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);
}
public void ReadParameterFile(string parameterFilePath, ref AnalysisOptions options)
{
MetaData metaData = new MetaData("PNNLProteomics");
metaData.ReadFile(parameterFilePath);
MetaNode msOptions = metaData.OpenChild("MSnLinker", false);
if (msOptions != null)
{
LoadParameterOptions(options.MSLinkerOptions, msOptions);
}
LoadParameterOptions(options.MassTagDatabaseOptions, metaData.OpenChild("MassTagDatabase"));
LoadParameterOptions(options.FeatureFindingOptions, metaData.OpenChild("LCMSFeatureFinding"));
msOptions = metaData.OpenChild("LCMSFeatureFilters", false);
if (msOptions != null)
{
LoadParameterOptions(options.FeatureFilterOptions, msOptions);
}
List<classAlignmentMZBoundary> boundaries = options.AlignmentOptions.MZBoundaries;
LoadParameterOptions(options.AlignmentOptions, metaData.OpenChild("Alignment"));
if (options.AlignmentOptions.DriftTimeBinSize <= 0)
{
options.AlignmentOptions.DriftTimeBinSize = 1;
}
options.AlignmentOptions.MZBoundaries = boundaries;
MetaNode node = metaData.OpenChild("DriftTimeAlignment", false);
if (node != null)
{
LoadParameterOptions(options.DriftTimeAlignmentOptions, node);
}
LoadParameterOptions(options.ClusterOptions, metaData.OpenChild("LCMSFeatureClustering"));
MetaNode stacNode = metaData.OpenChild("STAC", false);
if (stacNode != null)
{
LoadParameterOptions(options.STACOptions, stacNode);
}
MetaNode consolidatorNode = metaData.OpenChild("FeatureConsolidator", false);
if (consolidatorNode != null)
{
LoadParameterOptions(options.ConsolidationOptions, consolidatorNode);
}
}