import java.util.Hashtable;
import java.util.Map;
+import jalview.analysis.Conservation;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
void updateGroupAnnotationSettings(boolean applyGlobalSettings,
boolean preserveNewGroupSettings);
+ void setSequenceColour(SequenceI seq, Color col);
+
+ Color getSequenceColour(SequenceI seq);
+
+ void updateSequenceIdColours();
SequenceGroup getSelectionGroup();
SequenceI[] getSequenceSelection();
+ void clearSequenceColours();
CigarArray getViewAsCigars(boolean selectedRegionOnly);
char getGapCharacter();
+ void setColumnSelection(ColumnSelection cs);
+
+ void setConservation(Conservation cons);
+
}