X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FPIDColourScheme.java;h=66f180be4c72186c75934d0e2cb817a4dd865b8f;hb=4f01ddc72d2297c48c57d4f9c25af45b300df154;hp=9dc4c66aa729c9086b2d84d37a47f47432bea273;hpb=503ebba0021fa583fa7af58f9406f9234274fd7c;p=jalview.git

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index 9dc4c66..66f180b 100755
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -40,7 +40,7 @@ public class PIDColourScheme
     char res = s.charAt(0);
     if ('a' <= res && res <= 'z')
     {
-      s = Character.toString(res -= ('a' - 'A'));
+      s = String.valueOf(res -= ('a' - 'A'));
     }
 
 
@@ -49,9 +49,7 @@ public class PIDColourScheme
       return Color.white;
     }
 
-
-
-    Color c = Color.white;
+    currentColour = Color.white;
 
     double sc = 0;
 
@@ -66,7 +64,7 @@ public class PIDColourScheme
         {
           if (sc > thresholds[i])
           {
-            c = pidColours[i];
+            currentColour = pidColours[i];
 
             break;
           }
@@ -74,6 +72,9 @@ public class PIDColourScheme
       }
     }
 
-    return c;
+    if(conservationColouring)
+         applyConservation(j);
+
+    return currentColour;
   }
 }