import java.awt.Color;
import java.awt.Font;
import java.util.Hashtable;
+import java.util.Iterator;
import java.util.List;
import java.util.Map;
* - a group defined on sequences in the alignment held by the view
*/
void addSequenceGroup(SequenceGroup sequenceGroup);
+
+ /**
+ * Returns an interator over the [start, end] column positions of the visible
+ * regions of the alignment
+ *
+ * @param selectedRegionOnly
+ * if true, and the view has a selection region,
+ * then only the intersection of visible columns
+ * with the selection region is returned
+ * @return
+ */
+ Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly);
}