public void ChaoChaoPeptidomicsTesting1()
{
var executorParameters =
@"\\protoapps\DataPkgs\Public\2013\727_IQ_analysis_of_Peptidomics_data_First_attempts\Parameters\ExecutorParameters1.xml";
var alignmentParametersFile =
@"\\protoapps\DataPkgs\Public\2013\727_IQ_analysis_of_Peptidomics_data_First_attempts\Parameters\TargetedAlignmentWorkflowParameters1.xml";
var rawDatafile = @"D:\Data\From_ChaoChao\CPTAC_OT_Pep_JB_5439_60min_4May12_Legolas_11-07-64.raw";
var parameters = new BasicTargetedWorkflowExecutorParameters();
parameters.LoadParameters(executorParameters);
parameters.TargetedAlignmentIsPerformed = true;
var targetedAlignerWorkflowParameters = new TargetedAlignerWorkflowParameters();
targetedAlignerWorkflowParameters.LoadParameters(alignmentParametersFile);
var alignmentParametersOutputfile = alignmentParametersFile.Replace(".xml", "_autoGenerated.xml");
targetedAlignerWorkflowParameters.SaveParametersToXML(alignmentParametersOutputfile);
TargetedWorkflowExecutor executor = new BasicTargetedWorkflowExecutor(parameters, rawDatafile);
executor.Execute();
}
public void exportParameterTests1()
{
var exportedParametersFile = Path.Combine(FileRefs.OutputFolderPath, "exportedTargetedAlignmentWorkflowParameters.xml");
var parameters = new TargetedAlignerWorkflowParameters();
parameters.SaveParametersToXML(exportedParametersFile);
}