Its possible to use an alternate trustStore but its not recommended, see Atlassian doco, in a nutshell:
because if Java is told to use a custom keystore (eg. containing a self-signed certificate), then Java will not have access to the root certificates of signing authorities...
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Its more than likely your JRE cacerts file in JAVA_HOME/jre/lib/security/cacerts.
I wrote a trivial java app yonks ago when I did exacytly what you're trying to do. With SSLPoke you will be able to valiate JRE -> SSL Service connectiivty, because Java requires the SSL chain of trust to be established before it will allow a connection to be made. See http://confluence.atlassian.com/display/JIRA/Connecting+to+SSL+services fore more.
Specifically, the default cacerts file could be overridden but there are maintenance and other issues related, all discussed in the link above.
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