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The standard way would be to just set the protocol in the connection uri to imaps instead of _ imap. (same for smtp and pop3)
Java will then try to verify the certificate of the mail server by following the chain of certificates signing the server's certificate back to one of these well known CA certificates specified in the default java keystore file. (see SSLNOTES.txt of JavaMail API for details)
If the certificate has no chain (is self signed) then this chain following is impossible. For this case you have to specify the key store to use via system properties:
java -Djavax.net.ssl.trustStore=$HOME/.keystore ...
To import keys to that store you may use the keytool command.

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