*/
package jalview.api;
+import java.awt.Color;
+import java.awt.Font;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+
import jalview.analysis.Conservation;
import jalview.analysis.TreeModel;
import jalview.datamodel.AlignmentAnnotation;
import jalview.schemes.ColourSchemeI;
import jalview.viewmodel.ViewportRanges;
-import java.awt.Color;
-import java.awt.Font;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Map;
-
/**
* @author jimp
*
* - 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);
+
+ /**
+ * Show or hide annotation tracks for each type of sequence feature
+ *
+ * @param selected
+ */
+ void setShowSequenceFeatureCounts(boolean selected);
}