public Regression(List <Tuple <double[], double> > data, IRegressionFunction costFunction) { this.countInput = data[0].Item1.Length; this.data = data; this.costFunction = costFunction; sigmas = new double[countInput + 1]; }
public RetentionTimeValues Scale(IRegressionFunction regressionFunction) { if (null == regressionFunction) { return(this); } double startRetentionTime = regressionFunction.GetY(StartRetentionTime); double endRetentionTime = regressionFunction.GetY(EndRetentionTime); double retentionTime = regressionFunction.GetY(RetentionTime); double?fwhm; if (Fwhm.HasValue) { double t1 = regressionFunction.GetY(RetentionTime - Fwhm.Value / 2); double t2 = regressionFunction.GetY(RetentionTime + Fwhm.Value / 2); fwhm = t2 - t1; } else { fwhm = null; } return(new RetentionTimeValues { RetentionTime = retentionTime, StartRetentionTime = startRetentionTime, EndRetentionTime = endRetentionTime, Fwhm = fwhm, }); }
public RetentionTimeValues Scale(IRegressionFunction regressionFunction) { if (null == regressionFunction) { return(this); } double startRetentionTime = regressionFunction.GetY(StartRetentionTime); double endRetentionTime = regressionFunction.GetY(EndRetentionTime); double retentionTime = regressionFunction.GetY(RetentionTime); double?fwhm; if (Fwhm.HasValue) { double t1 = regressionFunction.GetY(RetentionTime - Fwhm.Value / 2); double t2 = regressionFunction.GetY(RetentionTime + Fwhm.Value / 2); fwhm = t2 - t1; } else { fwhm = null; } return(ChangeProp(ImClone(this), im => { im.RetentionTime = retentionTime; im.StartRetentionTime = startRetentionTime; im.EndRetentionTime = endRetentionTime; im.Fwhm = fwhm; })); }
public bool TryGetRegressionFunction(ChromFileInfoId chromFileInfoId, out IRegressionFunction regressionFunction) { if (ReferenceEquals(chromFileInfoId, ChromFileInfo.Id)) { regressionFunction = null; return(true); } Tuple <ChromatogramSet, ChromFileInfo> chromSetInfo; if (_chromSetInfos.TryGetValue(chromFileInfoId, out chromSetInfo)) { var retentionTimeAlignment = FileRetentionTimeAlignments.RetentionTimeAlignments.Find(chromSetInfo.Item2); if (null != retentionTimeAlignment) { regressionFunction = retentionTimeAlignment.RegressionLine; return(true); } } regressionFunction = null; return(false); }
private static void AddRetentionTimesToDict(IRetentionTimeProvider retentionTimes, IRegressionFunction regressionLine, IDictionary <Target, IrtPeptideAverages> dictPeptideAverages, IEnumerable <DbIrtPeptide> standardPeptideList) { var setStandards = new TargetMap <bool>(standardPeptideList.Select(peptide => new KeyValuePair <Target, bool>(peptide.Target, true))); foreach (var pepTime in retentionTimes.PeptideRetentionTimes.Where(p => !setStandards.ContainsKey(p.PeptideSequence))) { var peptideModSeq = pepTime.PeptideSequence; var timeSource = retentionTimes.GetTimeSource(peptideModSeq); var irt = regressionLine.GetY(pepTime.RetentionTime); if (!dictPeptideAverages.TryGetValue(peptideModSeq, out var pepAverage)) { dictPeptideAverages.Add(peptideModSeq, new IrtPeptideAverages(peptideModSeq, irt, timeSource)); } else { pepAverage.AddIrt(irt); } } }
public bool TryGetRegressionFunction(ChromFileInfoId chromFileInfoId, out IRegressionFunction regressionFunction) { regressionFunction = _retentionTimeRegression.GetUnconversion(chromFileInfoId); return(regressionFunction != null); }
public ChromGraphItem(TransitionGroupDocNode transitionGroupNode, TransitionDocNode transition, ChromatogramInfo chromatogram, TransitionChromInfo tranPeakInfo, IRegressionFunction timeRegressionFunction, bool[] annotatePeaks, double[] dotProducts, double bestProduct, bool isFullScanMs, bool isSummary, RawTimesInfoItem?displayRawTimes, int step, Color color, float fontSize, int width, FullScanInfo fullScanInfo = null) { TransitionGroupNode = transitionGroupNode; TransitionNode = transition; Chromatogram = chromatogram; TransitionChromInfo = tranPeakInfo; TimeRegressionFunction = timeRegressionFunction; Color = color; FullScanInfo = fullScanInfo; _step = step; _fontSpec = CreateFontSpec(color, fontSize); _width = width; _dotProducts = dotProducts; _bestProduct = bestProduct; _isFullScanMs = isFullScanMs; _isSummary = isSummary; _displayRawTimes = displayRawTimes; _arrayLabelIndexes = new int[annotatePeaks.Length]; if (chromatogram == null) { _measuredTimes = new double[0]; _displayTimes = _measuredTimes; _intensities = new double[0]; } else { // Cache values early to avoid accessing slow enumerators // which show up under profiling. Chromatogram.AsArrays(out _measuredTimes, out _intensities); if (TimeRegressionFunction == null) { _displayTimes = _measuredTimes; } else { _displayTimes = _measuredTimes.Select(TimeRegressionFunction.GetY).ToArray(); } // Add peak times to hash set for labeling int iLastStart = 0; for (int i = 0; i < chromatogram.NumPeaks; i++) { int maxIndex = -1; if (annotatePeaks[i]) { ChromPeak peak = chromatogram.GetPeak(i); maxIndex = GetMaxIndex(peak.StartTime, peak.EndTime, ref iLastStart); } _arrayLabelIndexes[i] = maxIndex; if (maxIndex != -1 && !_annotatedTimes.ContainsKey(maxIndex)) { _annotatedTimes.Add(maxIndex, i); } } // Calculate best peak index if (tranPeakInfo != null) { iLastStart = 0; _bestPeakTimeIndex = GetMaxIndex(tranPeakInfo.StartRetentionTime, tranPeakInfo.EndRetentionTime, ref iLastStart); } } }
private PointPair CalculatePointPair <TChromInfoData>(int iResult, IEnumerable <TChromInfoData> chromInfoDatas, Func <TChromInfoData, RetentionTimeValues?> getRetentionTimeValues) where TChromInfoData : ChromInfoData { var startTimes = new List <double>(); var endTimes = new List <double>(); var retentionTimes = new List <double>(); var fwhms = new List <double>(); foreach (var chromInfoData in chromInfoDatas) { var retentionTimeValues = getRetentionTimeValues(chromInfoData).GetValueOrDefault(); IRegressionFunction regressionFunction = null; if (null != RetentionTimeTransform.RtTransformOp) { RetentionTimeTransform.RtTransformOp.TryGetRegressionFunction(chromInfoData.ChromFileInfo.FileId, out regressionFunction); } if (regressionFunction == null) { startTimes.Add(retentionTimeValues.StartRetentionTime); endTimes.Add(retentionTimeValues.EndRetentionTime); retentionTimes.Add(retentionTimeValues.RetentionTime); fwhms.Add(retentionTimeValues.Fwhm ?? 0); } else { startTimes.Add(regressionFunction.GetY(retentionTimeValues.StartRetentionTime)); endTimes.Add(regressionFunction.GetY(retentionTimeValues.EndRetentionTime)); retentionTimes.Add(regressionFunction.GetY(retentionTimeValues.RetentionTime)); if (retentionTimeValues.Fwhm.HasValue) { fwhms.Add(regressionFunction.GetY(retentionTimeValues.RetentionTime + retentionTimeValues.Fwhm.Value / 2) - regressionFunction.GetY(retentionTimeValues.RetentionTime - retentionTimeValues.Fwhm.Value / 2)); } else { fwhms.Add(0); } } } if (RTPeptideValue.All == RTPeptideGraphPane.RTValue) { var point = HiLowMiddleErrorBarItem.MakePointPair(iResult, new Statistics(endTimes).Mean(), new Statistics(startTimes).Mean(), new Statistics(retentionTimes).Mean(), new Statistics(fwhms).Mean()); return(point.IsInvalid ? PointPairMissing(iResult) : point); } IEnumerable <double> values; switch (RTPeptideGraphPane.RTValue) { case RTPeptideValue.FWB: values = startTimes.Select((startTime, index) => endTimes[index] - startTime); break; case RTPeptideValue.FWHM: values = fwhms; break; default: values = retentionTimes; break; } return(RetentionTimeTransform.AggregateOp.MakeBarValue(iResult, values)); }
public ChromGraphItem(TransitionGroupDocNode transitionGroupNode, TransitionDocNode transition, ChromatogramInfo chromatogram, TransitionChromInfo tranPeakInfo, IRegressionFunction timeRegressionFunction, bool[] annotatePeaks, double[] dotProducts, double bestProduct, bool isFullScanMs, bool isSummary, int step, Color color, float fontSize, int width, FullScanInfo fullScanInfo = null) { TransitionGroupNode = transitionGroupNode; TransitionNode = transition; Chromatogram = chromatogram; TransitionChromInfo = tranPeakInfo; TimeRegressionFunction = timeRegressionFunction; Color = color; FullScanInfo = fullScanInfo; _step = step; _fontSpec = CreateFontSpec(color, fontSize); _width = width; _dotProducts = dotProducts; _bestProduct = bestProduct; _isFullScanMs = isFullScanMs; _isSummary = isSummary; _arrayLabelIndexes = new int[annotatePeaks.Length]; if (chromatogram == null) { _measuredTimes = new double[0]; _displayTimes = _measuredTimes; _intensities = new double[0]; } else { // Cache values early to avoid accessing slow enumerators // which show up under profiling. Chromatogram.AsArrays(out _measuredTimes, out _intensities); if (TimeRegressionFunction == null) { _displayTimes = _measuredTimes; } else { _displayTimes = _measuredTimes.Select(TimeRegressionFunction.GetY).ToArray(); } // Add peak times to hash set for labeling int iLastStart = 0; for (int i = 0; i < chromatogram.NumPeaks; i++) { int maxIndex = -1; if (annotatePeaks[i]) { ChromPeak peak = chromatogram.GetPeak(i); maxIndex = GetMaxIndex(peak.StartTime, peak.EndTime, ref iLastStart); } _arrayLabelIndexes[i] = maxIndex; if (maxIndex != -1 && !_annotatedTimes.ContainsKey(maxIndex)) _annotatedTimes.Add(maxIndex, i); } // Calculate best peak index if (tranPeakInfo != null) { iLastStart = 0; _bestPeakTimeIndex = GetMaxIndex(tranPeakInfo.StartRetentionTime, tranPeakInfo.EndRetentionTime, ref iLastStart); } } }
private void ShadeGraph(TransitionChromInfo tranPeakInfo, ChromatogramInfo info, IRegressionFunction timeRegressionFunction, double[] dotProducts, double bestProduct, bool isFullScanMs, int step, float fontSize, int width, FullScanInfo fullScanInfo, PaneKey graphPaneKey) { if (tranPeakInfo == null) return; // Nothing to shade float end = tranPeakInfo.EndRetentionTime; float start = tranPeakInfo.StartRetentionTime; double[] allTimes; double[] allIntensities; info.AsArrays(out allTimes, out allIntensities); var peakTimes = new List<float>(); var peakIntensities = new List<float>(); for (int j = 0; j < allTimes.Length; j++) { if (start > allTimes[j]) continue; if (end < allTimes[j]) break; peakTimes.Add((float) allTimes[j]); peakIntensities.Add((float) allIntensities[j]); } if (peakIntensities.Count == 0) return; // Add peak area shading float[] peakTimesArray = peakTimes.ToArray(); info = new ChromatogramInfo(peakTimesArray, peakIntensities.ToArray()); var peakShadeItem = new ChromGraphItem(null, null, info, null, timeRegressionFunction, new bool[info.NumPeaks], dotProducts, bestProduct, isFullScanMs, false, step, ChromGraphItem.ColorSelected, fontSize, width, fullScanInfo); var peakShadeCurveItem = _graphHelper.AddChromatogram(graphPaneKey, peakShadeItem); peakShadeCurveItem.Label.IsVisible = false; var lineItem = peakShadeCurveItem as LineItem; if (lineItem != null) { const int fillAlpha = 50; lineItem.Line.Fill = new Fill(Color.FromArgb(fillAlpha, lineItem.Color)); } // Add peak background shading float min = Math.Min(peakIntensities.First(), peakIntensities.Last()); info = new ChromatogramInfo(peakTimesArray, peakIntensities.Select(intensity => Math.Min(intensity, min)).ToArray()); var backgroundShadeItem = new ChromGraphItem(null, null, info, null, timeRegressionFunction, new bool[info.NumPeaks], dotProducts, bestProduct, isFullScanMs, false, step, Color.DarkGray, fontSize, 2, fullScanInfo); var backgroundShadeCurveItem = _graphHelper.AddChromatogram(graphPaneKey, backgroundShadeItem); backgroundShadeCurveItem.Label.IsVisible = false; var lineItem2 = backgroundShadeCurveItem as LineItem; if (lineItem2 != null) { const int fillAlpha = 70; lineItem2.Line.Fill = new Fill(Color.FromArgb(fillAlpha, Color.Black)); } }
private void DisplayTransitions(IRegressionFunction timeRegressionFunction, TransitionDocNode nodeTranSelected, ChromatogramSet chromatograms, float mzMatchTolerance, TransitionGroupDocNode nodeGroup, ChromatogramGroupInfo chromGroupInfo, PaneKey graphPaneKey, DisplayTypeChrom displayType, ref double bestStartTime, ref double bestEndTime) { var fileId = chromatograms.FindFile(chromGroupInfo); // Get points for all transitions, and pick maximum peaks. ChromatogramInfo[] arrayChromInfo; var displayTrans = GetDisplayTransitions(nodeGroup, displayType).ToArray(); int numTrans = displayTrans.Length; int numSteps = 0; bool allowEmpty = false; if (IsSingleTransitionDisplay && nodeTranSelected != null) { if (!displayTrans.Contains(nodeTranSelected)) { arrayChromInfo = new ChromatogramInfo[0]; displayTrans = new TransitionDocNode[0]; numTrans = 0; } else { arrayChromInfo = chromGroupInfo.GetAllTransitionInfo((float) nodeTranSelected.Mz, mzMatchTolerance, chromatograms.OptimizationFunction); if (chromatograms.OptimizationFunction != null) { // Make sure the number of steps matches what will show up in the summary // graphs, or the colors won't match up. int numStepsExpected = chromatograms.OptimizationFunction.StepCount*2 + 1; if (arrayChromInfo.Length != numStepsExpected) { arrayChromInfo = ResizeArrayChromInfo(arrayChromInfo, numStepsExpected); allowEmpty = true; } } numTrans = arrayChromInfo.Length; displayTrans = new TransitionDocNode[numTrans]; for (int i = 0; i < numTrans; i++) displayTrans[i] = nodeTranSelected; } numSteps = numTrans/2; } else { arrayChromInfo = new ChromatogramInfo[numTrans]; for (int i = 0; i < numTrans; i++) { var nodeTran = displayTrans[i]; // Get chromatogram info for this transition arrayChromInfo[i] = chromGroupInfo.GetTransitionInfo((float) nodeTran.Mz, mzMatchTolerance); } } int bestPeakTran = -1; TransitionChromInfo tranPeakInfo = null; float maxPeakHeight = float.MinValue; int numPeaks = chromGroupInfo.NumPeaks; var maxPeakTrans = new int[numPeaks]; var maxPeakHeights = new float[numPeaks]; for (int i = 0; i < numPeaks; i++) maxPeakHeights[i] = float.MinValue; var transform = Transform; // Prepare arrays of values for library dot-product double[] expectedIntensities = null; double[][] peakAreas = null; bool isShowingMs = displayTrans.Any(nodeTran => nodeTran.IsMs1); bool isShowingMsMs = displayTrans.Any(nodeTran => !nodeTran.IsMs1); bool isFullScanMs = DocumentUI.Settings.TransitionSettings.FullScan.IsEnabledMs && isShowingMs; if ((isFullScanMs && !isShowingMsMs && nodeGroup.HasIsotopeDist) || (!isFullScanMs && nodeGroup.HasLibInfo)) { expectedIntensities = new double[numTrans]; peakAreas = new double[numPeaks][]; for (int i = 0; i < numPeaks; i++) peakAreas[i] = new double[numTrans]; } // Find the transition with the maximum peak height for the best peak for (int i = 0; i < numTrans; i++) { var nodeTran = displayTrans[i]; int step = (numSteps > 0 ? i - numSteps : 0); var transitionChromInfo = GetTransitionChromInfo(nodeTran, _chromIndex, fileId, step); if (transitionChromInfo == null) continue; if (maxPeakHeight < transitionChromInfo.Height) { maxPeakHeight = transitionChromInfo.Height; bestPeakTran = i; tranPeakInfo = transitionChromInfo; } AddBestPeakTimes(transitionChromInfo, ref bestStartTime, ref bestEndTime); } for (int i = 0; i < numTrans; i++) { var nodeTran = displayTrans[i]; // Store library intensities for dot-product if (expectedIntensities != null) { if (isFullScanMs) expectedIntensities[i] = nodeTran.HasDistInfo ? nodeTran.IsotopeDistInfo.Proportion : 0; else expectedIntensities[i] = nodeTran.HasLibInfo ? nodeTran.LibInfo.Intensity : 0; } var info = arrayChromInfo[i]; if (info == null) continue; // Apply any active transform info.Transform(transform); for (int j = 0; j < numPeaks; j++) { var peak = info.GetPeak(j); // Exclude any peaks between the boundaries of the chosen peak. if (IntersectPeaks(peak, tranPeakInfo)) continue; // Store peak intensity for dot-product if (peakAreas != null) peakAreas[j][i] = peak.Area; // Keep track of which transition has the max height for each peak if (maxPeakHeights[j] < peak.Height) { maxPeakHeights[j] = peak.Height; maxPeakTrans[j] = i; } } } // Calculate library dot-products, if possible double[] dotProducts = null; double bestProduct = 0; int minProductTrans = isFullScanMs ? TransitionGroupDocNode.MIN_DOT_PRODUCT_MS1_TRANSITIONS : TransitionGroupDocNode.MIN_DOT_PRODUCT_TRANSITIONS; if (peakAreas != null && numTrans >= minProductTrans) { var tranGroupChromInfo = GetTransitionGroupChromInfo(nodeGroup, fileId, _chromIndex); double? dotProduct = null; if (tranGroupChromInfo != null) { dotProduct = isFullScanMs ? tranGroupChromInfo.IsotopeDotProduct : tranGroupChromInfo.LibraryDotProduct; } if (dotProduct.HasValue) { bestProduct = dotProduct.Value; var statExpectedIntensities = new Statistics(expectedIntensities); for (int i = 0; i < peakAreas.Length; i++) { var statPeakAreas = new Statistics(peakAreas[i]); double dotProductCurrent = statPeakAreas.NormalizedContrastAngleSqrt(statExpectedIntensities); // Only show products that are greater than the best peak product, // and by enough to be a significant improvement. Also the library product // on the group node is stored as a float, which means the version // hear calculated as a double can be larger, but really represent // the same number. if (dotProductCurrent > bestProduct && dotProductCurrent > 0.5 && dotProductCurrent - bestProduct > 0.05) { if (dotProducts == null) dotProducts = new double[numPeaks]; dotProducts[i] = dotProductCurrent; } } } } // Create graph items int iColor = 0; int lineWidth = LineWidth; float fontSize = FontSize; // We want the product ion colors to stay the same whether they are displayed: // 1. In a single pane with the precursor ions (Transitions -> All) // 2. In a separate pane of the split graph (Transitions -> All AND Transitions -> Split Graph) // 3. In a single pane by themselves (Transition -> Products) // We will use an offset in the colors array for cases 2 and 3 so that we do not reuse the precursor ion colors. var nodeDisplayType = GetDisplayType(DocumentUI, nodeGroup); int colorOffset = 0; if(displayType == DisplayTypeChrom.products && (nodeDisplayType != DisplayTypeChrom.single || (nodeDisplayType == DisplayTypeChrom.single && chromatograms.OptimizationFunction == null))) { colorOffset = GetDisplayTransitions(nodeGroup, DisplayTypeChrom.precursors).Count(); } for (int i = 0; i < numTrans; i++) { var info = arrayChromInfo[i]; if (info == null && !allowEmpty) continue; var nodeTran = displayTrans[i]; int step = numSteps != 0 ? i - numSteps : 0; Color color; bool shade = false; int width = lineWidth; if ((numSteps == 0 && ReferenceEquals(nodeTran, nodeTranSelected) || (numSteps > 0 && step == 0))) { color = ChromGraphItem.ColorSelected; shade = true; width++; } else { color = COLORS_LIBRARY[(iColor + colorOffset) % COLORS_LIBRARY.Length]; } TransitionChromInfo tranPeakInfoGraph = null; if (bestPeakTran == i) tranPeakInfoGraph = tranPeakInfo; var scanName = nodeTran.FragmentIonName; if (nodeTran.Transition.Charge != 1) // Positive singly charged is uninteresting scanName += Transition.GetChargeIndicator(nodeTran.Transition.Charge); if (nodeTran.Transition.MassIndex != 0) scanName += Environment.NewLine + Transition.GetMassIndexText(nodeTran.Transition.MassIndex); var fullScanInfo = new FullScanInfo { ChromInfo = info, ScanName = scanName }; if (fullScanInfo.ChromInfo != null && fullScanInfo.ChromInfo.ExtractionWidth > 0) _enableTrackingDot = true; var graphItem = new ChromGraphItem(nodeGroup, nodeTran, info, tranPeakInfoGraph, timeRegressionFunction, GetAnnotationFlags(i, maxPeakTrans, maxPeakHeights), dotProducts, bestProduct, isFullScanMs, false, step, color, fontSize, width, fullScanInfo); _graphHelper.AddChromatogram(graphPaneKey, graphItem); if (shade) { ShadeGraph(tranPeakInfo,info,timeRegressionFunction,dotProducts,bestProduct,isFullScanMs,step,fontSize,width,fullScanInfo,graphPaneKey); } iColor++; } var graphPane = _graphHelper.GetGraphPane(graphPaneKey); if (graphPane == null) _enableTrackingDot = false; if (_enableTrackingDot) { graphPane.CurveList.Insert(FULLSCAN_TRACKING_INDEX, CreateScanPoint(Color.Black)); graphPane.CurveList.Insert(FULLSCAN_SELECTED_INDEX, CreateScanPoint(Color.Red)); } }
private void DisplayTotals(IRegressionFunction timeRegressionFunction, ChromatogramSet chromatograms, float mzMatchTolerance, int countLabelTypes, ref double bestStartTime, ref double bestEndTime) { // Construct and add graph items for all relevant transition groups. float fontSize = FontSize; int lineWidth = LineWidth; int iCharge = -1; int? charge = null; var chromGroupInfos = ChromGroupInfos; for (int i = 0; i < _nodeGroups.Length; i++) { var nodeGroup = _nodeGroups[i]; var chromGroupInfo = chromGroupInfos[i]; if (chromGroupInfo == null) continue; ChromFileInfoId fileId = chromatograms.FindFile(chromGroupInfo); // Collect the chromatogram info for the transition children // of this transition group. ChromatogramInfo infoPrimary = null; TransitionChromInfo tranPeakInfo = null; float maxPeakHeight = float.MinValue; var listChromInfo = new List<ChromatogramInfo>(); foreach (TransitionDocNode nodeTran in nodeGroup.Children) { var info = chromGroupInfo.GetTransitionInfo((float)nodeTran.Mz, mzMatchTolerance); if (info == null) continue; listChromInfo.Add(info); // Keep track of which chromatogram owns the tallest member of // the peak on the document tree. var transitionChromInfo = GetTransitionChromInfo(nodeTran, _chromIndex, fileId, 0); if (transitionChromInfo == null) continue; if (transitionChromInfo.Height > maxPeakHeight) { maxPeakHeight = transitionChromInfo.Height; tranPeakInfo = transitionChromInfo; infoPrimary = info; } // Adjust best peak window used to zoom the graph to the best peak AddBestPeakTimes(transitionChromInfo, ref bestStartTime, ref bestEndTime); } // If any transitions are present for this group, add a graph item to // the graph for it. if (listChromInfo.Count > 0) { if (infoPrimary == null) infoPrimary = listChromInfo[0]; // Sum the intensities of all transitions into the first chromatogram infoPrimary.SumIntensities(listChromInfo); // Apply any transform the user has chosen infoPrimary.Transform(Transform); int iColor = GetColorIndex(nodeGroup, countLabelTypes, ref charge, ref iCharge); Color color = COLORS_GROUPS[iColor % COLORS_GROUPS.Length]; bool[] annotateAll = new bool[infoPrimary.NumPeaks]; for (int j = 0; j < annotateAll.Length; j++) { var peak = infoPrimary.GetPeak(j); if (peak.IsForcedIntegration) continue; // Exclude any peaks between the boundaries of the chosen peak. if (tranPeakInfo != null && tranPeakInfo.StartRetentionTime < peak.RetentionTime && peak.RetentionTime < tranPeakInfo.EndRetentionTime) continue; annotateAll[j] = true; } var graphItem = new ChromGraphItem(nodeGroup, null, infoPrimary, tranPeakInfo, timeRegressionFunction, annotateAll, null, 0, false, false, 0, color, fontSize, lineWidth); var graphPaneKey = new PaneKey(nodeGroup); _graphHelper.AddChromatogram(graphPaneKey, graphItem); } } }
/// <summary> /// Display summed transitions for multiple selected peptides. /// </summary> private void DisplayPeptides(IRegressionFunction timeRegressionFunction, ChromatogramSet chromatograms, float mzMatchTolerance, int countLabelTypes, IList<PeptideDocNode> peptideDocNodes, ref double bestStartTime, ref double bestEndTime, out double leftPeakWidth, out double rightPeakWidth) { leftPeakWidth = 0; rightPeakWidth = 0; // Construct and add graph items for all relevant transition groups. float fontSize = FontSize; int lineWidth = LineWidth; var chromGroupInfos = ChromGroupInfos; var lookupChromGroupInfoIndex = new Dictionary<int, int>(_nodeGroups.Length); for (int i = 0; i < _nodeGroups.Length; i++) lookupChromGroupInfoIndex[_nodeGroups[i].Id.GlobalIndex] = i; // Generate a unique short identifier for each peptide. var peptideNames = new Tuple<string,bool>[peptideDocNodes.Count]; for (int i = 0; i < peptideDocNodes.Count; i++) peptideNames[i] = new Tuple<string,bool>(peptideDocNodes[i].RawTextId, peptideDocNodes[i].IsProteomic); var uniqueNames = new UniquePrefixGenerator(peptideNames, 3); var displayPeptides = new List<DisplayPeptide>(); for (int peptideIndex = 0; peptideIndex < peptideDocNodes.Count; peptideIndex++) { var peptideDocNode = peptideDocNodes[peptideIndex]; TransitionChromInfo bestPeakInfo = null; ChromatogramInfo sumInfo = null; float maxPeakHeight = float.MinValue; foreach (var precursor in peptideDocNode.TransitionGroups) { int indexInfo; if (!lookupChromGroupInfoIndex.TryGetValue(precursor.Id.GlobalIndex, out indexInfo)) continue; var chromGroupInfo = chromGroupInfos[indexInfo]; if (chromGroupInfo == null) continue; ChromFileInfoId fileId = chromatograms.FindFile(chromGroupInfo); foreach (var nodeTran in precursor.Transitions) { var info = chromGroupInfo.GetTransitionInfo((float)nodeTran.Mz, mzMatchTolerance); if (info == null) continue; if (sumInfo == null) sumInfo = info; else { float[] sumTimes; float[] sumIntensities; if (!AddTransitions.Add( info.Times, info.Intensities, sumInfo.Times, sumInfo.Intensities, out sumTimes, out sumIntensities)) continue; sumInfo = new ChromatogramInfo(sumTimes, sumIntensities); } // Keep track of which chromatogram owns the tallest member of // the peak on the document tree. var transitionChromInfo = GetTransitionChromInfo(nodeTran, _chromIndex, fileId, 0); if (transitionChromInfo == null) continue; if (transitionChromInfo.Height > maxPeakHeight) { maxPeakHeight = transitionChromInfo.Height; bestPeakInfo = transitionChromInfo; } } } if (sumInfo != null && bestPeakInfo != null) { displayPeptides.Add(new DisplayPeptide { PeptideIndex = peptideIndex, SumInfo = sumInfo, BestPeakInfo = bestPeakInfo }); } } // Order the peptides by height of best peak. displayPeptides = displayPeptides.OrderByDescending(e => e.BestPeakInfo.Height).ToList(); // Display only the top peptides. int lastPeptideIndex = Math.Min(MaxPeptidesDisplayed, displayPeptides.Count); var graphItems = new List<ChromGraphItem>(); for (int i = lastPeptideIndex-1; i >= 0; i--) // smallest peaks first for good z-ordering in graph { var bestPeakInfo = displayPeptides[i].BestPeakInfo; var sumInfo = displayPeptides[i].SumInfo; var peptideDocNode = peptideDocNodes[displayPeptides[i].PeptideIndex]; // Intersect best peak with summed transition. if (bestPeakInfo != null && sumInfo.Times.Length > 0) { float startRetentionTime = Math.Max(bestPeakInfo.StartRetentionTime, sumInfo.Times[0]); float endRetentionTime = Math.Min(bestPeakInfo.EndRetentionTime, sumInfo.Times[sumInfo.Times.Length - 1]); if (endRetentionTime > startRetentionTime) { if (bestStartTime > startRetentionTime) { bestStartTime = startRetentionTime; leftPeakWidth = endRetentionTime - startRetentionTime; } if (bestEndTime < endRetentionTime) { bestEndTime = endRetentionTime; rightPeakWidth = endRetentionTime - startRetentionTime; } bestPeakInfo = new TransitionChromInfo(startRetentionTime, endRetentionTime); } } // Get peptide graph color from SequenceTree. var peptideGraphInfo = _stateProvider.GetPeptideGraphInfo(peptideDocNode); Color color = peptideGraphInfo.Color; sumInfo.Transform(Transform); bool[] annotateAll = new bool[sumInfo.NumPeaks]; ChromGraphItem graphItem = new ChromGraphItem(null, null, sumInfo, bestPeakInfo, timeRegressionFunction, annotateAll, null, 0, false, false, 0, color, fontSize, lineWidth) { CurveAnnotation = uniqueNames.GetUniquePrefix(peptideDocNode.RawTextId, peptideDocNode.IsProteomic), IdPath = _groupPaths[displayPeptides[i].PeptideIndex], GraphInfo = peptideGraphInfo }; if (peptideGraphInfo.IsSelected) graphItems.Insert(0, graphItem); else graphItems.Add(graphItem); } foreach (var graphItem in graphItems) { var curveItem = _graphHelper.AddChromatogram(new PaneKey(), graphItem); // Make the fill color under the curve more opaque if the curve is selected. var fillAlpha = graphItem.GraphInfo.IsSelected ? 60 : 15; ((LineItem)curveItem).Line.Fill = new Fill(Color.FromArgb(fillAlpha, graphItem.GraphInfo.Color)); } }
private void DisplayOptimizationTotals(IRegressionFunction timeRegressionFunction, ChromatogramSet chromatograms, float mzMatchTolerance, ref double bestStartTime, ref double bestEndTime) { // Construct and add graph items for all relevant transition groups. float fontSize = FontSize; int lineWidth = LineWidth; int iColor = 0; // Get the one and only group var nodeGroup = _nodeGroups[0]; var chromGroupInfo = ChromGroupInfos[0]; ChromFileInfoId fileId = chromatograms.FindFile(chromGroupInfo); int numPeaks = chromGroupInfo.NumPeaks; // Collect the chromatogram info for the transition children // of this transition group. var listChromInfoSets = new List<ChromatogramInfo[]>(); var listTranisitionChromInfoSets = new List<TransitionChromInfo[]>(); int totalOptCount = chromatograms.OptimizationFunction.StepCount*2 + 1; foreach (TransitionDocNode nodeTran in nodeGroup.Children) { var infos = chromGroupInfo.GetAllTransitionInfo((float) nodeTran.Mz, mzMatchTolerance, chromatograms.OptimizationFunction); if (infos.Length == 0) continue; // Make sure the total number of chrom info entries match the expected // no matter what, so that chromatogram colors will match up with peak // area charts. if (infos.Length != totalOptCount) infos = ResizeArrayChromInfo(infos, totalOptCount); listChromInfoSets.Add(infos); var transitionChromInfos = new TransitionChromInfo[totalOptCount]; int steps = infos.Length/2; int offset = totalOptCount/2 - steps; for (int i = 0; i < infos.Length; i++) { transitionChromInfos[i + offset] = GetTransitionChromInfo(nodeTran, _chromIndex, fileId, i - steps); } listTranisitionChromInfoSets.Add(transitionChromInfos); } if (listChromInfoSets.Count == 0 || totalOptCount == 0) throw new InvalidDataException(Resources.GraphChromatogram_DisplayOptimizationTotals_No_optimization_data_available); // Enumerate optimization steps, grouping the data into graph data by step var listGraphData = new List<OptimizationGraphData>(); for (int i = 0; i < listChromInfoSets.Count; i++) { var chromInfos = listChromInfoSets[i]; var transitionChromInfos = listTranisitionChromInfoSets[i]; for (int j = 0; j < chromInfos.Length; j++) { if (listGraphData.Count <= j) listGraphData.Add(new OptimizationGraphData(numPeaks)); listGraphData[j].Add(chromInfos[j], transitionChromInfos[j]); } } // Total and transform the data, and compute which optimization // set has the most intense peak for each peak group. int bestPeakData = -1; TransitionChromInfo tranPeakInfo = null; float maxPeakHeight = float.MinValue; var maxPeakData = new int[numPeaks]; var maxPeakHeights = new float[numPeaks]; for (int i = 0; i < numPeaks; i++) maxPeakHeights[i] = float.MinValue; var transform = Transform; for (int i = 0; i < listGraphData.Count; i++) { var graphData = listGraphData[i]; var infoPrimary = graphData.InfoPrimary; if (infoPrimary == null) continue; // Sum intensities of all transitions in this // optimization bucket infoPrimary.SumIntensities(graphData.ChromInfos); // Apply any transform the user has chosen infoPrimary.Transform(transform); for (int j = 0; j < numPeaks; j++) { float height = graphData.PeakHeights[j]; if (height > maxPeakHeights[j]) { maxPeakHeights[j] = height; maxPeakData[j] = i; } } if (maxPeakHeight < graphData.TotalHeight) { maxPeakHeight = graphData.TotalHeight; bestPeakData = i; tranPeakInfo = graphData.TransitionInfoPrimary; } AddBestPeakTimes(graphData.TransitionInfoPrimary, ref bestStartTime, ref bestEndTime); } // Hide all peaks between the best peak extents if (tranPeakInfo != null) { for (int j = 0; j < numPeaks; j++) { if (maxPeakHeights[j] == 0) continue; var graphData = listGraphData[maxPeakData[j]]; if (graphData.InfoPrimary == null) continue; ChromPeak peak = graphData.InfoPrimary.GetPeak(j); if (peak.IsForcedIntegration) continue; if (IntersectPeaks(peak, tranPeakInfo)) maxPeakHeights[j] = 0; } } // Create graph items int totalSteps = totalOptCount/2; for (int i = 0; i < listGraphData.Count; i++) { var graphData = listGraphData[i]; if (graphData.InfoPrimary != null) { int step = i - totalSteps; int width = lineWidth; Color color; if (step == 0) { color = ChromGraphItem.ColorSelected; width++; } else if (nodeGroup.HasLibInfo) color = COLORS_LIBRARY[iColor % COLORS_LIBRARY.Length]; else color = COLORS_LIBRARY[iColor % COLORS_LIBRARY.Length]; // color = COLORS_HEURISTIC[iColor % COLORS_HEURISTIC.Length]; TransitionChromInfo tranPeakInfoGraph = null; if (bestPeakData == i) tranPeakInfoGraph = tranPeakInfo; var graphItem = new ChromGraphItem(nodeGroup, null, graphData.InfoPrimary, tranPeakInfoGraph, timeRegressionFunction, GetAnnotationFlags(i, maxPeakData, maxPeakHeights), null, 0, false, false, step, color, fontSize, width); _graphHelper.AddChromatogram(PaneKey.PRECURSORS, graphItem); } iColor++; } }
private void DisplayAllIonsSummary(IRegressionFunction timeRegressionFunction, TransitionDocNode nodeTranSelected, ChromatogramSet chromatograms, ChromExtractor extractor, ref double bestStartTime, ref double bestEndTime) { if (ChromGroupInfos.Length == 0) { return; } var chromGroupInfo = ChromGroupInfos[0]; var info = chromGroupInfo.GetTransitionInfo(0, 0); var fileId = chromatograms.FindFile(chromGroupInfo); var nodeGroup = _nodeGroups != null ? _nodeGroups[0] : null; if (nodeGroup == null) nodeTranSelected = null; TransitionChromInfo tranPeakInfo = null; if (nodeGroup != null) { float maxPeakHeight = float.MinValue; foreach (TransitionDocNode nodeTran in nodeGroup.Children) { // Keep track of which chromatogram owns the tallest member of // the peak on the document tree. var transitionChromInfo = GetTransitionChromInfo(nodeTran, _chromIndex, fileId, 0); if (transitionChromInfo == null) continue; if (nodeTranSelected != null) { if (ReferenceEquals(nodeTran, nodeTranSelected)) tranPeakInfo = transitionChromInfo; } else if (transitionChromInfo.Height > maxPeakHeight) { maxPeakHeight = transitionChromInfo.Height; tranPeakInfo = transitionChromInfo; } // Adjust best peak window used to zoom the graph to the best peak AddBestPeakTimes(transitionChromInfo, ref bestStartTime, ref bestEndTime); } } // Apply active transform info.Transform(Transform); int numPeaks = info.NumPeaks; var annotationFlags = new bool[numPeaks]; for (int i = 0; i < numPeaks; i++) { // Exclude any peaks between the boundaries of the chosen peak. annotationFlags[i] = !IntersectPeaks(info.GetPeak(i), tranPeakInfo); } var graphItem = new ChromGraphItem(nodeGroup, nodeTranSelected, info, tranPeakInfo, timeRegressionFunction, annotationFlags, null, 0, true, true, 0, COLORS_GROUPS[(int)extractor], FontSize, LineWidth); _graphHelper.AddChromatogram(new PaneKey(nodeGroup), graphItem); }
public RetentionTimeValues Scale(IRegressionFunction regressionFunction) { if (null == regressionFunction) { return this; } double startRetentionTime = regressionFunction.GetY(StartRetentionTime); double endRetentionTime = regressionFunction.GetY(EndRetentionTime); double retentionTime = regressionFunction.GetY(RetentionTime); double? fwhm; if (Fwhm.HasValue) { double t1 = regressionFunction.GetY(RetentionTime - Fwhm.Value/2); double t2 = regressionFunction.GetY(RetentionTime + Fwhm.Value/2); fwhm = t2 - t1; } else { fwhm = null; } return new RetentionTimeValues { RetentionTime = retentionTime, StartRetentionTime = startRetentionTime, EndRetentionTime = endRetentionTime, Fwhm = fwhm, }; }