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Where's the data going to be housed? Is it going to be on the same system as the GUI?
Flex has no way to read local data like that. Flex is designed to extract data from a remote service - either through HTTP, WebService, or its own AMF protocol through the RemoteObject service.
If you have Java APIs that can access the data and that Java is going to be running on a server, remote from the GUI, Flex, which runs in the Flash Player on the user's desktop, needs to connect to it through some mechanism. You could use sockets - write a socket server which uses your Java APIs and Flex can connect to it through the Flash XMLSocket class. You could also use Apache as the server for your Java and then your Java could exchange XML data with Flex if you didn't want to use FDS (Flex Data Services).
Keep in mind that FDS Express is free!
On a similar topic (from a complete Flex newbie), I have exactly the same requirement. I need to build workflow applications that can have access to the local filesystem, because that's what we do in graphic arts. Is Apollo going to solve this problem? Thanks!
Apollo will allow access to the local file system through some new classes. You'll be able to read an entire directory, copy and move files, as well as read and write text and binary files.