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); } }