).setThreshold(threshold);\r
       }\r
-      else if (cs instanceof ScoreColourScheme)\r
-      {\r
-        ( (ScoreColourScheme) cs).setThreshold(threshold);\r
-      }\r
 \r
       viewport.setGlobalColourScheme(cs);\r
     }\r
@@ -760,10 +756,6 @@ public class AlignFrame
     {\r
       ( (ResidueColourScheme) cs).setThreshold(0);\r
     }\r
-    else if (cs instanceof ScoreColourScheme)\r
-    {\r
-      ( (ScoreColourScheme) cs).setThreshold(0);\r
-    }\r
 \r
     if (viewport.getConservationSelected())\r
     {\r
@@ -804,9 +796,16 @@ public class AlignFrame
       {\r
         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 \r
+        if(cs==null)\r
+        {\r
+          sg.cs = null;\r
+          continue;\r
+        }\r
         if (cs instanceof ClustalxColourScheme)\r
         {\r
-          sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
+          ClustalxColourScheme cxs = (ClustalxColourScheme) cs;\r
+          cxs.resetClustalX(viewport.alignment.getSequences(), viewport.alignment.getWidth());\r
+          sg.cs = cxs;\r
         }\r
         else\r
         {\r
@@ -827,10 +826,6 @@ public class AlignFrame
           {\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.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
         }\r