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I would like to find a FREE MP4 (container) writer for Java. I do not need an encoder, only something which can write the correct atoms given their expected values. Bonus for such a library that also can write “valid” F4V.
I would prefer a pure Java solution rather than something using JNI or external executables.
Even though my answer comes very late you could have a look into my MP4 Parser/Unparser at Github. You can parse MP4 files, modify them and write the result. You can even start from scratch creating boxes programatically and write your object representation to some sink.