You will link Java to SAP through JCo, the Java Connector, or within the Java Stack of a NetWeaver installation.
Your Java will connect to your SAP system and in terms of the ABAP stack will call various Function Modules and BAPI's written using ABAP.
If you are asking which is better, please search the forums as the topic has been asked and discussed enough. They both have the strengths and each group should decide on their own where to invest their time and resources.
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