JAL-2629 hmm search UI and structural improvements, inclusion thresholds

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

diff --git a/src/jalview/schemes/HMMMatchScoreColourScheme.java b/src/jalview/schemes/HMMMatchScoreColourScheme.java
index 0ee83a5..96eb26a 100644 (file)
--- a/src/jalview/schemes/HMMMatchScoreColourScheme.java
+++ b/src/jalview/schemes/HMMMatchScoreColourScheme.java
@@ -212,10 +212,11 @@ public class HMMMatchScoreColourScheme extends ResidueColourScheme
               .log(getHmm().getMatchEmissionProbability(column, symbol)
                       / hmm.getBackgroundFrequencies().get(symbol));
 
-      if (!probabilities.get(symbol).get(lengthBin)
+      if (!probabilities.containsKey(symbol)
+              || !probabilities.get(symbol).get(lengthBin)
               .containsKey(format(llr)))
       {
-        return Color.white;
+        return new Color(140, 140, 140);
       }