private SrmDocument EnsureAnnotation(SrmDocument document, string annotationName, bool addAnnotation, IEnumerable <string> annotationNames) { var containsQAnnotation = annotationNames.Contains(annotationName); if (!containsQAnnotation && addAnnotation) { var annotationTargets = AnnotationDef.AnnotationTargetSet.OfValues(AnnotationDef.AnnotationTarget.precursor_result); var newAnnotationDef = new AnnotationDef(annotationName, annotationTargets, AnnotationDef.AnnotationType.number, new string[0]); AnnotationDef existingAnnotationDef; // CONSIDER: Throw error instead of overwriting? if (!Settings.Default.AnnotationDefList.TryGetValue(annotationName, out existingAnnotationDef) && !Equals(existingAnnotationDef, newAnnotationDef)) { Settings.Default.AnnotationDefList.SetValue(newAnnotationDef); } else { // Use the existing annotation newAnnotationDef = existingAnnotationDef; } document = document.ChangeSettings(Document.Settings.ChangeAnnotationDefs(defs => { var defsNew = defs.ToList(); defsNew.Add(newAnnotationDef); return(defsNew); })); } else if (containsQAnnotation && !AddAnnotation) { document = document.ChangeSettings(Document.Settings.ChangeAnnotationDefs(defs => { var defsNew = defs.ToList(); defsNew.RemoveAll(def => Equals(def.Name, annotationName)); return(defsNew); })); var annotationNamesToKeep = document.Settings.DataSettings.AnnotationDefs.Select(def => def.Name).ToList(); document = (SrmDocument)document.StripAnnotationValues(annotationNamesToKeep); } return(document); }
public void GenerateComparison(SrmDocument docOriginal, IProgressMonitor progressMonitor) { DocOriginal = docOriginal; _docCompare = docOriginal; if (IsModel) { var handler = new MProphetResultsHandler(DocOriginal, PeakScoringModel) { AddAnnotation = true, AddMAnnotation = true }; handler.ScoreFeatures(progressMonitor); _docCompare = handler.ChangePeaks(progressMonitor); } else { // Add in the necessary annotation definitions so that ImportPeakBoundaries can read them _docCompare = AddAnnotationIfMissing(_docCompare, MProphetResultsHandler.AnnotationName); _docCompare = AddAnnotationIfMissing(_docCompare, MProphetResultsHandler.MAnnotationName); _docCompare = AddAnnotationIfMissing(_docCompare, APEX_ANNOTATION); // But strip the values of these annotations if there were any var annotationNamesToStrip = new List <string> { MProphetResultsHandler.AnnotationName, MProphetResultsHandler.MAnnotationName, APEX_ANNOTATION }; var annotationNamesToKeep = _docCompare.Settings.DataSettings.AnnotationDefs .Where(def => !annotationNamesToStrip.Contains(def.Name)) .Select(def => def.Name).ToList(); _docCompare = (SrmDocument)_docCompare.StripAnnotationValues(annotationNamesToKeep); Importer = new PeakBoundaryImporter(_docCompare); long lineCount = Helpers.CountLinesInFile(FilePath); // Peek at the file to see if it has a column called "Apex" using (var reader = new StreamReader(FilePath)) { var line = reader.ReadLine(); var fieldNames = PeakBoundaryImporter.FIELD_NAMES.ToList(); fieldNames.Add(new [] { APEX_ANNOTATION }); int fieldsTotal; int[] fieldIndices; var separator = PeakBoundaryImporter.DetermineCorrectSeparator(line, fieldNames, PeakBoundaryImporter.REQUIRED_NO_CHROM, out fieldIndices, out fieldsTotal); ApexPresent = separator != null && fieldIndices.Last() != -1; } _docCompare = Importer.Import(FilePath, progressMonitor, lineCount, true, !ApexPresent); } var matches = new List <PeakBoundsMatch>(); var truePeptides = DocOriginal.Molecules.ToList(); var pickedPeptides = _docCompare.Molecules.ToList(); int nTruePeptides = truePeptides.Count; var chromatogramSets = DocOriginal.Settings.MeasuredResults.Chromatograms; for (int i = 0; i < chromatogramSets.Count; i++) { var set = chromatogramSets[i]; for (int j = 0; j < nTruePeptides; j++) { var truePeptide = truePeptides[j]; var pickedPeptide = pickedPeptides[j]; // We don't care about peak picking performance for decoys if (truePeptide.IsDecoy) { continue; } // We don't care about peak picking performance for standard peptides if (truePeptide.GlobalStandardType != null) { continue; } var trueGroups = truePeptide.TransitionGroups.ToList(); var pickedGroups = pickedPeptide.TransitionGroups.ToList(); for (int k = 0; k < trueGroups.Count; k++) { var trueGroup = trueGroups[k]; var pickedGroup = pickedGroups[k]; var trueResults = trueGroup.Results[i]; var pickedResults = pickedGroup.Results[i]; if (trueResults == null) { continue; } int nChromInfos = trueResults.Count; for (int m = 0; m < nChromInfos; m++) { var trueInfo = trueResults[m]; var pickedInfo = pickedResults[m]; var fileInfo = set.GetFileInfo(trueInfo.FileId); var filePath = fileInfo.FilePath; var key = new MatchKey(trueGroup.Id.GlobalIndex, trueInfo.FileId.GlobalIndex); matches.Add(new PeakBoundsMatch(trueInfo, pickedInfo, key, filePath, trueGroup, HasNoQValues, HasNoScores, ApexPresent)); } } } } Matches = matches; // Detect if the apex time is in seconds, and if so adjust it to minutes if (ApexPresent) { double maxTime = matches.Where(match => match.PickedApex.HasValue) .Select(match => match.PickedApex.Value).Max(); if (maxTime > PeakBoundaryImporter.GetMaxRt(DocOriginal)) { foreach (var match in matches.Where(match => match.PickedApex.HasValue)) { match.PickedApex = match.PickedApex / 60; } } } }
public void GenerateComparison(SrmDocument docOriginal, IProgressMonitor progressMonitor) { DocOriginal = docOriginal; _docCompare = docOriginal; if (IsModel) { var handler = new MProphetResultsHandler(DocOriginal, PeakScoringModel); handler.ScoreFeatures(progressMonitor, true); _docCompare = handler.ChangePeaks(progressMonitor); } else { // Add in the necessary annotation definitions so that ImportPeakBoundaries can read them var annotationNamesToStrip = new List <string> { MProphetResultsHandler.AnnotationName, MProphetResultsHandler.MAnnotationName, APEX_ANNOTATION, START_TIME_ANNOTATION, END_TIME_ANNOTATION }; foreach (var annotationName in annotationNamesToStrip) { _docCompare = AddAnnotationIfMissing(_docCompare, annotationName); } // But strip the values of these annotations if there were any var annotationNamesToKeep = _docCompare.Settings.DataSettings.AnnotationDefs .Where(def => !annotationNamesToStrip.Contains(def.Name)) .Select(def => def.Name).ToList(); _docCompare = (SrmDocument)_docCompare.StripAnnotationValues(annotationNamesToKeep); Importer = new PeakBoundaryImporter(_docCompare); long lineCount = Helpers.CountLinesInFile(FilePath); // Peek at the file to see if it has a column called "Apex" using (var reader = new StreamReader(FilePath)) { var line = reader.ReadLine(); var fieldNames = PeakBoundaryImporter.FIELD_NAMES.ToList(); int fieldsTotal; int[] fieldIndices; var separator = PeakBoundaryImporter.DetermineCorrectSeparator(line, fieldNames, PeakBoundaryImporter.REQUIRED_NO_CHROM, out fieldIndices, out fieldsTotal); ApexPresent = separator != null && fieldIndices[(int)PeakBoundaryImporter.Field.apex_time] != -1; } _docCompare = Importer.Import(FilePath, progressMonitor, lineCount, true, !ApexPresent); if (progressMonitor.IsCanceled) { return; } } var matches = new List <PeakBoundsMatch>(); var truePeptides = DocOriginal.Molecules.ToList(); var pickedPeptides = _docCompare.Molecules.ToList(); int nTruePeptides = truePeptides.Count; var chromatogramSets = DocOriginal.Settings.MeasuredResults.Chromatograms; for (int i = 0; i < chromatogramSets.Count; i++) { var chromSet = chromatogramSets[i]; var set = chromatogramSets[i]; for (int j = 0; j < nTruePeptides; j++) { var truePeptide = truePeptides[j]; var pickedPeptide = pickedPeptides[j]; // We don't care about peak picking performance for decoys if (truePeptide.IsDecoy) { continue; } // We don't care about peak picking performance for standard peptides if (truePeptide.GlobalStandardType != null) { continue; } var trueGroups = truePeptide.TransitionGroups.ToList(); var pickedGroups = pickedPeptide.TransitionGroups.ToList(); for (int k = 0; k < trueGroups.Count; k++) { var trueGroup = trueGroups[k]; var pickedGroup = pickedGroups[k]; var trueResults = trueGroup.Results[i]; var pickedResults = pickedGroup.Results[i]; if (trueResults.IsEmpty) { continue; } int nChromInfos = trueResults.Count; for (int m = 0; m < nChromInfos; m++) { var trueInfo = trueResults[m]; var pickedInfo = pickedResults[m]; // For TRIC testing at the moment // double? qvaluePicked = PeakBoundsMatch.GetScoreValue(pickedInfo, // MProphetResultsHandler.AnnotationName, ci => pickedInfo.QValue); // if (qvaluePicked.HasValue && qvaluePicked.Value > 0.01) // continue; var fileInfo = set.GetFileInfo(trueInfo.FileId); var filePath = fileInfo.FilePath; var key = new MatchKey(trueGroup.Id.GlobalIndex, trueInfo.FileId.GlobalIndex); matches.Add(new PeakBoundsMatch(trueInfo, pickedInfo, key, chromSet, filePath, trueGroup, truePeptide, HasNoQValues, HasNoScores, ApexPresent)); } } } } Matches = matches; // Detect if the apex time is in seconds, and if so adjust it to minutes if (ApexPresent) { // ReSharper disable PossibleMultipleEnumeration var matchesWithApex = matches.Where(match => match.PickedApex.HasValue).ToArray(); double maxTime = 0; if (matchesWithApex.Length > 0) { maxTime = matchesWithApex.Select(match => match.PickedApex.Value).Max(); } if (maxTime > PeakBoundaryImporter.GetMaxRt(DocOriginal)) { foreach (var match in matchesWithApex) { // If the end is greater than the Apex, then it must also be in seconds (otherwise minutes) if (match.PickedEndBoundary.HasValue && match.PickedEndBoundary > match.PickedApex) { match.PickedEndBoundary = match.PickedEndBoundary / 60; } match.PickedApex = match.PickedApex / 60; // If the start is now greater than the apex, then it must also be in seconds (otherwise minutes) if (match.PickedStartBoundary.HasValue && match.PickedStartBoundary > match.PickedApex) { match.PickedStartBoundary = match.PickedStartBoundary / 60; } } } // ReSharper restore PossibleMultipleEnumeration } }
private SrmDocument EnsureAnnotation(SrmDocument document, string annotationName, bool addAnnotation, IEnumerable<string> annotationNames) { var containsQAnnotation = annotationNames.Contains(annotationName); if (!containsQAnnotation && addAnnotation) { var annotationTargets = AnnotationDef.AnnotationTargetSet.OfValues(AnnotationDef.AnnotationTarget.precursor_result); var newAnnotationDef = new AnnotationDef(annotationName, annotationTargets, AnnotationDef.AnnotationType.number, new string[0]); AnnotationDef existingAnnotationDef; // CONSIDER: Throw error instead of overwriting? if (!Settings.Default.AnnotationDefList.TryGetValue(annotationName, out existingAnnotationDef) && !Equals(existingAnnotationDef, newAnnotationDef)) { Settings.Default.AnnotationDefList.SetValue(newAnnotationDef); } else { // Use the existing annotation newAnnotationDef = existingAnnotationDef; } document = document.ChangeSettings(Document.Settings.ChangeAnnotationDefs(defs => { var defsNew = defs.ToList(); defsNew.Add(newAnnotationDef); return defsNew; })); } else if (containsQAnnotation && !AddAnnotation) { document = document.ChangeSettings(Document.Settings.ChangeAnnotationDefs(defs => { var defsNew = defs.ToList(); defsNew.RemoveAll(def => Equals(def.Name, annotationName)); return defsNew; })); var annotationNamesToKeep = document.Settings.DataSettings.AnnotationDefs.Select(def => def.Name).ToList(); document = (SrmDocument) document.StripAnnotationValues(annotationNamesToKeep); } return document; }
public void GenerateComparison(SrmDocument docOriginal, IProgressMonitor progressMonitor) { DocOriginal = docOriginal; _docCompare = docOriginal; if (IsModel) { var handler = new MProphetResultsHandler(DocOriginal, PeakScoringModel) { AddAnnotation = true, AddMAnnotation = true }; handler.ScoreFeatures(progressMonitor); _docCompare = handler.ChangePeaks(progressMonitor); } else { // Add in the necessary annotation definitions so that ImportPeakBoundaries can read them _docCompare = AddAnnotationIfMissing(_docCompare, MProphetResultsHandler.AnnotationName); _docCompare = AddAnnotationIfMissing(_docCompare, MProphetResultsHandler.MAnnotationName); _docCompare = AddAnnotationIfMissing(_docCompare, APEX_ANNOTATION); // But strip the values of these annotations if there were any var annotationNamesToStrip = new List<string> { MProphetResultsHandler.AnnotationName, MProphetResultsHandler.MAnnotationName, APEX_ANNOTATION }; var annotationNamesToKeep = _docCompare.Settings.DataSettings.AnnotationDefs .Where(def => !annotationNamesToStrip.Contains(def.Name)) .Select(def => def.Name).ToList(); _docCompare = (SrmDocument)_docCompare.StripAnnotationValues(annotationNamesToKeep); Importer = new PeakBoundaryImporter(_docCompare); long lineCount = Helpers.CountLinesInFile(FilePath); // Peek at the file to see if it has a column called "Apex" using (var reader = new StreamReader(FilePath)) { var line = reader.ReadLine(); var fieldNames = PeakBoundaryImporter.FIELD_NAMES.ToList(); fieldNames.Add(new [] {APEX_ANNOTATION}); int fieldsTotal; int[] fieldIndices; var separator = PeakBoundaryImporter.DetermineCorrectSeparator(line, fieldNames, PeakBoundaryImporter.REQUIRED_NO_CHROM, out fieldIndices, out fieldsTotal); ApexPresent = separator != null && fieldIndices.Last() != -1; } _docCompare = Importer.Import(FilePath, progressMonitor, lineCount, true, !ApexPresent); } var matches = new List<PeakBoundsMatch>(); var truePeptides = DocOriginal.Molecules.ToList(); var pickedPeptides = _docCompare.Molecules.ToList(); int nTruePeptides = truePeptides.Count; var chromatogramSets = DocOriginal.Settings.MeasuredResults.Chromatograms; for (int i = 0; i < chromatogramSets.Count; i++) { var set = chromatogramSets[i]; for (int j = 0; j < nTruePeptides; j++) { var truePeptide = truePeptides[j]; var pickedPeptide = pickedPeptides[j]; // We don't care about peak picking performance for decoys if (truePeptide.IsDecoy) continue; // We don't care about peak picking performance for standard peptides if (truePeptide.GlobalStandardType != null) continue; var trueGroups = truePeptide.TransitionGroups.ToList(); var pickedGroups = pickedPeptide.TransitionGroups.ToList(); for (int k = 0; k < trueGroups.Count; k++) { var trueGroup = trueGroups[k]; var pickedGroup = pickedGroups[k]; var trueResults = trueGroup.Results[i]; var pickedResults = pickedGroup.Results[i]; if (trueResults == null) continue; int nChromInfos = trueResults.Count; for (int m = 0; m < nChromInfos; m++) { var trueInfo = trueResults[m]; var pickedInfo = pickedResults[m]; var fileInfo = set.GetFileInfo(trueInfo.FileId); var filePath = fileInfo.FilePath; var key = new MatchKey(trueGroup.Id.GlobalIndex, trueInfo.FileId.GlobalIndex); matches.Add(new PeakBoundsMatch(trueInfo, pickedInfo, key, filePath, trueGroup, HasNoQValues, HasNoScores, ApexPresent)); } } } } Matches = matches; // Detect if the apex time is in seconds, and if so adjust it to minutes if (ApexPresent) { double maxTime = matches.Where(match => match.PickedApex.HasValue) .Select(match => match.PickedApex.Value).Max(); if (maxTime > PeakBoundaryImporter.GetMaxRt(DocOriginal)) { foreach (var match in matches.Where(match => match.PickedApex.HasValue)) { match.PickedApex = match.PickedApex / 60; } } } }