Conservation colour scheme is no more

[jalview.git] / src / jalview / schemes / ClustalxColourScheme.java

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index addf00f..353accf 100755 (executable)
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -255,18 +255,18 @@ public class ClustalxColourScheme
 \r
     int i = ( (Integer) ResidueProperties.aaHash.get(s)).intValue();\r
 \r
-    Color c = Color.white;\r
+    currentColour = Color.white;\r
 \r
     if (i > 19)\r
     {\r
-      return c;\r
+      return currentColour;\r
     }\r
 \r
     for (int k = 0; k < ResidueColour[i].conses.length; k++)\r
     {\r
       if (ResidueColour[i].conses[k].isConserved(cons2, j, size))\r
       {\r
-        c = ResidueColour[i].c;\r
+        currentColour = ResidueColour[i].c;\r
       }\r
     }\r
 \r
@@ -274,11 +274,14 @@ public class ClustalxColourScheme
     {\r
       if (conses[27].isConserved(cons2, j, size))\r
       {\r
-        c = (Color) colhash.get("PINK");\r
+        currentColour = (Color) colhash.get("PINK");\r
       }\r
     }\r
 \r
-    return c;\r
+    if(conservationColouring)\r
+         applyConservation(j);\r
+\r
+    return currentColour;\r
   }\r
 }\r
 \r