X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FHiddenMarkovModel.java;h=6b8b09562dcdc9011c9d910201630d068ed37c78;hb=747167089ecf8d6afc70d417f5a20352e029bd95;hp=a4270cd9791f8466af07b737efe1c058d2bf034b;hpb=bb9cbefb3041ef5aba75b9e41d2fa3b2bb891e89;p=jalview.git

diff --git a/src/jalview/datamodel/HiddenMarkovModel.java b/src/jalview/datamodel/HiddenMarkovModel.java
index a4270cd..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
    */
@@ -82,11 +85,13 @@ public class HiddenMarkovModel
   }
 
   /**
-   * Copy constructor
+   * Copy constructor given a new aligned sequence with which to associate the
+   * HMM profile
    * 
    * @param hmm
+   * @param sq
    */
-  public HiddenMarkovModel(HiddenMarkovModel hmm)
+  public HiddenMarkovModel(HiddenMarkovModel hmm, SequenceI sq)
   {
     super();
     this.fileProperties = new HashMap<>(hmm.fileProperties);
@@ -94,6 +99,19 @@ public class HiddenMarkovModel
     this.nodes = new ArrayList<>(hmm.nodes);
     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
+      this.mapToHmmConsensus = hmm.mapToHmmConsensus;
+    }
+    else
+    {
+      // different dataset sequence e.g. after loading HMM from project
+      this.mapToHmmConsensus = new Mapping(sq.getDatasetSequence(),
+              hmm.mapToHmmConsensus.getMap());
+    }
   }
 
   /**
@@ -506,12 +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 - start + 1];
+    char[] sequence = new char[endResNo];
 
     int lastResNo = start - 1;
-    int seqOffset = 0;
+    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);
@@ -522,7 +547,7 @@ public class HiddenMarkovModel
        */
       while (resNo > lastResNo + 1)
       {
-        sequence[seqOffset++] = '-';
+        sequence[seqOffset++] = GAP_DASH;
         lastResNo++;
         gapCount++;
       }
@@ -549,8 +574,6 @@ public class HiddenMarkovModel
             lastResNo - gapCount);
     seq.createDatasetSequence();
     seq.setHMM(this);
-    seq.setIsHMMConsensusSequence(true);
-
     this.hmmSeq = seq;
 
     /*
@@ -606,7 +629,44 @@ public class HiddenMarkovModel
   public void setNodes(List<HMMNode> nodeList)
   {
     nodes = nodeList;
-    buildConsensusSequence();
+    if (nodes.size() > 1)
+    {
+      buildConsensusSequence();
+    }
+  }
+
+  /**
+   * Sets the aligned consensus sequence this HMM is the model for
+   * 
+   * @param hmmSeq
+   */
+  public void setHmmSeq(SequenceI hmmSeq)
+  {
+    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;
+  }
+
 }