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Calling Apex Class methods from Java using WSDL

I have the generated code from custom Apex class WSDL. The stub generated does not have any properties to set the organization URL, which is there in the stub generated from enterprise WSDL. How can a custom Apex class code be called from Java client? I would like to use both the standard and custom class methods defined in Salesforce. But when u initially login, the stibs have to be properly bound to a organization URL and there are other header settings.