JAL-2629 choice of hmm profile now a parameter not a selection, apis simplified

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

diff --git a/src/jalview/schemes/HmmerGlobalBackground.java b/src/jalview/schemes/HmmerGlobalBackground.java
index d5508f1..31bcadf 100644 (file)
--- a/src/jalview/schemes/HmmerGlobalBackground.java
+++ b/src/jalview/schemes/HmmerGlobalBackground.java
@@ -1,6 +1,7 @@
 package jalview.schemes;
 
 import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
 
 /**
  * An HMM colour scheme that uses global ('Uniprot') background frequencies for
@@ -18,13 +19,13 @@ public class HmmerGlobalBackground extends HmmerColourScheme
   private static final float MAX_LOG_RATIO = 4.519f;
 
   /**
-   * Constructor given a Hidden Markov Model
+   * Constructor given a sequence collection
    * 
-   * @param markov
+   * @param ac
    */
-  public HmmerGlobalBackground(AnnotatedCollectionI ac)
+  public HmmerGlobalBackground(SequenceCollectionI ac)
   {
-    super(ac.getHmmConsensus());
+    super(ac.getHmmSequences());
     String alphabetType = getHmm() == null
             ? ResidueProperties.ALPHABET_AMINO
             : getHmm().getAlphabetType();