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Using JCo, you are not limited solely to calling R/3 BAPIs. The power of JCo allows you to call ANY RFC-enabled ABAP application within SAP.
You can import your ABAP application into SAP's Function Builder, describe the required set of input/output parameters, and call your new RFC using JCo. However, a major caveat here is that SAP does not allow you to directly call existing R/3 function modules even from within an ABAP application. The purpose of the BAPI interface is to provide prescribed methods for calling SAP function modules from outside SAP. Calling these modules directly, even if a BAPI doesn't exist, is done so at your own risk.
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