for (int i=0; i < allpages.size(); i++)
{
PDPage apage = (PDPage) allpages.get(i);
List annotations = apage.getAnnotations();
PDAnnotationRubberStamp rs = new PDAnnotationRubberStamp();
rs.setName(PDAnnotationRubberStamp.NAME_TOP_SECRET);
rs.setRectangle(new PDRectangle(100,100));
rs.setContents("A top secret note");
annotations.add(rs);
}
document.save( args[1] );