Java Security

Hi, i am new to java.
I have a Digitally signed document, i wanna verify this signed document against the original one.
i got the idea from this link:
http://help.sap.com/saphelp_45b/helpdata/en/8d/517619da7d11d1a5ab0000e835363f/content.htm

i signed a pdf doc with my SmartCard. the third party signing tool passed me the PKCS7 digital signature and i stored it in database. the problem arose when i retrieved this digital signature from DB and verified against the original doc using the message digest method. the base64 result strings are always not equal.

I am sure about this:
-the retrieved digital signature was GOOD.
-the original doc was GOOD.
but why i can't get the same 2 message digests? can somebody please help?

below is part of my code:

..
..
while (rsetDs.next()) 
{
	InputStream DSName2 = rsetDs.getBinaryStream(1);
	ByteArrayOutputStream byteStream = new ByteArrayOutputStream();

	byte[] myByte = Base64.decode(byteStream.toString());
	ByteArrayInputStream newStream = new ByteArrayInputStream(myByte);


	CertificateFactory cf = CertificateFactory.getInstance("X.509");
	Collection c = cf.generateCertificates(newStream2);
	Iterator i = c.iterator();

	while (i.hasNext()) 
	{
		Certificate cert = (Certificate)i.next();
		X509Certificate cert1 = (X509Certificate)cert;
	
		try
		{
			java.security.MessageDigest md = java.security.MessageDigest.getInstance("MD5");

			/*=============DB MD (BEGIN)==================*/

			byte [] pubkeyByte = cert1.getPublicKey().getEncoded();

			md.update(myByte);
			md.update(pubkeyByte);
			byte[] raw = md.digest();

			String db_md = Base64.encode(raw);

			/*============DB MD (end)============*/

			/*=============PDF MD (BEGIN)==================*/
		
			DataInputStream m_disFile = new DataInputStream(new FileInputStream("C:\\" + "original_doc.pdf"));
			int m_iNum = m_disFile.available();
			byte[] msgBytes = new byte[m_iNum];
			m_iNum = m_disFile.read(msgBytes, 0, m_iNum);

			md.update(msgBytes);
			byte[] digestMd = md.digest();
			md.reset();

			String pdf_md = Base64.encode(digestMd);

			/*=============PDF MD (END)==================*/

		}
	}
}
..
..

thanks in advance.