Specific configuration settings can be defined using one of the {@link ch.javasoft.metabolic.efm.config.Config#initForJUnitTest(java.lang.String, ch.javasoft.metabolic.compress.CompressionMethod[], ch.javasoft.metabolic.efm.config.Arithmetic) Config#initForJUnitTest(..)} methods.
The following code initializes a typical EFM computaion:
MetabolicNetwork network = ... //initialize ElementaryFluxModes.setImpl(null);//important to clear previous settings Config.initForJUnitTest(PatternTreeMinZerosAdjacencyEnumerator.NAME, SortUtil.DEFAULT_SORTER, CompressionMethod.STANDARD_NO_DUPLICATE, false, Arithmetic.fractional, Norm.min); Iterable modes = ElementaryFluxModes.calculateAndReturnEfms(network);