public void SaveFeaturesToTextfile(string outputFolder)
{
var exportTargetedFeaturesFile = Path.Combine(outputFolder, Run.DatasetName + "_alignedFeatures.txt");
var exporter = new UnlabelledTargetedResultToTextExporter(exportTargetedFeaturesFile);
exporter.ExportResults(_targetedResultRepository.Results);
}
public void exporterTest1()
{
var testFile = DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var peaksTestFile = DeconTools.UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500;
var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\qcshew_standard_file_NETVals0.3-0.33.txt";
var exportedResultFile = Path.Combine(FileRefs.OutputFolderPath, "UnlabelledTargetedResultsExporterOutput1.txt");
if (File.Exists(exportedResultFile))
{
File.Delete(exportedResultFile);
}
var run = RunUtilities.CreateAndAlignRun(testFile, peaksTestFile);
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var selectedMassTags = mtc.TargetList.OrderBy(p => p.ID).Take(10).ToList();
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
var workflow = new BasicTargetedWorkflow(run, parameters);
foreach (var mt in selectedMassTags)
{
run.CurrentMassTag = mt;
workflow.Execute();
}
var repo = new TargetedResultRepository();
repo.AddResults(run.ResultCollection.GetMassTagResults());
var exporter = new UnlabelledTargetedResultToTextExporter(exportedResultFile);
exporter.ExportResults(repo.Results);
}
public void Execute()
{
Check.Require(_run != null, "Run has not been defined.");
//Use Features file if it exists; if not, find the quality Features
List <MassTagResultBase> resultsPassingCriteria;
_targetedResultRepository = new TargetedResultRepository();
if (ImportedFeaturesFilename == null || ImportedFeaturesFilename.Length == 0)
{
Check.Require(_run.ResultCollection.MSPeakResultList != null && _run.ResultCollection.MSPeakResultList.Count > 0, "Dataset's Peak-level data is empty. This is needed for chromatogram generation.");
resultsPassingCriteria = FindTargetsThatPassCriteria();
_targetedResultRepository.AddResults(resultsPassingCriteria);
if (AreFeaturesSavedToTextFile)
{
string outputfolder;
if (ExportAlignmentFolder == null || ExportAlignmentFolder.Length == 0)
{
outputfolder = _run.DataSetPath;
}
else
{
outputfolder = ExportAlignmentFolder;
}
string exportTargetedFeaturesFile = Path.Combine(outputfolder, _run.DatasetName + "_alignedFeatures.txt");
UnlabelledTargetedResultToTextExporter exporter = new UnlabelledTargetedResultToTextExporter(exportTargetedFeaturesFile);
exporter.ExportResults(_targetedResultRepository.Results);
}
}
else
{
//load them from the Features file
UnlabelledTargetedResultFromTextImporter importer = new UnlabelledTargetedResultFromTextImporter(ImportedFeaturesFilename);
TargetedResultRepository repo = importer.Import();
_targetedResultRepository.Results = repo.Results;
}
//do alignment
NETAndMassAligner aligner = new NETAndMassAligner();
aligner.SetFeaturesToBeAligned(_targetedResultRepository.Results);
aligner.SetReferenceMassTags(this.MassTagList);
aligner.Execute(this._run);
//save the alignment data
if (IsAlignmentInfoExported)
{
string outputfolder;
if (ExportAlignmentFolder == null || ExportAlignmentFolder.Length == 0)
{
outputfolder = _run.DataSetPath;
}
else
{
outputfolder = ExportAlignmentFolder;
}
string exportNETAlignmentFilename = Path.Combine(outputfolder, _run.DatasetName + "_NETAlignment.txt");
string exportMZAlignmentFilename = Path.Combine(outputfolder, _run.DatasetName + "_MZAlignment.txt");
MassAlignmentInfoToTextExporter mzAlignmentExporter = new MassAlignmentInfoToTextExporter(exportMZAlignmentFilename);
mzAlignmentExporter.ExportAlignmentInfo(_run.AlignmentInfo);
NETAlignmentInfoToTextExporter netAlignmentExporter = new NETAlignmentInfoToTextExporter(exportNETAlignmentFilename);
netAlignmentExporter.ExportAlignmentInfo(_run.AlignmentInfo);
}
}