import jalview.util.Comparison;
import java.awt.Color;
-import java.util.List;
import java.util.Map;
/**
public ColourSchemeI getInstance(AnnotatedCollectionI sg,
Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
{
- HiddenMarkovModel model = null;
- List<SequenceI> seqs = sg.getHMMConsensusSequences();
- if (!seqs.isEmpty())
- {
- model = seqs.get(0).getHMM();
- }
+ SequenceI hmmSeq = sg.getHmmConsensus();
+ HiddenMarkovModel model = hmmSeq == null ? null : hmmSeq.getHMM();
+
HMMERColourScheme colour = new HMMERColourScheme(model);
return colour;
}
return false;
}
+ /**
+ * Answers true if the sequence collection has an HMM consensus sequence, else
+ * false
+ */
@Override
public boolean isApplicableTo(AnnotatedCollectionI ac)
{
- return !ac.getHMMConsensusSequences().isEmpty();
+ return ac.getHmmConsensus() != null;
}
}