JAL-2668 add tests for HMMER commands, annotation and io

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

diff --git a/src/jalview/schemes/HMMERColourScheme.java b/src/jalview/schemes/HMMERColourScheme.java
index 7a8ef94..f3691f0 100644 (file)
--- a/src/jalview/schemes/HMMERColourScheme.java
+++ b/src/jalview/schemes/HMMERColourScheme.java
@@ -79,13 +79,13 @@ public class HMMERColourScheme extends ResidueColourScheme
     {
       return new Color(230, 0, 0);
     }
-    Double value = Math.log(prob / freq) / Math.log(2);
+    Double value = Math.log(prob / freq);
     Color colour = null;
     if (value > 0)
     {
 
       colour = ColorUtils.getGraduatedColour(value.floatValue(), 0,
-              Color.WHITE, 6.52f, Color.blue);
+              Color.WHITE, 4.52f, Color.blue);
     }
     else if (value < 0)
     {