JAL-2599 fix background frequency storage and correct colour scheme

[jalview.git] / src / jalview / util / HMMProbabilityDistributionAnalyser.java

diff --git a/src/jalview/util/HMMProbabilityDistributionAnalyser.java b/src/jalview/util/HMMProbabilityDistributionAnalyser.java
index 24b3bc3..c84b177 100644 (file)
--- a/src/jalview/util/HMMProbabilityDistributionAnalyser.java
+++ b/src/jalview/util/HMMProbabilityDistributionAnalyser.java
@@ -372,7 +372,7 @@ public class HMMProbabilityDistributionAnalyser
         alignPos = hmm.getNodeAlignmentColumn(length);
 
         symbol = sequences.get(width).getCharAt(alignPos);
-        if (ResidueProperties.aminoBackgroundFrequencies
+        if (ResidueProperties.backgroundFrequencies.get("amino")
                 .containsKey(symbol))
         {
           count++;
@@ -406,14 +406,15 @@ public class HMMProbabilityDistributionAnalyser
         alignPos = hmm.getNodeAlignmentColumn(length);
         
         symbol = sequences.get(width).getCharAt(alignPos);
-        if (ResidueProperties.aminoBackgroundFrequencies
+        if (ResidueProperties.backgroundFrequencies.get("amino")
                 .containsKey(symbol))
         {
           Double prob;
           Float bfreq;
           Double llr;
           prob = hmm.getMatchEmissionProbability(alignPos, symbol);
-          bfreq = ResidueProperties.aminoBackgroundFrequencies.get(symbol);
+          bfreq = ResidueProperties.backgroundFrequencies.get("amino")
+                  .get(symbol);
           if (prob == 0 || bfreq == 0)
           {
             System.out.println("error");