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I've to access to files on the software user and I don't know if it's better to use a full JS app with HTML5 File Api rules or use Java and communicate with it ?

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Do all of your user's browsers support the File API? –  Jeremy Heiler Jun 10 '12 at 21:27
    
No because they don't have Chrome so no File API –  philien Jun 11 '12 at 19:40
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up vote 2 down vote accepted

If you have the option to use the HTML file api and you are not worried about browser compatibility then you should avoid using 3rd party things like java as a far as possible and keep as close as possible to bare bones.

Java requires a JRE to be installed on the client PC, which adds a deployment layer, however simple it may be.

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