X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FHMMERColourScheme.java;h=f545fe6a625c68be88d4aa2a4a3b2479c9ebff31;hb=refs%2Fheads%2Ffeatures%2Fhmmer_statistics;hp=a7fc8b85460df2d4e2617b93c634558e558346bd;hpb=96356075a122b745936738f478a8ee33ac7e0f0a;p=jalview.git

diff --git a/src/jalview/schemes/HMMERColourScheme.java b/src/jalview/schemes/HMMERColourScheme.java
index a7fc8b8..f545fe6 100644
--- a/src/jalview/schemes/HMMERColourScheme.java
+++ b/src/jalview/schemes/HMMERColourScheme.java
@@ -51,19 +51,22 @@ public class HMMERColourScheme extends ResidueColourScheme
     }
     Double prob;
     prob = hmm.getMatchEmissionProbability(position, symbol);
+    if (prob == 0)
+    {
+      return Color.red;
+    }
     double freq = ResidueProperties.aminoBackgroundFrequencies.get(symbol);
-    Double value = prob - freq;
-
+    Double value = Math.log(prob / freq);
     Color colour = null;
-    if (value >= 0)
+    if (value > 0)
     {
 
       colour = ColorUtils.getGraduatedColour(value.floatValue(), 0,
-              Color.WHITE, 1f, Color.green);
+              Color.WHITE, 3f, Color.blue);
     }
     else if (value < 0)
     {
-      return Color.YELLOW;
+      return Color.ORANGE;
 
     }
     return colour;