I am trying to establish a connection between my mail server and a java program to parse the mail using protocol MAPI.. now the connection is working fine with a mock mailbox us
It seems like Java Supports POP3 and IMAP very well out of the box.
But for other protocols you can use one of the vendors found at JavaMail API - Third Party Products.
I've had problems communicating with the Novell Groupwise Protocol, luckily they have a IMAP bridge I could have used instead.
The Moonrug Exchange Connector looks like the one you are looking for, but you will have to purchase.
OpenMAPI looks like a promising one, but it is still in development.