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Although there is a richer C++ API to FemtoZip, the C API is the preferred way to use FemtoZip in order to insulate clients from C++ API changes.
The C API is documented in the femtozip.h header, currently found at femtozip header.
For a simple example, check out example.c.
The primary class for using the Pure Java API is org.toubassi.femtozip.CompressionModel. See the associated javadoc for more info.
For a simple example check out ExampleTest.java.
In order to use the native JNI interface to FemtoZip, make sure you have built and installed the shared library. The primary class for using the JNI interface to FemtoZip is org.toubassi.femtozip.models.NativeCompressionModel. See the associated javadoc for more info.
For a simple example check out NativeCompressionModelTest.java.