JAL_1426 JAL-3066 update Apache James mime parser and fix deprecation warnings with...

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

diff --git a/src/jalview/schemes/HmmerColourScheme.java b/src/jalview/schemes/HmmerColourScheme.java
index 9ea468d..05c9b66 100644 (file)
--- a/src/jalview/schemes/HmmerColourScheme.java
+++ b/src/jalview/schemes/HmmerColourScheme.java
@@ -1,13 +1,14 @@
 package jalview.schemes;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.HiddenMarkovModel;
-import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
 import jalview.util.ColorUtils;
 import jalview.util.Comparison;
 
 import java.awt.Color;
+import java.util.List;
 import java.util.Map;
 
 /**
@@ -45,15 +46,15 @@ public abstract class HmmerColourScheme extends ResidueColourScheme
   private Map<Character, Float> frequencies;
 
   /**
-   * Constructor given a Hidden Markov Model consensus sequence. This provides
-   * the HMM profile from which we can read the emission probabilities that
-   * determine the colour.
+   * Constructor given a list of Hidden Markov Model consensus sequences. The
+   * first sequence provides the HMM profile from which we can read the emission
+   * probabilities that determine the colour.
    * 
-   * @param consensusSeq
+   * @param hmmSeqs
    */
-  public HmmerColourScheme(SequenceI consensusSeq)
+  public HmmerColourScheme(List<SequenceI> hmmSeqs)
   {
-    hmmSeq = consensusSeq;
+    hmmSeq = hmmSeqs.isEmpty() ? null : hmmSeqs.get(0);
     hmm = hmmSeq == null ? null : hmmSeq.getHMM();
   }
 
@@ -144,8 +145,8 @@ public abstract class HmmerColourScheme extends ResidueColourScheme
    * in ac that has an HMM
    */
   @Override
-  public ColourSchemeI getInstance(AnnotatedCollectionI ac,
-          Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+  public ColourSchemeI getInstance(AlignViewportI viewport,
+          AnnotatedCollectionI ac)
   {
     return newInstance(ac);
   }
@@ -171,7 +172,7 @@ public abstract class HmmerColourScheme extends ResidueColourScheme
   @Override
   public boolean isApplicableTo(AnnotatedCollectionI ac)
   {
-    return ac.getHmmConsensus() != null;
+    return !ac.getHmmSequences().isEmpty();
   }
 
   protected Map<Character, Float> getFrequencies()