package jalview.api;
import java.util.Hashtable;
+import java.util.Map;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
import jalview.schemes.ColourSchemeI;
+import jalview.schemes.RNAHelicesColour;
/**
* @author jimp
AlignmentAnnotation getAlignmentQualityAnnot();
AlignmentAnnotation getAlignmentConservationAnnotation();
+ /**
+ * get the container for alignment consensus annotation
+ * @return
+ */
+ AlignmentAnnotation getAlignmentConsensusAnnotation();
/**
* Test to see if viewport is still open and active
*
*/
public int getConsPercGaps();
+
+ /**
+ * set the consensus result object for the viewport
+ * @param hconsensus
+ */
+ void setSequenceConsensusHash(Hashtable[] hconsensus);
+
+ /**
+ *
+ * @return the alignment annotatino row for the structure consensus calculation
+ */
+ AlignmentAnnotation getAlignmentStrucConsensusAnnotation();
+
+ /**
+ * set the Rna structure consensus result object for the viewport
+ * @param hStrucConsensus
+ */
+ void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus);
+
+ /**
+ * set global colourscheme
+ * @param rhc
+ */
+ void setGlobalColourScheme(ColourSchemeI rhc);
+
+ Map<SequenceI, SequenceCollectionI> getHiddenRepSequences();
+
+ void setHiddenRepSequences(
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences);
+
}