Joined: May 30, 2005
You can choose what CAPI system stores to use when you work with certificates in JCAPI. The class you should work with is named JCAPIProperties.
Here is an example of how you can do:
KeyStore ks = KeyStore.getInstance("msks", "JCAPI");
JCAPIProperties.getInstance().setExclusiveMSCertStore(ks, "Root"); //This will tell JCAPI to only use the CAPI system store Root.
..Do your stuff here...
JCAPIProperties.getInstance().resetMSCertStoreNames(); //Use the usual CAPI system stores again.
Just let us know if it doesn't work out for you.