Read certificates from windows store

If you are on Java 6, you can use the MSCAPI keystore to read it. Just open your keystore like this,

KeyStore ks = KeyStore.getInstance("Windows-MY", "SunMSCAPI");
ks.load(null, null);
java.util.Enumeration en = ks.aliases();

while (en.hasMoreElements()) {
  String aliasKey = (String) en.nextElement();
  Certificate[] chain = ks.getCertificateChain(aliasKey);
  X509Certificate x509 = ((X509Certificate) chain[0]);

  boolean keyUsage[] = x509.getKeyUsage();

  //keyUsage[0] -> digitalSignature
  //keyUsage[1] -> nonRepudiation
  //keyUsage[2] -> keyEncipherment
  //keyUsage[3] -> dataEncipherment
  //keyUsage[4] -> keyAgreement
  //keyUsage[5] -> keyCertSign
  //keyUsage[6] -> cRLSign
  //keyUsage[7] -> encipherOnly
  //keyUsage[8] -> decipherOnly
}

To load windows root certificates simple replace the first line (highlighted) with this,

KeyStore ks = KeyStore.getInstance("Windows-MY", "Windows-ROOT");

To know more about the subject please read this