X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FPIDColourScheme.java;h=66f180be4c72186c75934d0e2cb817a4dd865b8f;hb=4f01ddc72d2297c48c57d4f9c25af45b300df154;hp=8cea5071aa04572c3a7fb34f1d1a56137cc03c08;hpb=96786b7b949dc261a9556e13a17870166915d0e9;p=jalview.git

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index 8cea507..66f180b 100755
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -37,12 +37,19 @@ public class PIDColourScheme
 
   public Color findColour(String s, int j)
   {
+    char res = s.charAt(0);
+    if ('a' <= res && res <= 'z')
+    {
+      s = String.valueOf(res -= ('a' - 'A'));
+    }
+
+
     if ( (threshold != 0) && !aboveThreshold(s, j))
     {
       return Color.white;
     }
 
-    Color c = Color.white;
+    currentColour = Color.white;
 
     double sc = 0;
 
@@ -51,13 +58,13 @@ public class PIDColourScheme
     {
       sc = ((Float)consensus[j].get(ignoreGaps)).floatValue();
 
-      if (!jalview.util.Comparison.isGap( (s.charAt(0))))
+      if (!jalview.util.Comparison.isGap( res ))
       {
         for (int i = 0; i < thresholds.length; i++)
         {
           if (sc > thresholds[i])
           {
-            c = pidColours[i];
+            currentColour = pidColours[i];
 
             break;
           }
@@ -65,6 +72,9 @@ public class PIDColourScheme
       }
     }
 
-    return c;
+    if(conservationColouring)
+         applyConservation(j);
+
+    return currentColour;
   }
 }