public void ExportNET_andMass_AlignmentDataTest1()
{
string exportNETFilename = Path.Combine(FileRefs.OutputFolderPath, "exportedNETAlignmentInfo1.txt");
string exportMassFilename = Path.Combine(FileRefs.OutputFolderPath, "exportedMassAlignmentInfo1.txt");
RunFactory rf = new RunFactory();
Run run = rf.CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
string deconToolsResultFile = @"D:\Temp\output7\targetedFeatures.txt";
UnlabelledTargetedResultFromTextImporter importer = new UnlabelledTargetedResultFromTextImporter(deconToolsResultFile);
TargetedResultRepository repo = importer.Import();
string massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\qcshew_standard_file_allMassTags.txt";
MassTagCollection mtc = new MassTagCollection();
MassTagFromTextFileImporter mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
NETAndMassAligner aligner = new NETAndMassAligner();
aligner.SetFeaturesToBeAligned(repo.Results);
aligner.SetReferenceMassTags(mtc.MassTagList);
aligner.Execute(run);
NETAlignmentInfoToTextExporter exporter = new NETAlignmentInfoToTextExporter(exportNETFilename);
exporter.ExportAlignmentInfo(run.AlignmentInfo);
MassAlignmentInfoToTextExporter massInfoexporter = new MassAlignmentInfoToTextExporter(exportMassFilename);
massInfoexporter.ExportAlignmentInfo(run.AlignmentInfo);
}
public void ExportNET_andMass_AlignmentDataTest1()
{
var exportNETFilename = Path.Combine(FileRefs.OutputFolderPath, "exportedNETAlignmentInfo1.txt");
var exportMassFilename = Path.Combine(FileRefs.OutputFolderPath, "exportedMassAlignmentInfo1.txt");
var rf = new RunFactory();
var run = rf.CreateRun(DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var deconToolsResultFile = Path.Combine(FileRefs.ImportedData, "QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_targetedFeatures.txt");
var importer = new UnlabelledTargetedResultFromTextImporter(deconToolsResultFile);
var repo = importer.Import();
var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\qcshew_standard_file_allMassTags.txt";
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var aligner = new NETAndMassAligner();
aligner.SetFeaturesToBeAligned(repo.Results);
aligner.SetReferenceMassTags(mtc.TargetList);
aligner.Execute(run);
var exporter = new NETAlignmentInfoToTextExporter(exportNETFilename);
exporter.ExportAlignmentInfo(run.AlignmentInfo);
var massInfoexporter = new MassAlignmentInfoToTextExporter(exportMassFilename);
massInfoexporter.ExportAlignmentInfo(run.AlignmentInfo);
}
public void SaveAlignmentData(string outputFolder)
{
var exportNETAlignmentFilename = Path.Combine(outputFolder, Run.DatasetName + "_NETAlignment.txt");
var exportMZAlignmentFilename = Path.Combine(outputFolder, Run.DatasetName + "_MZAlignment.txt");
var mzAlignmentExporter = new MassAlignmentInfoToTextExporter(exportMZAlignmentFilename);
mzAlignmentExporter.ExportAlignmentInfo(Run.AlignmentInfo);
var netAlignmentExporter = new NETAlignmentInfoToTextExporter(exportNETAlignmentFilename);
netAlignmentExporter.ExportAlignmentInfo(Run.AlignmentInfo);
}
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);
}
}
