import java.awt.Rectangle;
import java.util.ArrayList;
import java.util.Hashtable;
-import java.util.Iterator;
import java.util.List;
import javax.swing.JInternalFrame;
}
/**
- * returns the visible column regions of the alignment
- *
- * @param selectedRegionOnly
- * true to just return the contigs intersecting with the selected
- * area
- * @return
- */
- public Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly)
- {
- int start = 0;
- int end = 0;
- if (selectedRegionOnly && selectionGroup != null)
- {
- start = selectionGroup.getStartRes();
- end = selectionGroup.getEndRes() + 1;
- }
- else
- {
- end = alignment.getWidth();
- }
- return (alignment.getHiddenColumns().getVisContigsIterator(start, end,
- false));
- }
-
- /**
* get hash of undo and redo list for the alignment
*
* @return long[] { historyList.hashCode, redoList.hashCode };