X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FHiddenMarkovModel.java;h=6b8b09562dcdc9011c9d910201630d068ed37c78;hb=bea1d9b563d2fea018de3dbde9112dd59149126e;hp=975bacbf9648082975a9057ed7711b87c8b0b807;hpb=d5477e299373c07a2b1f92421dcf454b0fe40b56;p=jalview.git

diff --git a/src/jalview/datamodel/HiddenMarkovModel.java b/src/jalview/datamodel/HiddenMarkovModel.java
index 975bacb..6b8b095 100644
--- a/src/jalview/datamodel/HiddenMarkovModel.java
+++ b/src/jalview/datamodel/HiddenMarkovModel.java
@@ -74,6 +74,9 @@ public class HiddenMarkovModel
    */
   private Mapping mapToHmmConsensus;
 
+  // stores background frequencies of alignment from which this model came
+  private Map<Character, Float> backgroundFrequencies;
+
   /**
    * Constructor
    */
@@ -97,6 +100,7 @@ public class HiddenMarkovModel
     this.symbolIndexLookup = hmm.symbolIndexLookup;
     this.fileHeader = new String(hmm.fileHeader);
     this.hmmSeq = sq;
+    this.backgroundFrequencies = hmm.getBackgroundFrequencies();
     if (sq.getDatasetSequence() == hmm.mapToHmmConsensus.getTo())
     {
       // same dataset sequence e.g. after realigning search results
@@ -640,5 +644,29 @@ public class HiddenMarkovModel
   {
     this.hmmSeq = hmmSeq;
   }
+
+  public void setBackgroundFrequencies(Map<Character, Float> bkgdFreqs)
+  {
+    backgroundFrequencies = bkgdFreqs;
+  }
+
+  public void setBackgroundFrequencies(ResidueCount bkgdFreqs)
+  {
+    backgroundFrequencies = new HashMap<>();
+
+    int total = bkgdFreqs.getTotalResidueCount();
+
+    for (char c : bkgdFreqs.getSymbolCounts().symbols)
+    {
+      backgroundFrequencies.put(c, bkgdFreqs.getCount(c) * 1f / total);
+    }
+
+  }
+
+  public Map<Character, Float> getBackgroundFrequencies()
+  {
+    return backgroundFrequencies;
+  }
+
 }