private static PointPair CreatePointPair(int iGroup, ICollection <double> listTimes, IEnumerable <double> listStarts, IEnumerable <double> listEnds, IEnumerable <double> listFwhms, ref double maxY, ref double minY) { if (listTimes.Count == 0) { return(RTPointPairMissing(iGroup)); } var statTimes = new Statistics(listTimes); var statStarts = new Statistics(listStarts); var statEnds = new Statistics(listEnds); var statFwhms = new Statistics(listFwhms); double endY = statEnds.Mean(); double startY = statStarts.Mean(); var pointPair = HiLowMiddleErrorBarItem.MakePointPair(iGroup, endY, startY, statTimes.Mean(), statFwhms.Mean()); maxY = Math.Max(maxY, endY); minY = Math.Min(minY, startY); return(pointPair); }
private CurveItem CreateMultiSelectBarItem(string label, PointPairList pointPairList, Color color) { for (var index = 0; index < pointPairList.Count; index++) { PointPair pp = pointPairList[index]; var middle = pp.Y - (pp.Y - pp.LowValue) / 2; if (!double.IsNaN(middle)) { pp.Tag = new MiddleErrorTag(middle, 0); } } var curveItem = new HiLowMiddleErrorBarItem(label, pointPairList, color, color); BarSettings.Type = BarType.SortedOverlay; return(curveItem); }
public override void UpdateGraph(bool selectionChanged) { Clear(); TransitionGroupDocNode selectedGroup = null; PeptideGroupDocNode selectedProtein = null; var selectedTreeNode = GraphSummary.StateProvider.SelectedNode as SrmTreeNode; if (selectedTreeNode != null) { if (selectedTreeNode is TransitionTreeNode) { selectedGroup = (TransitionGroupDocNode)selectedTreeNode.SrmParent.Model; } else if (selectedTreeNode is TransitionGroupTreeNode) { selectedGroup = (TransitionGroupDocNode)selectedTreeNode.Model; } else { var node = selectedTreeNode as PeptideTreeNode; if (node != null) { var nodePep = node.DocNode; selectedGroup = nodePep.TransitionGroups.FirstOrDefault(); } } var proteinTreeNode = selectedTreeNode.GetNodeOfType <PeptideGroupTreeNode>(); if (proteinTreeNode != null) { selectedProtein = proteinTreeNode.DocNode; } } SrmDocument document = GraphSummary.DocumentUIContainer.DocumentUI; var displayType = GraphChromatogram.GetDisplayType(document, selectedTreeNode); _graphData = CreateGraphData(document, selectedProtein, selectedGroup, displayType); int iColor = 0; int colorOffset = 0; if (selectedGroup != null && displayType == DisplayTypeChrom.products) { // If we are only displaying product ions, we want to use an offset in the colors array // so that we do not re-use colors that would be used for any precursor ions. colorOffset = GraphChromatogram.GetDisplayTransitions(selectedGroup, DisplayTypeChrom.precursors).Count(); } foreach (var pointPairList in _graphData.PointPairLists) { Color color = displayType == DisplayTypeChrom.total ? COLORS_GROUPS[iColor++ % COLORS_GROUPS.Count] : COLORS_TRANSITION[(iColor++ + colorOffset) % COLORS_TRANSITION.Count]; BarItem curveItem; if (HiLowMiddleErrorBarItem.IsHiLoMiddleErrorList(pointPairList)) { curveItem = new HiLowMiddleErrorBarItem(string.Empty, pointPairList, color, Color.Black); } else { curveItem = new MeanErrorBarItem(string.Empty, pointPairList, color, Color.Black); } curveItem.Bar.Border.IsVisible = false; curveItem.Bar.Fill.Brush = new SolidBrush(color); CurveList.Add(curveItem); } if (ShowSelection && SelectedIndex != -1) { double yValue = _graphData.SelectedMaxY; double yMin = _graphData.SelectedMinY; double height = yValue - yMin; GraphObjList.Add(new BoxObj(SelectedIndex + .5, yValue, 0.99, height, Color.Black, Color.Empty) { IsClippedToChartRect = true, }); } UpdateAxes(); }
public override void UpdateGraph(bool selectionChanged) { SrmDocument document = GraphSummary.DocumentUIContainer.DocumentUI; var results = document.Settings.MeasuredResults; bool resultsAvailable = results != null; Clear(); if (!resultsAvailable) { Title.Text = Resources.RTReplicateGraphPane_UpdateGraph_No_results_available; EmptyGraph(document); return; } var selectedTreeNode = GraphSummary.StateProvider.SelectedNode as SrmTreeNode ?? GraphSummary.StateProvider.SelectedNodes.OfType <SrmTreeNode>().FirstOrDefault(); if (selectedTreeNode == null || document.FindNode(selectedTreeNode.Path) == null) { EmptyGraph(document); return; } Title.Text = null; DisplayTypeChrom displayType = GraphChromatogram.GetDisplayType(document, selectedTreeNode); DocNode selectedNode = selectedTreeNode.Model; IdentityPath selectedPath = selectedTreeNode.Path; DocNode parentNode = selectedNode; IdentityPath parentPath = selectedTreeNode.Path; // If the selected tree node is a transition, then its siblings are displayed. if (selectedTreeNode is TransitionTreeNode) { if (displayType != DisplayTypeChrom.single) { SrmTreeNode parentTreeNode = selectedTreeNode.SrmParent; parentNode = parentTreeNode.Model; selectedPath = parentTreeNode.Path; } } // If the selected node is a peptide with one child, then show the children, // unless chromatogram display type is total else if (selectedTreeNode is PeptideTreeNode) { var children = ((DocNodeParent)selectedNode).Children; if (children.Count == 1 && displayType != DisplayTypeChrom.total) { selectedNode = parentNode = children[0]; selectedPath = new IdentityPath(parentPath, children[0].Id); } } else if (!(selectedTreeNode is PeptideGroupTreeNode) && !(selectedTreeNode is TransitionGroupTreeNode)) { Title.Text = Resources.RTReplicateGraphPane_UpdateGraph_Select_a_peptide_to_see_the_retention_time_graph; CanShowRTLegend = false; return; } // If a precursor is going to be displayed with display type single if (parentNode is TransitionGroupDocNode && displayType == DisplayTypeChrom.single) { // If no optimization data, then show all the transitions if (!results.Chromatograms.Contains(chrom => chrom.OptimizationFunction != null)) { displayType = DisplayTypeChrom.all; } } var rtTransformOp = GraphSummary.StateProvider.GetRetentionTimeTransformOperation(); var rtValue = RTPeptideGraphPane.RTValue; GraphValues.ReplicateGroupOp replicateGroupOp; if (rtValue == RTPeptideValue.All) { replicateGroupOp = GraphValues.ReplicateGroupOp.FromCurrentSettings(document.Settings, GraphValues.AggregateOp.MEAN); } else { replicateGroupOp = GraphValues.ReplicateGroupOp.FromCurrentSettings(document.Settings); } var retentionTimeValue = new GraphValues.RetentionTimeTransform(rtValue, rtTransformOp, replicateGroupOp.AggregateOp); YAxis.Title.Text = retentionTimeValue.GetAxisTitle(); var peptidePaths = GetSelectedPeptides().GetUniquePeptidePaths().ToList(); // if PeptideGroupTreeNode is selected but has only one child isMultiSelect should still be true IsMultiSelect = peptidePaths.Count > 1 || (peptidePaths.Count == 1 && GraphSummary.StateProvider.SelectedNodes.FirstOrDefault() is PeptideGroupTreeNode); GraphData graphData = new RTGraphData(document, IsMultiSelect ? peptidePaths : new[] { selectedPath }.AsEnumerable(), displayType, retentionTimeValue, replicateGroupOp); CanShowRTLegend = graphData.DocNodes.Count != 0; InitFromData(graphData); int selectedReplicateIndex = SelectedIndex; double minRetentionTime = double.MaxValue; double maxRetentionTime = -double.MaxValue; int iColor = 0, iCharge = -1; var charge = Adduct.EMPTY; int countLabelTypes = document.Settings.PeptideSettings.Modifications.CountLabelTypes; int colorOffset = 0; var transitionGroupDocNode = parentNode as TransitionGroupDocNode; if (transitionGroupDocNode != null && displayType == DisplayTypeChrom.products) { // If we are only displaying product ions, we want to use an offset in the colors array // so that we do not re-use colors that would be used for any precursor ions. colorOffset = GraphChromatogram.GetDisplayTransitions(transitionGroupDocNode, DisplayTypeChrom.precursors).Count(); } for (int i = 0; i < graphData.DocNodes.Count; i++) { var docNode = graphData.DocNodes[i]; var identityPath = graphData.DocNodePaths[i]; var pointPairLists = graphData.PointPairLists[i]; int numSteps = pointPairLists.Count / 2; for (int iStep = 0; iStep < pointPairLists.Count; iStep++) { int step = iStep - numSteps; var pointPairList = pointPairLists[iStep]; Color color; var isSelected = false; var nodeGroup = docNode as TransitionGroupDocNode; if (IsMultiSelect) { var peptides = peptidePaths.Select(path => document.FindNode(path)) .Cast <PeptideDocNode>().ToArray(); var peptideDocNode = peptides.FirstOrDefault( peptide => 0 <= peptide.FindNodeIndex(docNode.Id)); if (peptideDocNode == null) { continue; } color = GraphSummary.StateProvider.GetPeptideGraphInfo(peptideDocNode).Color; if (identityPath.Equals(selectedTreeNode.Path) && step == 0) { color = ChromGraphItem.ColorSelected; isSelected = true; } } else if (parentNode is PeptideDocNode) { // Resharper code inspection v9.0 on TC gets this one wrong // ReSharper disable ExpressionIsAlwaysNull int iColorGroup = GetColorIndex(nodeGroup, countLabelTypes, ref charge, ref iCharge); // ReSharper restore ExpressionIsAlwaysNull color = COLORS_GROUPS[iColorGroup % COLORS_GROUPS.Count]; } else if (displayType == DisplayTypeChrom.total) { color = COLORS_GROUPS[iColor % COLORS_GROUPS.Count]; } else if (ReferenceEquals(docNode, selectedNode) && step == 0) { color = ChromGraphItem.ColorSelected; isSelected = true; } else { color = COLORS_TRANSITION[(iColor + colorOffset) % COLORS_TRANSITION.Count]; } iColor++; string label = graphData.DocNodeLabels[i]; if (step != 0) { label = string.Format(Resources.RTReplicateGraphPane_UpdateGraph_Step__0__, step); } CurveItem curveItem; if (IsMultiSelect) { if (rtValue != RTPeptideValue.All) { curveItem = CreateLineItem(label, pointPairList, color); } else { curveItem = CreateMultiSelectBarItem(label, pointPairList, color); } } else if (HiLowMiddleErrorBarItem.IsHiLoMiddleErrorList(pointPairList)) { curveItem = new HiLowMiddleErrorBarItem(label, pointPairList, color, Color.Black); BarSettings.Type = BarType.Cluster; } else if (rtValue == RTPeptideValue.All) { curveItem = new MeanErrorBarItem(label, pointPairList, color, Color.Black); BarSettings.Type = BarType.Cluster; } else { curveItem = CreateLineItem(label, pointPairList, color); } if (curveItem != null) { curveItem.Tag = identityPath; var barItem = curveItem as BarItem; if (barItem != null) { barItem.Bar.Border.IsVisible = false; barItem.Bar.Fill.Brush = GetBrushForNode(docNode, color); if (!isSelected) { barItem.SortedOverlayPriority = 1; } } CurveList.Add(curveItem); if (selectedReplicateIndex != -1 && selectedReplicateIndex < pointPairList.Count) { PointPair pointPair = pointPairList[selectedReplicateIndex]; if (!pointPair.IsInvalid) { minRetentionTime = Math.Min(minRetentionTime, pointPair.Z); maxRetentionTime = Math.Max(maxRetentionTime, pointPair.Y); } } } } } // Draw a box around the currently selected replicate if (ShowSelection && minRetentionTime != double.MaxValue) { AddSelection(selectedReplicateIndex, maxRetentionTime, minRetentionTime); } // Reset the scale when the parent node changes if (_parentNode == null || !ReferenceEquals(_parentNode.Id, parentNode.Id)) { XAxis.Scale.MaxAuto = XAxis.Scale.MinAuto = true; YAxis.Scale.MaxAuto = YAxis.Scale.MinAuto = true; } _parentNode = parentNode; Legend.IsVisible = !IsMultiSelect && Settings.Default.ShowRetentionTimesLegend; GraphSummary.GraphControl.Invalidate(); AxisChange(); }
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 static PointPair RTPointPairMissing(int xValue) { return(HiLowMiddleErrorBarItem.MakePointPair(xValue, PointPairBase.Missing, PointPairBase.Missing, PointPairBase.Missing, 0)); }
public override void UpdateGraph(bool checkData) { SrmDocument document = GraphSummary.DocumentUIContainer.DocumentUI; var results = document.Settings.MeasuredResults; bool resultsAvailable = results != null; Clear(); if (!resultsAvailable) { Title.Text = Resources.RTReplicateGraphPane_UpdateGraph_No_results_available; EmptyGraph(document); return; } var selectedTreeNode = GraphSummary.StateProvider.SelectedNode as SrmTreeNode; if (selectedTreeNode == null || document.FindNode(selectedTreeNode.Path) == null) { EmptyGraph(document); return; } Title.Text = null; DisplayTypeChrom displayType = GraphChromatogram.GetDisplayType(document, selectedTreeNode); DocNode selectedNode = selectedTreeNode.Model; DocNode parentNode = selectedNode; IdentityPath identityPath = selectedTreeNode.Path; // If the selected tree node is a transition, then its siblings are displayed. if (selectedTreeNode is TransitionTreeNode) { if (displayType != DisplayTypeChrom.single) { SrmTreeNode parentTreeNode = selectedTreeNode.SrmParent; parentNode = parentTreeNode.Model; identityPath = parentTreeNode.Path; } } // If the selected node is a peptide with one child, then show the children, // unless chromatogram display type is total else if (selectedTreeNode is PeptideTreeNode) { var children = ((DocNodeParent)selectedNode).Children; if (children.Count == 1 && displayType != DisplayTypeChrom.total) { selectedNode = parentNode = children[0]; identityPath = new IdentityPath(identityPath, parentNode.Id); } } else if (!(selectedTreeNode is TransitionGroupTreeNode)) { Title.Text = Resources.RTReplicateGraphPane_UpdateGraph_Select_a_peptide_to_see_the_retention_time_graph; CanShowRTLegend = false; return; } // If a precursor is going to be displayed with display type single if (parentNode is TransitionGroupDocNode && displayType == DisplayTypeChrom.single) { // If no optimization data, then show all the transitions if (!results.Chromatograms.Contains(chrom => chrom.OptimizationFunction != null)) { displayType = DisplayTypeChrom.all; } } var rtTransformOp = GraphSummary.StateProvider.GetRetentionTimeTransformOperation(); var rtValue = RTPeptideGraphPane.RTValue; GraphValues.ReplicateGroupOp replicateGroupOp; if (rtValue == RTPeptideValue.All) { replicateGroupOp = GraphValues.ReplicateGroupOp.FromCurrentSettings(document.Settings, GraphValues.AggregateOp.MEAN); } else { replicateGroupOp = GraphValues.ReplicateGroupOp.FromCurrentSettings(document.Settings); } var retentionTimeValue = new GraphValues.RetentionTimeTransform(rtValue, rtTransformOp, replicateGroupOp.AggregateOp); YAxis.Title.Text = retentionTimeValue.GetAxisTitle(); GraphData graphData = new RTGraphData(document, parentNode, displayType, retentionTimeValue, replicateGroupOp); CanShowRTLegend = graphData.DocNodes.Count != 0; InitFromData(graphData); int selectedReplicateIndex = SelectedIndex; double minRetentionTime = double.MaxValue; double maxRetentionTime = -double.MaxValue; int iColor = 0, iCharge = -1; int? charge = null; int countLabelTypes = document.Settings.PeptideSettings.Modifications.CountLabelTypes; int colorOffset = 0; var transitionGroupDocNode = parentNode as TransitionGroupDocNode; if (transitionGroupDocNode != null && displayType == DisplayTypeChrom.products) { // If we are only displaying product ions, we want to use an offset in the colors array // so that we do not re-use colors that would be used for any precursor ions. colorOffset = GraphChromatogram.GetDisplayTransitions(transitionGroupDocNode, DisplayTypeChrom.precursors).Count(); } for (int i = 0; i < graphData.DocNodes.Count; i++) { var docNode = graphData.DocNodes[i]; var pointPairLists = graphData.PointPairLists[i]; int numSteps = pointPairLists.Count / 2; for (int iStep = 0; iStep < pointPairLists.Count; iStep++) { int step = iStep - numSteps; var pointPairList = pointPairLists[iStep]; Color color; var nodeGroup = docNode as TransitionGroupDocNode; if (parentNode is PeptideDocNode) { // Resharper code inspection v9.0 on TC gets this one wrong // ReSharper disable ExpressionIsAlwaysNull int iColorGroup = GetColorIndex(nodeGroup, countLabelTypes, ref charge, ref iCharge); // ReSharper restore ExpressionIsAlwaysNull color = COLORS_GROUPS[iColorGroup % COLORS_GROUPS.Length]; } else if (displayType == DisplayTypeChrom.total) { color = COLORS_GROUPS[iColor % COLORS_GROUPS.Length]; } else if (docNode.Equals(selectedNode) && step == 0) { color = ChromGraphItem.ColorSelected; } else { color = COLORS_TRANSITION[(iColor + colorOffset) % COLORS_TRANSITION.Length]; } iColor++; string label = graphData.DocNodeLabels[i]; if (step != 0) { label = string.Format(Resources.RTReplicateGraphPane_UpdateGraph_Step__0__, step); } BarItem curveItem; if (HiLowMiddleErrorBarItem.IsHiLoMiddleErrorList(pointPairList)) { curveItem = new HiLowMiddleErrorBarItem(label, pointPairList, color, Color.Black); } else { curveItem = new MeanErrorBarItem(label, pointPairList, color, Color.Black); } if (selectedReplicateIndex != -1 && selectedReplicateIndex < pointPairList.Count) { PointPair pointPair = pointPairList[selectedReplicateIndex]; if (!pointPair.IsInvalid) { minRetentionTime = Math.Min(minRetentionTime, pointPair.Z); maxRetentionTime = Math.Max(maxRetentionTime, pointPair.Y); } } curveItem.Bar.Border.IsVisible = false; curveItem.Bar.Fill.Brush = new SolidBrush(color); curveItem.Tag = new IdentityPath(identityPath, docNode.Id); CurveList.Add(curveItem); } } // Draw a box around the currently selected replicate if (ShowSelection && minRetentionTime != double.MaxValue) { GraphObjList.Add(new BoxObj(selectedReplicateIndex + .5, maxRetentionTime, 1, maxRetentionTime - minRetentionTime, Color.Black, Color.Empty) { IsClippedToChartRect = true, }); } // Reset the scale when the parent node changes if (_parentNode == null || !ReferenceEquals(_parentNode.Id, parentNode.Id)) { XAxis.Scale.MaxAuto = XAxis.Scale.MinAuto = true; YAxis.Scale.MaxAuto = YAxis.Scale.MinAuto = true; } _parentNode = parentNode; Legend.IsVisible = Settings.Default.ShowRetentionTimesLegend; AxisChange(); }
public override void UpdateGraph(bool checkData) { Clear(); TransitionGroupDocNode selectedGroup = null; PeptideGroupDocNode selectedProtein = null; var selectedTreeNode = GraphSummary.StateProvider.SelectedNode as SrmTreeNode; if (selectedTreeNode != null) { if (selectedTreeNode is TransitionTreeNode) selectedGroup = (TransitionGroupDocNode)selectedTreeNode.SrmParent.Model; else if (selectedTreeNode is TransitionGroupTreeNode) selectedGroup = (TransitionGroupDocNode)selectedTreeNode.Model; else { var node = selectedTreeNode as PeptideTreeNode; if (node != null) { var nodePep = node.DocNode; selectedGroup = nodePep.TransitionGroups.FirstOrDefault(); } } var proteinTreeNode = selectedTreeNode.GetNodeOfType<PeptideGroupTreeNode>(); if (proteinTreeNode != null) selectedProtein = proteinTreeNode.DocNode; } SrmDocument document = GraphSummary.DocumentUIContainer.DocumentUI; var displayType = GraphChromatogram.GetDisplayType(document, selectedTreeNode); _graphData = CreateGraphData(document, selectedProtein, selectedGroup, displayType); int iColor = 0; int colorOffset = 0; if(selectedGroup != null && displayType == DisplayTypeChrom.products) { // If we are only displaying product ions, we want to use an offset in the colors array // so that we do not re-use colors that would be used for any precursor ions. colorOffset = GraphChromatogram.GetDisplayTransitions(selectedGroup, DisplayTypeChrom.precursors).Count(); } foreach (var pointPairList in _graphData.PointPairLists) { Color color = displayType == DisplayTypeChrom.total ? COLORS_GROUPS[iColor++ % COLORS_GROUPS.Length] : COLORS_TRANSITION[(iColor++ + colorOffset)% COLORS_TRANSITION.Length]; BarItem curveItem; if (HiLowMiddleErrorBarItem.IsHiLoMiddleErrorList(pointPairList)) curveItem = new HiLowMiddleErrorBarItem(string.Empty, pointPairList, color, Color.Black); else curveItem = new MeanErrorBarItem(string.Empty, pointPairList, color, Color.Black); curveItem.Bar.Border.IsVisible = false; curveItem.Bar.Fill.Brush = new SolidBrush(color); CurveList.Add(curveItem); } if (ShowSelection && SelectedIndex != -1) { double yValue = _graphData.SelectedMaxY; double yMin = _graphData.SelectedMinY; GraphObjList.Add(new BoxObj(SelectedIndex + .5, yValue, 0.99, yValue - yMin, Color.Black, Color.Empty) { IsClippedToChartRect = true, }); } UpdateAxes(); }