Conservation colour scheme is no more

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

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index db120e1..c98322e 100755 (executable)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -553,27 +553,26 @@ public class SeqPanel extends JPanel
             av.getSelectionGroup().recalcConservation();\r
         }\r
 \r
-        if (cs instanceof ConservationColourScheme)\r
+        if (cs.conservationApplied())\r
         {\r
-            ConservationColourScheme ccs = (ConservationColourScheme) cs;\r
             Conservation c = new Conservation("All",\r
                     ResidueProperties.propHash, 3, av.alignment.getSequences(),\r
                     0, av.alignment.getWidth() - 1);\r
             c.calculate();\r
             c.verdict(false, av.ConsPercGaps);\r
 \r
-            if (ccs.cs instanceof ClustalxColourScheme)\r
+            if (cs instanceof ClustalxColourScheme)\r
             {\r
-                ClustalxColourScheme cxs = (ClustalxColourScheme) ccs.cs;\r
+                ClustalxColourScheme cxs = (ClustalxColourScheme) cs;\r
                 cxs.resetClustalX(av.alignment.getSequences(),\r
                     av.alignment.getWidth());\r
-                ccs = new ConservationColourScheme(c, cxs);\r
-                av.setGlobalColourScheme(ccs);\r
+                cs.setConservation(c);\r
+                av.setGlobalColourScheme(cs);\r
             }\r
             else\r
             {\r
-                ccs = new ConservationColourScheme(c, ccs.cs);\r
-                av.setGlobalColourScheme(ccs);\r
+                cs.setConservation(c);\r
+                av.setGlobalColourScheme(cs);\r
             }\r
         }\r
 \r
@@ -707,25 +706,26 @@ public class SeqPanel extends JPanel
             return;\r
         }\r
 \r
-        if (stretchGroup.cs instanceof ClustalxColourScheme)\r
+        if(stretchGroup.cs!=null)\r
         {\r
-            ((ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup.sequences,\r
+          if (stretchGroup.cs instanceof ClustalxColourScheme)\r
+          {\r
+            ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup.\r
+                sequences,\r
                 stretchGroup.getWidth());\r
-        }\r
+          }\r
 \r
-        if (stretchGroup.cs instanceof ConservationColourScheme)\r
-        {\r
-            ConservationColourScheme ccs = (ConservationColourScheme) stretchGroup.cs;\r
-            stretchGroup.cs = ccs;\r
+          if (stretchGroup.cs.conservationApplied())\r
+          {\r
             SliderPanel.setConservationSlider(ap, stretchGroup.cs,\r
-                stretchGroup.getName());\r
-        }\r
-        else\r
-        {\r
+                                              stretchGroup.getName());\r
+          }\r
+          else\r
+          {\r
             SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,\r
-                stretchGroup.getName());\r
+                                           stretchGroup.getName());\r
+          }\r
         }\r
-\r
         changeEndRes = false;\r
         changeStartRes = false;\r
         stretchGroup = null;\r