JAL-2629 update spikes/mungo to latest

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

diff --git a/src/jalview/schemes/HmmerLocalBackground.java b/src/jalview/schemes/HmmerLocalBackground.java
index d7a5e65..2fe775c 100644 (file)
--- a/src/jalview/schemes/HmmerLocalBackground.java
+++ b/src/jalview/schemes/HmmerLocalBackground.java
@@ -2,6 +2,7 @@ package jalview.schemes;
 
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.ResidueCount;
+import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
 
 import java.util.HashMap;
@@ -19,15 +20,13 @@ public class HmmerLocalBackground extends HmmerColourScheme
   float logTotalCount;
 
   /**
-   * Constructor given a Hidden Markov Model
+   * Constructor given a sequence collection
    * 
-   * @param sg
-   * 
-   * @param markov
+   * @param ac
    */
   public HmmerLocalBackground(AnnotatedCollectionI ac)
   {
-    super(ac.getHmmConsensus());
+    super(ac.getHmmSequences());
     countFrequencies(ac);
   }
 
@@ -48,9 +47,9 @@ public class HmmerLocalBackground extends HmmerColourScheme
    * Counts and stores the relative frequency of every residue in the alignment
    * (apart from any HMM consensus sequences)
    * 
-   * @param sg
+   * @param sc
    */
-  public void countFrequencies(AnnotatedCollectionI sg)
+  public void countFrequencies(SequenceCollectionI sc)
   {
     // TODO or total counts in Consensus Profile (how do we get at it?)?
     Map<Character, Float> freqs = new HashMap<>();
@@ -59,10 +58,10 @@ public class HmmerLocalBackground extends HmmerColourScheme
      * count symbols, excluding any HMM consensus sequences
      */
     ResidueCount counts = new ResidueCount();
-    List<SequenceI> seqs = sg.getSequences();
+    List<SequenceI> seqs = sc.getSequences();
     for (SequenceI seq : seqs)
     {
-      if (!seq.isHMMConsensusSequence())
+      if (!seq.hasHMMProfile())
       {
         for (char c : seq.getSequence())
         {