PdfDocument doc = new PdfDocument();
PdfPageBase pdfPage = doc.getPages().add();
ArrayList inkList = new ArrayList();
int[] intPoints = new int[]
     {
         100,800,
         200,800,
         200,700
     };
inkList.add(intPoints);
Rectangle2D rect = new Rectangle2D.Float();
rect.setFrame(new Point2D.Float(0, 0), new Dimension((int)pdfPage.getActualSize().getWidth(), (int)pdfPage.getActualSize().getHeight()));
PdfInkAnnotation ink= new PdfInkAnnotation(rect,inkList);
ink.setColor(new PdfRGBColor(Color.RED));
ink.getBorder().setWidth(12);
ink.setText("e-iceblue");
pdfPage.getAnnotations().add(ink);
doc.saveToFile("inkAnnotation.pdf");

PdfPageBase page = pdf.getPages().get(0);
StringBuilder stringBuilder = new StringBuilder();
java.util.List<PdfJavaScriptAction> list = pdf.getNames().getJavaScripts();
stringBuilder.append(list.get(2).getScript()+"\r\n");
list.get(0).setScript("new javaScript code");
PdfAnnotationCollection annotationCollection = page.getAnnotations();
for(int i = 0;i < annotationCollection.getCount();i++){
    PdfLinkAnnotationWidget annotation = (PdfLinkAnnotationWidget) annotationCollection.get(i);
    stringBuilder.append("Method name:"+"\r\n");
    String script = ((PdfJavaScriptAction) annotation.getAction()).getScript();
    stringBuilder.append(script+"\r\n");
}

CompareOptions options=new CompareOptions();
Options.IgnoreHeadersAndFooters=true;//Default is false