There are quite a few intergration software out there that you can sychronize your sharepoint with Java but most of them are very expensive and not powerful enough to be customized. There is a innovating software tool the CNS Media GateWay which is both cheap and very easy to implement.
The CNS Media GateWay (MGW) is an innovative integration tool that strives to combine the cost-effectiveness and flexibility of custom code and the power and maintainability of integration suites.
You can connect from any custom application like java to MS SharePoint, MS Exchange (2000 – 2013), , Dynamics CRM, Dynamics NAV and many more via the CNS ODBC and JDBC driver, thus accessing, for example, the entire Exchange mailbox from your custom application.
Please let mek now if you need some more information.