InputStream in1, in2, in3;
in1 = new ByteArrayInputStream(X509_FOO);
in2 = new ByteArrayInputStream(X509_INTERMEDIATE_CA);
in3 = new ByteArrayInputStream(X509_ROOT_CA);
X509Certificate[] chain = new X509Certificate[3];
chain[0] = (X509Certificate) cf.generateCertificate(in1);
chain[1] = (X509Certificate) cf.generateCertificate(in2);
chain[2] = (X509Certificate) cf.generateCertificate(in3);
ks.setKeyEntry("RSA_KEY", pk, pwd, chain);
ks.setCertificateEntry("CERT", chain[2]); // Let's trust ourselves. :-)