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;
* 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);
}
package jalview.schemes;
+import jalview.api.AlignViewportI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
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);
+ }
+
}