Also see this article:

http://www.javaworld.com/javaworld/jw-07-2004/jw-0726-security.html

J2EE security: Container versus custom
Choose the appropriate type of security for your application

Summary
This article covers the factors to consider when choosing between custom
security and J2EE standard security, also known as container security. It
briefly covers how each type of security works and then illustrates their
differences, strengths, and weaknesses. Although J2EE security itself
applies to all components of an enterprise application, this discussion's
main focus is Web application security or, more specifically,
authentication. (6,000 words; July 26, 2004) 


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