Please read the docs on Identity.  You can call the methods from anywhere, including Java code.  For instance, you could call login()

I have written this class.

public class SeamUtil {

  public static void login(Client client){
    Identity.instance().setUsername(client.getEmail());
    Identity.instance().setPassword(client.getPassword());
    Identity.instance().login();    
  }  

}

I can make this call with an injected client:

SeamUtil.login(client);

The seamspace example logs in the user automatically after registration, you could look there for pointers.