There are some examples on the jave2 github page, but not many. if you want to get real-time messages (progress information) you need to use the Threaded version of the library. There are 2 b4xlibs attached and a test project for each (you will have to change at least the source and target filenames to use the test projects). With the library, users of your app won't have to install FFMpeg on their machines. The library jars are quite large, so if you only want to use it for the odd conversion it might be better to use the Shell option. Useful to integrate FFMpeg into your app without having to use jShell. After using FFMpeg from the command line, I came across Jave2 (Java Audio Video Encoder) a java wrapper based on FFMpeg.
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