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

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 1a6853b..3a707de 100755 (executable)
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -370,14 +370,35 @@ public class SeqPanel extends Panel
     av.updateConservation();\r
     av.updateConsensus();\r
 \r
+    // Y O Y CLUSTALX\r
     ColourSchemeI cs = av.getGlobalColourScheme();\r
     if(cs instanceof ConservationColourScheme)\r
-      cs = ( (ConservationColourScheme) cs).cs;\r
+    {\r
+      ConservationColourScheme ccs =  (ConservationColourScheme) cs;\r
+      if(ccs.cs instanceof ClustalxColourScheme)\r
+     {\r
+        jalview.analysis.Conservation c = new jalview.analysis.Conservation\r
+            ("All",\r
+            ResidueProperties.propHash, 3,\r
+            av.alignment.getSequences(), 0,\r
+            av.alignment.getWidth() - 1);\r
+        c.calculate();\r
+        c.verdict(false, av.ConsPercGaps);\r
+\r
+        ClustalxColourScheme cxs = (ClustalxColourScheme)ccs.cs;\r
+        cxs.resetClustalX(av.alignment.getSequences(),  av.alignment.getWidth());\r
+        ccs = new ConservationColourScheme(c, cxs);\r
+        av.setGlobalColourScheme(ccs);\r
+     }\r
+    }\r
 \r
     if(cs instanceof ClustalxColourScheme)\r
-      cs = new ClustalxColourScheme(av.alignment.getSequences(), av.alignment.getWidth());\r
+    {\r
+      ((ClustalxColourScheme)cs).resetClustalX(av.alignment.getSequences(),\r
+                                    av.alignment.getWidth());\r
+      av.setGlobalColourScheme(cs);\r
+    }\r
 \r
-    ap.alignFrame.changeColour(cs);\r
 \r
   }\r
 \r