X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FHmmerGlobalBackground.java;h=a24b7ab7130c579694af7227efcb9abd586f2c71;hb=5d9222f19e4fbdd9b396853a0442b0e6c5eb98a4;hp=d5508f16b46941373ea559e8652df284d730d109;hpb=9b0d1162a0c5a08aa477b87b033bc841d840ea95;p=jalview.git

diff --git a/src/jalview/schemes/HmmerGlobalBackground.java b/src/jalview/schemes/HmmerGlobalBackground.java
index d5508f1..a24b7ab 100644
--- a/src/jalview/schemes/HmmerGlobalBackground.java
+++ b/src/jalview/schemes/HmmerGlobalBackground.java
@@ -1,6 +1,8 @@
 package jalview.schemes;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
 
 /**
  * An HMM colour scheme that uses global ('Uniprot') background frequencies for
@@ -18,13 +20,13 @@ 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();
@@ -57,4 +59,15 @@ public class HmmerGlobalBackground extends HmmerColourScheme
     return MAX_LOG_RATIO;
   }
 
+  /**
+   * Answers a new colour scheme instance based on the HMM of the first sequence
+   * in alignment that has an HMM
+   */
+  @Override
+  public ColourSchemeI getInstance(AlignViewportI viewport,
+          AnnotatedCollectionI ac)
+  {
+    return newInstance(ac);
+  }
+
 }