X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FHiddenMarkovModel.java;h=6b8b09562dcdc9011c9d910201630d068ed37c78;hb=bea1d9b563d2fea018de3dbde9112dd59149126e;hp=e9174744441847284b94c05f75fe28c4dee5e140;hpb=f452bcb5ddecb4378e952447031ddb076bdf8268;p=jalview.git

diff --git a/src/jalview/datamodel/HiddenMarkovModel.java b/src/jalview/datamodel/HiddenMarkovModel.java
index e917474..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
@@ -520,18 +524,19 @@ public class HiddenMarkovModel
     int start = hasMap ? getNode(1).getResidueNumber() : 1;
     int endResNo = hasMap ? getNode(nodes.size() - 1).getResidueNumber()
             : (start + getLength() - 1);
-    char[] sequence = new char[endResNo + 1];
+    char[] sequence = new char[endResNo];
 
     int lastResNo = start - 1;
     int seqOffset = -1;
     int gapCount = 0;
 
+
     for (int seqN = 0; seqN < start; seqN++)
     {
       sequence[seqN] = GAP_DASH;
       seqOffset++;
     }
-
+    
     for (int nodeNo = 1; nodeNo < nodes.size(); nodeNo++)
     {
       HMMNode node = nodes.get(nodeNo);
@@ -639,5 +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;
+  }
+
 }