String[] files = new String[] {"input1.pdf", "input2.pdf"};
String outputFile = "output.pdf";
int firstPage=1;
Document document = new Document();
PdfWriter writer = PdfWriter.getInstance(document, new FileOutputStream(outputFile));
document.setPageSize(PageSize.A4);
float W = PageSize.A4.getWidth() / 2;
float H = PageSize.A4.getHeight() / 2;
document.open();
PdfContentByte cb = writer.getDirectContent();
for (int i = 0; i < files.length; i++) {
PdfReader currentReader = new PdfReader(files[i]);
currentReader.consolidateNamedDestinations();
for (int page = 1; page <= currentReader.getNumberOfPages(); page++) {
PdfImportedPage importedPage = writer.getImportedPage(currentReader, page);
float a = 0.5f;
float e = (page % 2 == 0) ? W : 0;
float f = (page % 4 == 1 || page % 4 == 2) ? H : 0;
ArrayList links = currentReader.getLinks(page);
cb.addTemplate(importedPage, a, 0, 0, a, e, f);
for (int j = 0; j < links.size(); j++) {
PdfAnnotation.PdfImportedLink link = (PdfAnnotation.PdfImportedLink)links.get(j);
if (link.isInternal()) {
int dPage = link.getDestinationPage();
int newDestPage = (dPage-1)/4 + firstPage;
float ee = (dPage % 2 == 0) ? W : 0;
float ff = (dPage % 4 == 1 || dPage % 4 == 2) ? H : 0;
link.setDestinationPage(newDestPage);
link.transformDestination(a, 0, 0, a, ee, ff);
}
link.transformRect(a, 0, 0, a, e, f);
writer.addAnnotation(link.createAnnotation(writer));
}
if (page % 4 == 0)
document.newPage();
}
if (i < files.length - 1)
document.newPage();
firstPage += (currentReader.getNumberOfPages()+3)/4;
}
document.close();

since: 2.1.3 -

 public PdfAnnotation(PdfWriter writer,
    Rectangle rect) 
{
    
    // constructors
        this.writer = writer;
        if (rect != null)
            put(PdfName.RECT, new PdfRectangle(rect));
}

 public PdfAnnotation(PdfWriter writer,
    float llx,
    float lly,
    float urx,
    float ury,
    PdfAction action) 
{
        this.writer = writer;
        put(PdfName.SUBTYPE, PdfName.LINK);
        put(PdfName.RECT, new PdfRectangle(llx, lly, urx, ury));
        put(PdfName.A, action);
        put(PdfName.BORDER, new PdfBorderArray(0, 0, 0));
        put(PdfName.C, new PdfColor(0x00, 0x00, 0xFF));
}

Constructs a new PdfAnnotation of subtype link (Action).

Parameters:

writer -

llx -

lly -

urx -

ury -

action -

 public PdfAnnotation(PdfWriter writer,
    float llx,
    float lly,
    float urx,
    float ury,
    PdfString title,
    PdfString content) 
{
        this.writer = writer;
        put(PdfName.SUBTYPE, PdfName.TEXT);
        put(PdfName.T, title);
        put(PdfName.RECT, new PdfRectangle(llx, lly, urx, ury));
        put(PdfName.CONTENTS, content);
}

Constructs a new PdfAnnotation of subtype text.

Parameters:

writer -

llx -

lly -

urx -

ury -

title -

content -

 public static PdfAnnotation createFileAttachment(PdfWriter writer,
    Rectangle rect,
    String contents,
    PdfFileSpecification fs) throws IOException 
{
        PdfAnnotation annot = new PdfAnnotation(writer, rect);
        annot.put(PdfName.SUBTYPE, PdfName.FILEATTACHMENT);
        if (contents != null)
            annot.put(PdfName.CONTENTS, new PdfString(contents, PdfObject.TEXT_UNICODE));
        annot.put(PdfName.FS, fs.getReference());
        return annot;
}

Creates a file attachment annotation

 public static PdfAnnotation createFileAttachment(PdfWriter writer,
    Rectangle rect,
    String contents,
    byte[] fileStore,
    String file,
    String fileDisplay) throws IOException 
{
        return createFileAttachment(writer, rect, contents, PdfFileSpecification.fileEmbedded(writer, file, fileDisplay, fileStore));
}

Creates a file attachment annotation.

 public static PdfAnnotation createFreeText(PdfWriter writer,
    Rectangle rect,
    String contents,
    PdfContentByte defaultAppearance) 
{
        PdfAnnotation annot = new PdfAnnotation(writer, rect);
        annot.put(PdfName.SUBTYPE, PdfName.FREETEXT);
        annot.put(PdfName.CONTENTS, new PdfString(contents, PdfObject.TEXT_UNICODE));
        annot.setDefaultAppearanceString(defaultAppearance);
        return annot;
}

Add some free text to the document.

 public static PdfAnnotation createInk(PdfWriter writer,
    Rectangle rect,
    String contents,
    float[][] inkList) 
{
        PdfAnnotation annot = new PdfAnnotation(writer, rect);
        annot.put(PdfName.SUBTYPE, PdfName.INK);
        annot.put(PdfName.CONTENTS, new PdfString(contents, PdfObject.TEXT_UNICODE));
        PdfArray outer = new PdfArray();
        for (int k = 0; k <  inkList.length; ++k) {
            PdfArray inner = new PdfArray();
            float deep[] = inkList[k];
            for (int j = 0; j <  deep.length; ++j)
                inner.add(new PdfNumber(deep[j]));
            outer.add(inner);
        }
        annot.put(PdfName.INKLIST, outer);
        return annot;
}

 public static PdfAnnotation createLine(PdfWriter writer,
    Rectangle rect,
    String contents,
    float x1,
    float y1,
    float x2,
    float y2) 
{
        PdfAnnotation annot = new PdfAnnotation(writer, rect);
        annot.put(PdfName.SUBTYPE, PdfName.LINE);
        annot.put(PdfName.CONTENTS, new PdfString(contents, PdfObject.TEXT_UNICODE));
        PdfArray array = new PdfArray(new PdfNumber(x1));
        array.add(new PdfNumber(y1));
        array.add(new PdfNumber(x2));
        array.add(new PdfNumber(y2));
        annot.put(PdfName.L, array);
        return annot;
}

Adds a line to the document. Move over the line and a tooltip is shown.

 protected static PdfAnnotation createLink(PdfWriter writer,
    Rectangle rect,
    PdfName highlight) 
{
        PdfAnnotation annot = new PdfAnnotation(writer, rect);
        annot.put(PdfName.SUBTYPE, PdfName.LINK);
        if (!highlight.equals(HIGHLIGHT_INVERT))
            annot.put(PdfName.H, highlight);
        return annot;
}

Creates a link.

 public static PdfAnnotation createLink(PdfWriter writer,
    Rectangle rect,
    PdfName highlight,
    PdfAction action) 
{
        PdfAnnotation annot = createLink(writer, rect, highlight);
        annot.putEx(PdfName.A, action);
        return annot;
}

Creates an Annotation with an Action.

 public static PdfAnnotation createLink(PdfWriter writer,
    Rectangle rect,
    PdfName highlight,
    String namedDestination) 
{
        PdfAnnotation annot = createLink(writer, rect, highlight);
        annot.put(PdfName.DEST, new PdfString(namedDestination));
        return annot;
}

Creates an Annotation with an local destination.

 public static PdfAnnotation createLink(PdfWriter writer,
    Rectangle rect,
    PdfName highlight,
    int page,
    PdfDestination dest) 
{
        PdfAnnotation annot = createLink(writer, rect, highlight);
        PdfIndirectReference ref = writer.getPageReference(page);
        dest.addPage(ref);
        annot.put(PdfName.DEST, dest);
        return annot;
}

Creates an Annotation with a PdfDestination.

 public static PdfAnnotation createMarkup(PdfWriter writer,
    Rectangle rect,
    String contents,
    int type,
    float[] quadPoints) 
{
        PdfAnnotation annot = new PdfAnnotation(writer, rect);
        PdfName name = PdfName.HIGHLIGHT;
        switch (type) {
            case MARKUP_UNDERLINE:
                name = PdfName.UNDERLINE;
                break;
            case MARKUP_STRIKEOUT:
                name = PdfName.STRIKEOUT;
                break;
            case MARKUP_SQUIGGLY:
                name = PdfName.SQUIGGLY;
                break;
        }
        annot.put(PdfName.SUBTYPE, name);
        annot.put(PdfName.CONTENTS, new PdfString(contents, PdfObject.TEXT_UNICODE));
        PdfArray array = new PdfArray();
        for (int k = 0; k <  quadPoints.length; ++k)
        	array.add(new PdfNumber(quadPoints[k]));
        annot.put(PdfName.QUADPOINTS, array);
        return annot;
}

 public static PdfAnnotation createPopup(PdfWriter writer,
    Rectangle rect,
    String contents,
    boolean open) 
{
        PdfAnnotation annot = new PdfAnnotation(writer, rect);
        annot.put(PdfName.SUBTYPE, PdfName.POPUP);
        if (contents != null)
            annot.put(PdfName.CONTENTS, new PdfString(contents, PdfObject.TEXT_UNICODE));
        if (open)
            annot.put(PdfName.OPEN, PdfBoolean.PDFTRUE);
        return annot;
}

Adds a popup to your document.

 public static PdfAnnotation createScreen(PdfWriter writer,
    Rectangle rect,
    String clipTitle,
    PdfFileSpecification fs,
    String mimeType,
    boolean playOnDisplay) throws IOException 
{
        PdfAnnotation ann = new PdfAnnotation(writer, rect);
        ann.put(PdfName.SUBTYPE, PdfName.SCREEN);
        ann.put (PdfName.F, new PdfNumber(FLAGS_PRINT));
        ann.put(PdfName.TYPE, PdfName.ANNOT);
        ann.setPage();
        PdfIndirectReference ref = ann.getIndirectReference();
        PdfAction action = PdfAction.rendition(clipTitle,fs,mimeType, ref);
        PdfIndirectReference actionRef = writer.addToBody(action).getIndirectReference();
        // for play on display add trigger event
        if (playOnDisplay)
        {
            PdfDictionary aa = new PdfDictionary();
            aa.put(new PdfName("PV"), actionRef);
            ann.put(PdfName.AA, aa);
        }
        ann.put(PdfName.A, actionRef);
        return ann;
}

Creates a screen PdfAnnotation

 public static PdfAnnotation createSquareCircle(PdfWriter writer,
    Rectangle rect,
    String contents,
    boolean square) 
{
        PdfAnnotation annot = new PdfAnnotation(writer, rect);
        if (square)
            annot.put(PdfName.SUBTYPE, PdfName.SQUARE);
        else
            annot.put(PdfName.SUBTYPE, PdfName.CIRCLE);
        annot.put(PdfName.CONTENTS, new PdfString(contents, PdfObject.TEXT_UNICODE));
        return annot;
}

Adds a circle or a square that shows a tooltip when you pass over it.

 public static PdfAnnotation createStamp(PdfWriter writer,
    Rectangle rect,
    String contents,
    String name) 
{
        PdfAnnotation annot = new PdfAnnotation(writer, rect);
        annot.put(PdfName.SUBTYPE, PdfName.STAMP);
        annot.put(PdfName.CONTENTS, new PdfString(contents, PdfObject.TEXT_UNICODE));
        annot.put(PdfName.NAME, new PdfName(name));
        return annot;
}

Adds a Stamp to your document. Move over the stamp and a tooltip is shown

 public static PdfAnnotation createText(PdfWriter writer,
    Rectangle rect,
    String title,
    String contents,
    boolean open,
    String icon) 
{
        PdfAnnotation annot = new PdfAnnotation(writer, rect);
        annot.put(PdfName.SUBTYPE, PdfName.TEXT);
        if (title != null)
            annot.put(PdfName.T, new PdfString(title, PdfObject.TEXT_UNICODE));
        if (contents != null)
            annot.put(PdfName.CONTENTS, new PdfString(contents, PdfObject.TEXT_UNICODE));
        if (open)
            annot.put(PdfName.OPEN, PdfBoolean.PDFTRUE);
        if (icon != null) {
            annot.put(PdfName.NAME, new PdfName(icon));
        }
        return annot;
}

 public PdfIndirectReference getIndirectReference() 
{
        if (reference == null) {
            reference = writer.getPdfIndirectReference();
        }
        return reference;
}

 PdfDictionary getMK() 
{
        PdfDictionary mk = (PdfDictionary)get(PdfName.MK);
        if (mk == null) {
            mk = new PdfDictionary();
            put(PdfName.MK, mk);
        }
        return mk;
}

 public static PdfArray getMKColor(Color color) 
{
        PdfArray array = new PdfArray();
        int type = ExtendedColor.getType(color);
        switch (type) {
            case ExtendedColor.TYPE_GRAY: {
                array.add(new PdfNumber(((GrayColor)color).getGray()));
                break;
            }
            case ExtendedColor.TYPE_CMYK: {
                CMYKColor cmyk = (CMYKColor)color;
                array.add(new PdfNumber(cmyk.getCyan()));
                array.add(new PdfNumber(cmyk.getMagenta()));
                array.add(new PdfNumber(cmyk.getYellow()));
                array.add(new PdfNumber(cmyk.getBlack()));
                break;
            }
            case ExtendedColor.TYPE_SEPARATION:
            case ExtendedColor.TYPE_PATTERN:
            case ExtendedColor.TYPE_SHADING:
                throw new RuntimeException("Separations, patterns and shadings are not allowed in MK dictionary.");
            default:
                array.add(new PdfNumber(color.getRed() / 255f));
                array.add(new PdfNumber(color.getGreen() / 255f));
                array.add(new PdfNumber(color.getBlue() / 255f));
        }
        return array;
}

 public int getPlaceInPage() 
{
        return placeInPage;
}

Getter for property placeInPage.

 public HashMap getTemplates() 
{
        return templates;
}

 public boolean isAnnotation() 
{
        return annotation;
}

Getter for property annotation.

 public boolean isForm() 
{
        return form;
}

Getter for property form.

 public boolean isUsed() 
{
        return used;
}

Getter for property used.

 public  void setAction(PdfAction action) 
{
        put(PdfName.A, action);
}

 public  void setAdditionalActions(PdfName key,
    PdfAction action) 
{
        PdfDictionary dic;
        PdfObject obj = get(PdfName.AA);
        if (obj != null && obj.isDictionary())
            dic = (PdfDictionary)obj;
        else
            dic = new PdfDictionary();
        dic.put(key, action);
        put(PdfName.AA, dic);
}

 public  void setAppearance(PdfName ap,
    PdfTemplate template) 
{
        PdfDictionary dic = (PdfDictionary)get(PdfName.AP);
        if (dic == null)
            dic = new PdfDictionary();
        dic.put(ap, template.getIndirectReference());
        put(PdfName.AP, dic);
        if (!form)
            return;
        if (templates == null)
            templates = new HashMap();
        templates.put(template, null);
}

 public  void setAppearance(PdfName ap,
    String state,
    PdfTemplate template) 
{
        PdfDictionary dicAp = (PdfDictionary)get(PdfName.AP);
        if (dicAp == null)
            dicAp = new PdfDictionary();
        PdfDictionary dic;
        PdfObject obj = dicAp.get(ap);
        if (obj != null && obj.isDictionary())
            dic = (PdfDictionary)obj;
        else
            dic = new PdfDictionary();
        dic.put(new PdfName(state), template.getIndirectReference());
        dicAp.put(ap, dic);
        put(PdfName.AP, dicAp);
        if (!form)
            return;
        if (templates == null)
            templates = new HashMap();
        templates.put(template, null);
}

 public  void setAppearanceState(String state) 
{
        if (state == null) {
            remove(PdfName.AS);
            return;
        }
        put(PdfName.AS, new PdfName(state));
}

 public  void setBorder(PdfBorderArray border) 
{
        put(PdfName.BORDER, border);
}

 public  void setBorderStyle(PdfBorderDictionary border) 
{
        put(PdfName.BS, border);
}

 public  void setColor(Color color) 
{
        put(PdfName.C, new PdfColor(color));
}

 public  void setDefaultAppearanceString(PdfContentByte cb) 
{
        byte b[] = cb.getInternalBuffer().toByteArray();
        int len = b.length;
        for (int k = 0; k <  len; ++k) {
            if (b[k] == '\n")
                b[k] = 32;
        }
        put(PdfName.DA, new PdfString(b));
}

 public  void setFlags(int flags) 
{
        if (flags == 0)
            remove(PdfName.F);
        else
            put(PdfName.F, new PdfNumber(flags));
}

 public  void setHighlighting(PdfName highlight) 
{
        if (highlight.equals(HIGHLIGHT_INVERT))
            remove(PdfName.H);
        else
            put(PdfName.H, highlight);
}

Sets the annotation's highlighting mode. The values can be HIGHLIGHT_NONE, HIGHLIGHT_INVERT, HIGHLIGHT_OUTLINE and HIGHLIGHT_PUSH;

 public  void setLayer(PdfOCG layer) 
{
        put(PdfName.OC, layer.getRef());
}

Sets the layer this annotation belongs to.

 public  void setMKAlternateCaption(String caption) 
{
        getMK().put(PdfName.AC, new PdfString(caption, PdfObject.TEXT_UNICODE));
}

 public  void setMKAlternateIcon(PdfTemplate template) 
{
        getMK().put(PdfName.IX, template.getIndirectReference());
}

 public  void setMKBackgroundColor(Color color) 
{
        if (color == null)
            getMK().remove(PdfName.BG);
        else
            getMK().put(PdfName.BG, getMKColor(color));
}

 public  void setMKBorderColor(Color color) 
{
        if (color == null)
            getMK().remove(PdfName.BC);
        else
            getMK().put(PdfName.BC, getMKColor(color));
}

 public  void setMKIconFit(PdfName scale,
    PdfName scalingType,
    float leftoverLeft,
    float leftoverBottom,
    boolean fitInBounds) 
{
        PdfDictionary dic = new PdfDictionary();
        if (!scale.equals(PdfName.A))
            dic.put(PdfName.SW, scale);
        if (!scalingType.equals(PdfName.P))
            dic.put(PdfName.S, scalingType);
        if (leftoverLeft != 0.5f || leftoverBottom != 0.5f) {
            PdfArray array = new PdfArray(new PdfNumber(leftoverLeft));
            array.add(new PdfNumber(leftoverBottom));
            dic.put(PdfName.A, array);
        }
        if (fitInBounds)
            dic.put(PdfName.FB, PdfBoolean.PDFTRUE);
        getMK().put(PdfName.IF, dic);
}

 public  void setMKNormalCaption(String caption) 
{
        getMK().put(PdfName.CA, new PdfString(caption, PdfObject.TEXT_UNICODE));
}

 public  void setMKNormalIcon(PdfTemplate template) 
{
        getMK().put(PdfName.I, template.getIndirectReference());
}

 public  void setMKRolloverCaption(String caption) 
{
        getMK().put(PdfName.RC, new PdfString(caption, PdfObject.TEXT_UNICODE));
}

 public  void setMKRolloverIcon(PdfTemplate template) 
{
        getMK().put(PdfName.RI, template.getIndirectReference());
}

 public  void setMKRotation(int rotation) 
{
        getMK().put(PdfName.R, new PdfNumber(rotation));
}

 public  void setMKTextPosition(int tp) 
{
        getMK().put(PdfName.TP, new PdfNumber(tp));
}

 public  void setName(String name) 
{
    	put(PdfName.NM, new PdfString(name));
}

Sets the name of the annotation. With this name the annotation can be identified among all the annotations on a page (it has to be unique).

 public  void setPage() 
{
        put(PdfName.P, writer.getCurrentPage());
}

 public  void setPage(int page) 
{
        put(PdfName.P, writer.getPageReference(page));
}

 public  void setPlaceInPage(int placeInPage) 
{
        this.placeInPage = placeInPage;
}

Places the annotation in a specified page that must be greater or equal to the current one. With PdfStamper the page can be any. The first page is 1.

 public  void setPopup(PdfAnnotation popup) 
{
        put(PdfName.POPUP, popup.getIndirectReference());
        popup.put(PdfName.PARENT, getIndirectReference());
}

 public  void setRotate(int v) 
{
        put(PdfName.ROTATE, new PdfNumber(v));
}

 public  void setTitle(String title) 
{
        if (title == null) {
            remove(PdfName.T);
            return;
        }
        put(PdfName.T, new PdfString(title, PdfObject.TEXT_UNICODE));
}

 public  void setUsed() 
{
        used = true;
}

Setter for property used.