public void WriteParameterFile(string parameterFilePath, AnalysisOptions options)
{
MetaData metaData = new MetaData("PNNLProteomics");
ReflectParameterOptions(options.MSLinkerOptions, metaData.OpenChild("MSnLinker"));
ReflectParameterOptions(options.FeatureFindingOptions, metaData.OpenChild("LCMSFeatureFinding"));
ReflectParameterOptions(options.FeatureFilterOptions, metaData.OpenChild("LCMSFeatureFilters"));
ReflectParameterOptions(options.MassTagDatabaseOptions, metaData.OpenChild("MassTagDatabase"));
ReflectParameterOptions(options.AlignmentOptions, metaData.OpenChild("Alignment"));
ReflectParameterOptions(options.DriftTimeAlignmentOptions, metaData.OpenChild("DriftTimeAlignment"));
ReflectParameterOptions(options.ClusterOptions, metaData.OpenChild("LCMSFeatureClustering"));
ReflectParameterOptions(options.STACOptions, metaData.OpenChild("STAC"));
ReflectParameterOptions(options.ConsolidationOptions, metaData.OpenChild("FeatureConsolidator"));
metaData.WriteFile(parameterFilePath);
}
