John,
Thanks for asking this question...
The book explores a full case-study (Chapter 14) illustrating "How to design and implement security for a Web-based application PORTAL (eRewards Portal) right from scratch" that integrates
J2EE applications and B2B Web services. The case study digs deep from identifying the security requirements, architecture, design, security infrastructure design, risk analysis, trade-off analysis, applying security
patterns, security architecture components (web-tier, bus-tier, web-service tier), Policy design, tier and factor analysis, implementation model, testing....and finally deployment, monitoring.
To enable multi-factor authentication, we have dedicated a chapter (Chapter 15) on "Architecture and Implementation strategies for incorporating Smartcards and Biometrics" in J2EE applications. We also highlighted the best practices and pitfalls while choosing these practices.
Hope this helps.
/Ramesh