public static void main(String[] args) throws IOException, SOMToolboxException { // register and parse all options for the JSAPResult config = OptionFactory.parseResults( args, OptionFactory.getOptInputVectorFile(true), OptionFactory.getOptClassInformationFile(true), OptionFactory.getOptOutputFileName(true), OptionFactory.getOptOutputDirectory(false)); String vectorFileName = config.getString("inputVectorFile"); String classInfoFile = config.getString("classInformationFile"); String outputDir = config.getString("outputDirectory", "."); String outputFileName = config.getString("output"); SOMLibSparseInputData inputData = new SOMLibSparseInputData(vectorFileName); SOMLibClassInformation classInfo = new SOMLibClassInformation(classInfoFile); classInfo.removeNotPresentElements(inputData); InputDataWriter.writeAsSOMLib(classInfo, outputDir + File.separator + outputFileName); }