Conservation colour scheme is no more

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

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index 3d1c18b..66f180b 100755 (executable)
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -49,9 +49,7 @@ public class PIDColourScheme
       return Color.white;\r
     }\r
 \r
-\r
-\r
-    Color c = Color.white;\r
+    currentColour = Color.white;\r
 \r
     double sc = 0;\r
 \r
@@ -66,7 +64,7 @@ public class PIDColourScheme
         {\r
           if (sc > thresholds[i])\r
           {\r
-            c = pidColours[i];\r
+            currentColour = pidColours[i];\r
 \r
             break;\r
           }\r
@@ -74,6 +72,9 @@ public class PIDColourScheme
       }\r
     }\r
 \r
-    return c;\r
+    if(conservationColouring)\r
+         applyConservation(j);\r
+\r
+    return currentColour;\r
   }\r
 }\r