private static PointPair CreatePointPair(int iGroup, ICollection <double> listValues, ref double maxY, ref double minY)
{
if (listValues.Count == 0)
{
return(PointPairMissing(iGroup));
}
var statValues = new Statistics(listValues);
PointPair pointPair;
if (Settings.Default.ShowPeptideCV)
{
double cvRatio = statValues.StdDev() / statValues.Mean();
if (!Settings.Default.PeakDecimalCv)
{
cvRatio *= 100;
}
pointPair = MeanErrorBarItem.MakePointPair(iGroup, cvRatio, 0);
}
else
{
pointPair = MeanErrorBarItem.MakePointPair(iGroup, statValues.Mean(), statValues.StdDev());
}
maxY = Math.Max(maxY, MeanErrorBarItem.GetYTotal(pointPair));
minY = Math.Min(minY, MeanErrorBarItem.GetYMin(pointPair));
return(pointPair);
}
public PointPair MakeBarValue(double xValue, IEnumerable <double> values)
{
var statValues = new Statistics(values);
if (Cv)
{
var cv = statValues.StdDev() / statValues.Mean();
return(MeanErrorBarItem.MakePointPair(xValue, CvDecimal ? cv : cv *100, 0));
}
return(MeanErrorBarItem.MakePointPair(xValue, statValues.Mean(), statValues.StdDev()));
}
private void UpdateGraph()
{
if (!IsHandleCreated)
{
return;
}
zedGraphControl.GraphPane.GraphObjList.Clear();
zedGraphControl.GraphPane.CurveList.Clear();
_barGraph = null;
_rows = null;
var points = new PointPairList();
var groupComparisonModel = FoldChangeBindingSource.GroupComparisonModel;
var groupComparisonDef = groupComparisonModel.GroupComparisonDef;
var document = groupComparisonModel.Document;
var sequences = new List<Tuple<string, bool>>();
foreach (var nodePep in document.Molecules)
sequences.Add(new Tuple<string, bool>(nodePep.RawTextId, nodePep.IsProteomic));
var uniquePrefixGenerator = new UniquePrefixGenerator(sequences, 3);
var textLabels = new List<string>();
var rows = _bindingListSource.OfType<RowItem>()
.Select(rowItem => rowItem.Value)
.OfType<FoldChangeBindingSource.FoldChangeRow>()
.ToArray();
bool showLabelType = rows.Select(row => row.IsotopeLabelType).Distinct().Count() > 1;
bool showMsLevel = rows.Select(row => row.MsLevel).Distinct().Count() > 1;
bool showGroup = rows.Select(row => row.Group).Distinct().Count() > 1;
foreach (var row in rows)
{
var foldChangeResult = row.FoldChangeResult;
double error = Math.Log(foldChangeResult.MaxFoldChange/foldChangeResult.FoldChange, 2.0);
var point = MeanErrorBarItem.MakePointPair(points.Count, foldChangeResult.Log2FoldChange, error);
points.Add(point);
string label;
if (null != row.Peptide)
{
label = uniquePrefixGenerator.GetUniquePrefix(row.Peptide.GetDocNode().RawTextId, row.Peptide.GetDocNode().IsProteomic);
}
else
{
label = row.Protein.Name;
}
if (showMsLevel && row.MsLevel.HasValue)
{
label += " MS" + row.MsLevel; // Not L10N;
}
if (showLabelType && row.IsotopeLabelType != null)
{
label += " (" + row.IsotopeLabelType.Title + ")"; // Not L10N
}
if (showGroup && !Equals(row.Group, default(GroupIdentifier)))
{
label += " " + row.Group; // Not L10N
}
textLabels.Add(label);
if (IsSelected(row))
{
double y, height;
if (foldChangeResult.Log2FoldChange >= 0)
{
y = foldChangeResult.Log2FoldChange + error;
height = y;
}
else
{
y = 0;
height = error - foldChangeResult.Log2FoldChange;
}
zedGraphControl.GraphPane.GraphObjList.Add(new BoxObj(point.X + .5, y, .99, height)
{
ZOrder = ZOrder.E_BehindCurves,
IsClippedToChartRect = true
});
}
}
zedGraphControl.GraphPane.XAxis.Title.Text = groupComparisonDef.PerProtein ? GroupComparisonStrings.FoldChangeBarGraph_UpdateGraph_Protein : GroupComparisonStrings.FoldChangeBarGraph_UpdateGraph_Peptide;
zedGraphControl.GraphPane.YAxis.Title.Text = GroupComparisonStrings.FoldChangeBarGraph_UpdateGraph_Log_2_Fold_Change;
var barGraph = new MeanErrorBarItem(null, points, Color.Black, Color.Blue);
zedGraphControl.GraphPane.CurveList.Add(barGraph);
zedGraphControl.GraphPane.XAxis.Type = AxisType.Text;
zedGraphControl.GraphPane.XAxis.Scale.TextLabels = textLabels.ToArray();
_axisLabelScaler.ScaleAxisLabels();
zedGraphControl.GraphPane.AxisChange();
zedGraphControl.Invalidate();
_barGraph = barGraph;
_rows = rows;
}
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();
}
protected static PointPair PointPairMissing(int iGroup)
{
return(MeanErrorBarItem.MakePointPair(iGroup, PointPairBase.Missing, PointPairBase.Missing));
}
public override void UpdateGraph(bool checkData)
{
_dotpLabels = new GraphObjList();
SrmDocument document = GraphSummary.DocumentUIContainer.DocumentUI;
var results = document.Settings.MeasuredResults;
bool resultsAvailable = results != null;
Clear();
if (!resultsAvailable)
{
Title.Text = Resources.AreaReplicateGraphPane_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;
}
BarSettings.Type = BarType;
Title.Text = null;
DisplayTypeChrom displayType;
if (Equals(PaneKey, PaneKey.PRECURSORS))
{
displayType = DisplayTypeChrom.precursors;
}
else if (Equals(PaneKey, PaneKey.PRODUCTS))
{
displayType = DisplayTypeChrom.products;
}
else
{
displayType = GraphChromatogram.GetDisplayType(document, selectedTreeNode);
}
DocNode selectedNode = selectedTreeNode.Model;
DocNode parentNode = selectedNode;
IdentityPath identityPath = selectedTreeNode.Path;
bool optimizationPresent = results.Chromatograms.Contains(
chrom => chrom.OptimizationFunction != null);
// If the selected tree node is a transition, then its siblings are displayed.
if (selectedTreeNode is TransitionTreeNode)
{
if (displayType == DisplayTypeChrom.single)
{
BarSettings.Type = BarType.Cluster;
}
else
{
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 = ((PeptideDocNode)selectedNode).TransitionGroups
.Where(PaneKey.IncludesTransitionGroup)
.ToArray();
if (children.Length == 1 && displayType != DisplayTypeChrom.total)
{
selectedNode = parentNode = children[0];
identityPath = new IdentityPath(identityPath, parentNode.Id);
}
else
{
BarSettings.Type = BarType.Cluster;
}
}
else if (!(selectedTreeNode is TransitionGroupTreeNode))
{
Title.Text = Resources.AreaReplicateGraphPane_UpdateGraph_Select_a_peptide_to_see_the_peak_area_graph;
CanShowPeakAreaLegend = false;
CanShowDotProduct = false;
return;
}
var parentGroupNode = parentNode as TransitionGroupDocNode;
// If a precursor is going to be displayed with display type single
if (parentGroupNode != null && displayType == DisplayTypeChrom.single)
{
// If no optimization data, then show all the transitions
if (!optimizationPresent)
{
displayType = DisplayTypeChrom.all;
}
// Otherwise, do not stack the bars
else
{
BarSettings.Type = BarType.Cluster;
}
}
int ratioIndex = AreaGraphData.RATIO_INDEX_NONE;
var standardType = IsotopeLabelType.light;
var areaView = AreaGraphController.AreaView;
if (areaView == AreaNormalizeToView.area_ratio_view)
{
ratioIndex = GraphSummary.RatioIndex;
standardType = document.Settings.PeptideSettings.Modifications.RatioInternalStandardTypes[ratioIndex];
}
else if (areaView == AreaNormalizeToView.area_global_standard_view)
{
if (document.Settings.HasGlobalStandardArea)
{
ratioIndex = ChromInfo.RATIO_INDEX_GLOBAL_STANDARDS;
}
else
{
areaView = AreaNormalizeToView.none;
}
}
// Sets normalizeData to optimization, maximum_stack, maximum, total, or none
AreaNormalizeToData normalizeData;
if (optimizationPresent && displayType == DisplayTypeChrom.single &&
areaView == AreaNormalizeToView.area_percent_view)
{
normalizeData = AreaNormalizeToData.optimization;
}
else if (areaView == AreaNormalizeToView.area_maximum_view)
{
normalizeData = BarSettings.Type == BarType.Stack
? AreaNormalizeToData.maximum_stack
: AreaNormalizeToData.maximum;
}
else if (BarSettings.Type == BarType.PercentStack)
{
normalizeData = AreaNormalizeToData.total;
}
else
{
normalizeData = AreaNormalizeToData.none;
}
// Calculate graph data points
// IsExpectedVisible depends on ExpectedVisible
ExpectedVisible = AreaExpectedValue.none;
if (parentGroupNode != null &&
displayType != DisplayTypeChrom.total &&
areaView != AreaNormalizeToView.area_ratio_view &&
!(optimizationPresent && displayType == DisplayTypeChrom.single))
{
var displayTrans = GraphChromatogram.GetDisplayTransitions(parentGroupNode, displayType).ToArray();
bool isShowingMs = displayTrans.Any(nodeTran => nodeTran.IsMs1);
bool isShowingMsMs = displayTrans.Any(nodeTran => !nodeTran.IsMs1);
bool isFullScanMs = document.Settings.TransitionSettings.FullScan.IsEnabledMs && isShowingMs;
if (isFullScanMs)
{
if (!isShowingMsMs && parentGroupNode.HasIsotopeDist)
{
ExpectedVisible = AreaExpectedValue.isotope_dist;
}
}
else
{
if (parentGroupNode.HasLibInfo)
{
ExpectedVisible = AreaExpectedValue.library;
}
}
}
var expectedValue = IsExpectedVisible ? ExpectedVisible : AreaExpectedValue.none;
var replicateGroupOp = GraphValues.ReplicateGroupOp.FromCurrentSettings(document.Settings);
var graphData = new AreaGraphData(document,
parentNode,
displayType,
replicateGroupOp,
ratioIndex,
normalizeData,
expectedValue,
PaneKey);
var aggregateOp = replicateGroupOp.AggregateOp;
// Avoid stacking CVs
if (aggregateOp.Cv || aggregateOp.CvDecimal)
{
BarSettings.Type = BarType.Cluster;
}
int countNodes = graphData.DocNodes.Count;
if (countNodes == 0)
{
ExpectedVisible = AreaExpectedValue.none;
}
CanShowDotProduct = ExpectedVisible != AreaExpectedValue.none &&
areaView != AreaNormalizeToView.area_percent_view;
CanShowPeakAreaLegend = countNodes != 0;
InitFromData(graphData);
// Add data to the graph
int selectedReplicateIndex = SelectedIndex;
if (IsExpectedVisible)
{
if (GraphSummary.ActiveLibrary)
{
selectedReplicateIndex = 0;
}
}
double maxArea = -double.MaxValue;
double sumArea = 0;
// An array to keep track of height of all bars to determine
// where each dot product annotation (if showing) should be placed
var sumAreas = new double[graphData.ReplicateGroups.Count];
// If only one bar to show, then use cluster instead of stack bar type, since nothing to stack
// Important for mean error bar checking below
if (BarSettings.Type == BarType.Stack && countNodes == 1 && graphData.PointPairLists[0].Count == 1)
{
BarSettings.Type = BarType.Cluster;
}
int colorOffset = 0;
if (parentGroupNode != null)
{
// 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 = GraphChromatogram.GetDisplayType(document, selectedTreeNode);
if (displayType == DisplayTypeChrom.products &&
(nodeDisplayType != DisplayTypeChrom.single ||
(nodeDisplayType == DisplayTypeChrom.single && !optimizationPresent)))
{
colorOffset =
GraphChromatogram.GetDisplayTransitions(parentGroupNode, DisplayTypeChrom.precursors).Count();
}
}
int iColor = 0, iCharge = -1;
int?charge = null;
int countLabelTypes = document.Settings.PeptideSettings.Modifications.CountLabelTypes;
for (int i = 0; i < countNodes; 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)
{
int iColorGroup = GetColorIndex(nodeGroup, countLabelTypes, ref charge, ref iCharge);
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++;
// If showing ratios, do not add the standard type to the graph,
// since it will always be empty, but make sure the colors still
// correspond with the other graphs.
if (nodeGroup != null && ratioIndex >= 0)
{
var labelType = nodeGroup.TransitionGroup.LabelType;
if (ReferenceEquals(labelType, standardType))
{
continue;
}
}
string label = graphData.DocNodeLabels[i];
if (step != 0)
{
label = string.Format(Resources.AreaReplicateGraphPane_UpdateGraph_Step__0_, step);
}
BarItem curveItem;
// Only use a MeanErrorBarItem if bars are not going to be stacked.
// TODO(nicksh): AreaGraphData.NormalizeTo does not know about MeanErrorBarItem
if (BarSettings.Type != BarType.Stack && BarSettings.Type != BarType.PercentStack && normalizeData == AreaNormalizeToData.none)
{
curveItem = new MeanErrorBarItem(label, pointPairList, color, Color.Black);
}
else
{
curveItem = new BarItem(label, pointPairList, color);
}
if (0 <= selectedReplicateIndex && selectedReplicateIndex < pointPairList.Count)
{
PointPair pointPair = pointPairList[selectedReplicateIndex];
if (!pointPair.IsInvalid)
{
sumArea += pointPair.Y;
maxArea = Math.Max(maxArea, pointPair.Y);
}
}
// Add area for this transition to each area entry
AddAreasToSums(pointPairList, sumAreas);
curveItem.Bar.Border.IsVisible = false;
curveItem.Bar.Fill.Brush = new SolidBrush(color);
curveItem.Tag = new IdentityPath(identityPath, docNode.Id);
CurveList.Add(curveItem);
}
}
ParentGroupNode = parentGroupNode;
SumAreas = sumAreas;
// Draw a box around the currently selected replicate
if (ShowSelection && maxArea > -double.MaxValue)
{
double yValue;
switch (BarSettings.Type)
{
case BarType.Stack:
// The Math.Min(sumArea, .999) makes sure that if graph is in normalized view
// height of the selection rectangle does not exceed 1, so that top of the rectangle
// can be viewed when y-axis scale maximum is at 1
yValue = (areaView == AreaNormalizeToView.area_maximum_view ? Math.Min(sumArea, .999) : sumArea);
break;
case BarType.PercentStack:
yValue = 99.99;
break;
default:
// Scale the selection box to fit exactly the bar height
yValue = (areaView == AreaNormalizeToView.area_maximum_view ? Math.Min(maxArea, .999) : maxArea);
break;
}
GraphObjList.Add(new BoxObj(selectedReplicateIndex + .5, yValue, 0.99,
yValue, Color.Black, Color.Empty)
{
IsClippedToChartRect = true,
});
}
// Reset the scale when the parent node changes
bool resetAxes = (_parentNode == null || !ReferenceEquals(_parentNode.Id, parentNode.Id));
_parentNode = parentNode;
UpdateAxes(resetAxes, aggregateOp, normalizeData, areaView, standardType);
}
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();
}
public LineErrorBarItem(String label,
double[] xValues, double[] yValues, double[] errorValues,
Color color, Color errorColor)
: this(label, MeanErrorBarItem.MakePointPairList(xValues, yValues, errorValues), color, errorColor)
{
}
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)
{
_dotpLabels = new GraphObjList();
SrmDocument document = GraphSummary.DocumentUIContainer.DocumentUI;
var results = document.Settings.MeasuredResults;
bool resultsAvailable = results != null;
Clear();
if (!resultsAvailable)
{
Title.Text = Resources.AreaReplicateGraphPane_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;
}
BarSettings.Type = BarType;
Title.Text = null;
DisplayTypeChrom displayType;
if (Equals(PaneKey, PaneKey.PRECURSORS))
{
displayType = DisplayTypeChrom.precursors;
}
else if (Equals(PaneKey, PaneKey.PRODUCTS))
{
displayType = DisplayTypeChrom.products;
}
else
{
displayType = GraphChromatogram.GetDisplayType(document, selectedTreeNode);
}
DocNode selectedNode = selectedTreeNode.Model;
DocNode parentNode = selectedNode;
IdentityPath identityPath = selectedTreeNode.Path;
bool optimizationPresent = results.Chromatograms.Contains(
chrom => chrom.OptimizationFunction != null);
// If the selected tree node is a transition, then its siblings are displayed.
if (selectedTreeNode is TransitionTreeNode)
{
if (displayType == DisplayTypeChrom.single)
{
BarSettings.Type = BarType.Cluster;
}
else
{
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 = ((PeptideDocNode) selectedNode).TransitionGroups
.Where(PaneKey.IncludesTransitionGroup)
.ToArray();
if (children.Length == 1 && displayType != DisplayTypeChrom.total)
{
selectedNode = parentNode = children[0];
identityPath = new IdentityPath(identityPath, parentNode.Id);
}
else
{
BarSettings.Type = BarType.Cluster;
}
}
else if (!(selectedTreeNode is TransitionGroupTreeNode))
{
Title.Text = Resources.AreaReplicateGraphPane_UpdateGraph_Select_a_peptide_to_see_the_peak_area_graph;
CanShowPeakAreaLegend = false;
CanShowDotProduct = false;
return;
}
var parentGroupNode = parentNode as TransitionGroupDocNode;
// If a precursor is going to be displayed with display type single
if (parentGroupNode != null && displayType == DisplayTypeChrom.single)
{
// If no optimization data, then show all the transitions
if (!optimizationPresent)
displayType = DisplayTypeChrom.all;
// Otherwise, do not stack the bars
else
BarSettings.Type = BarType.Cluster;
}
int ratioIndex = AreaGraphData.RATIO_INDEX_NONE;
var standardType = IsotopeLabelType.light;
var areaView = AreaGraphController.AreaView;
if (areaView == AreaNormalizeToView.area_ratio_view)
{
ratioIndex = GraphSummary.RatioIndex;
standardType = document.Settings.PeptideSettings.Modifications.RatioInternalStandardTypes[ratioIndex];
}
else if (areaView == AreaNormalizeToView.area_global_standard_view)
{
if (document.Settings.HasGlobalStandardArea)
ratioIndex = ChromInfo.RATIO_INDEX_GLOBAL_STANDARDS;
else
areaView = AreaNormalizeToView.none;
}
// Sets normalizeData to optimization, maximum_stack, maximum, total, or none
AreaNormalizeToData normalizeData;
if (optimizationPresent && displayType == DisplayTypeChrom.single &&
areaView == AreaNormalizeToView.area_percent_view)
{
normalizeData = AreaNormalizeToData.optimization;
}
else if (areaView == AreaNormalizeToView.area_maximum_view)
{
normalizeData = BarSettings.Type == BarType.Stack
? AreaNormalizeToData.maximum_stack
: AreaNormalizeToData.maximum;
}
else if (BarSettings.Type == BarType.PercentStack)
{
normalizeData = AreaNormalizeToData.total;
}
else
{
normalizeData = AreaNormalizeToData.none;
}
// Calculate graph data points
// IsExpectedVisible depends on ExpectedVisible
ExpectedVisible = AreaExpectedValue.none;
if (parentGroupNode != null &&
displayType != DisplayTypeChrom.total &&
areaView != AreaNormalizeToView.area_ratio_view &&
!(optimizationPresent && displayType == DisplayTypeChrom.single))
{
var displayTrans = GraphChromatogram.GetDisplayTransitions(parentGroupNode, displayType).ToArray();
bool isShowingMs = displayTrans.Any(nodeTran => nodeTran.IsMs1);
bool isShowingMsMs = displayTrans.Any(nodeTran => !nodeTran.IsMs1);
bool isFullScanMs = document.Settings.TransitionSettings.FullScan.IsEnabledMs && isShowingMs;
if (isFullScanMs)
{
if (!isShowingMsMs && parentGroupNode.HasIsotopeDist)
ExpectedVisible = AreaExpectedValue.isotope_dist;
}
else
{
if (parentGroupNode.HasLibInfo)
ExpectedVisible = AreaExpectedValue.library;
}
}
var expectedValue = IsExpectedVisible ? ExpectedVisible : AreaExpectedValue.none;
var replicateGroupOp = GraphValues.ReplicateGroupOp.FromCurrentSettings(document.Settings);
var graphData = new AreaGraphData(document,
parentNode,
displayType,
replicateGroupOp,
ratioIndex,
normalizeData,
expectedValue,
PaneKey);
var aggregateOp = replicateGroupOp.AggregateOp;
// Avoid stacking CVs
if (aggregateOp.Cv || aggregateOp.CvDecimal)
BarSettings.Type = BarType.Cluster;
int countNodes = graphData.DocNodes.Count;
if (countNodes == 0)
ExpectedVisible = AreaExpectedValue.none;
CanShowDotProduct = ExpectedVisible != AreaExpectedValue.none &&
areaView != AreaNormalizeToView.area_percent_view;
CanShowPeakAreaLegend = countNodes != 0;
InitFromData(graphData);
// Add data to the graph
int selectedReplicateIndex = SelectedIndex;
if (IsExpectedVisible)
{
if (GraphSummary.ActiveLibrary)
selectedReplicateIndex = 0;
}
double maxArea = -double.MaxValue;
double sumArea = 0;
// An array to keep track of height of all bars to determine
// where each dot product annotation (if showing) should be placed
var sumAreas = new double[graphData.ReplicateGroups.Count];
// If only one bar to show, then use cluster instead of stack bar type, since nothing to stack
// Important for mean error bar checking below
if (BarSettings.Type == BarType.Stack && countNodes == 1 && graphData.PointPairLists[0].Count == 1)
BarSettings.Type = BarType.Cluster;
int colorOffset = 0;
if(parentGroupNode != null)
{
// 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 = GraphChromatogram.GetDisplayType(document, selectedTreeNode);
if (displayType == DisplayTypeChrom.products &&
(nodeDisplayType != DisplayTypeChrom.single ||
(nodeDisplayType == DisplayTypeChrom.single && !optimizationPresent)))
{
colorOffset =
GraphChromatogram.GetDisplayTransitions(parentGroupNode, DisplayTypeChrom.precursors).Count();
}
}
int iColor = 0, iCharge = -1;
int? charge = null;
int countLabelTypes = document.Settings.PeptideSettings.Modifications.CountLabelTypes;
for (int i = 0; i < countNodes; 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)
{
int iColorGroup = GetColorIndex(nodeGroup, countLabelTypes, ref charge, ref iCharge);
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++;
// If showing ratios, do not add the standard type to the graph,
// since it will always be empty, but make sure the colors still
// correspond with the other graphs.
if (nodeGroup != null && ratioIndex >= 0)
{
var labelType = nodeGroup.TransitionGroup.LabelType;
if (ReferenceEquals(labelType, standardType))
continue;
}
string label = graphData.DocNodeLabels[i];
if (step != 0)
label = string.Format(Resources.AreaReplicateGraphPane_UpdateGraph_Step__0_, step);
BarItem curveItem;
// Only use a MeanErrorBarItem if bars are not going to be stacked.
// TODO(nicksh): AreaGraphData.NormalizeTo does not know about MeanErrorBarItem
if (BarSettings.Type != BarType.Stack && BarSettings.Type != BarType.PercentStack && normalizeData == AreaNormalizeToData.none)
{
curveItem = new MeanErrorBarItem(label, pointPairList, color, Color.Black);
}
else
{
curveItem = new BarItem(label, pointPairList, color);
}
if (0 <= selectedReplicateIndex && selectedReplicateIndex < pointPairList.Count)
{
PointPair pointPair = pointPairList[selectedReplicateIndex];
if (!pointPair.IsInvalid)
{
sumArea += pointPair.Y;
maxArea = Math.Max(maxArea, pointPair.Y);
}
}
// Add area for this transition to each area entry
AddAreasToSums(pointPairList, sumAreas);
curveItem.Bar.Border.IsVisible = false;
curveItem.Bar.Fill.Brush = new SolidBrush(color);
curveItem.Tag = new IdentityPath(identityPath, docNode.Id);
CurveList.Add(curveItem);
}
}
ParentGroupNode = parentGroupNode;
SumAreas = sumAreas;
// Draw a box around the currently selected replicate
if (ShowSelection && maxArea > -double.MaxValue)
{
double yValue;
switch (BarSettings.Type)
{
case BarType.Stack:
// The Math.Min(sumArea, .999) makes sure that if graph is in normalized view
// height of the selection rectangle does not exceed 1, so that top of the rectangle
// can be viewed when y-axis scale maximum is at 1
yValue = (areaView == AreaNormalizeToView.area_maximum_view ? Math.Min(sumArea, .999) : sumArea);
break;
case BarType.PercentStack:
yValue = 99.99;
break;
default:
// Scale the selection box to fit exactly the bar height
yValue = (areaView == AreaNormalizeToView.area_maximum_view ? Math.Min(maxArea, .999) : maxArea);
break;
}
GraphObjList.Add(new BoxObj(selectedReplicateIndex + .5, yValue, 0.99,
yValue, Color.Black, Color.Empty)
{
IsClippedToChartRect = true,
});
}
// Reset the scale when the parent node changes
bool resetAxes = (_parentNode == null || !ReferenceEquals(_parentNode.Id, parentNode.Id));
_parentNode = parentNode;
UpdateAxes(resetAxes, aggregateOp, normalizeData, areaView, standardType);
}
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();
}
public override void UpdateGraph(bool selectionChanged)
{
CurveList.Clear();
GraphObjList.Clear();
SrmDocument document = GraphSummary.DocumentUIContainer.DocumentUI;
var selectedTreeNode = GraphSummary.StateProvider.SelectedNode as SrmTreeNode;
if (selectedTreeNode == null || document.FindNode(selectedTreeNode.Path) == null)
{
Title.Text = Helpers.PeptideToMoleculeTextMapper.Translate(Resources.MassErrorReplicateGraphPane_UpdateGraph_Select_a_peptide_to_see_the_mass_error_graph, document.DocumentType);
EmptyGraph(document);
return;
}
if (!document.Settings.HasResults)
{
Title.Text = Resources.AreaReplicateGraphPane_UpdateGraph_No_results_available;
EmptyGraph(document);
return;
}
DisplayTypeChrom displayType;
if (Equals(PaneKey, PaneKey.PRECURSORS))
{
displayType = DisplayTypeChrom.precursors;
}
else if (Equals(PaneKey, PaneKey.PRODUCTS))
{
displayType = DisplayTypeChrom.products;
}
else
{
displayType = GraphChromatogram.GetDisplayType(document, selectedTreeNode);
}
Title.Text = null;
var aggregateOp = GraphValues.AggregateOp.FromCurrentSettings();
YAxis.Title.Text = aggregateOp.Cv
? aggregateOp.AnnotateTitle(Resources.MassErrorReplicateGraphPane_UpdateGraph_Mass_Error_No_Ppm)
: Resources.MassErrorReplicateGraphPane_UpdateGraph_Mass_Error;
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 = ((PeptideDocNode)selectedNode).TransitionGroups
.Where(PaneKey.IncludesTransitionGroup)
.ToArray();
if (children.Length == 1 && displayType != DisplayTypeChrom.total)
{
selectedNode = parentNode = children[0];
identityPath = new IdentityPath(identityPath, parentNode.Id);
}
}
else if (!(selectedTreeNode is TransitionGroupTreeNode))
{
Title.Text = Helpers.PeptideToMoleculeTextMapper.Translate(Resources.MassErrorReplicateGraphPane_UpdateGraph_Select_a_peptide_to_see_the_mass_error_graph, document.DocumentType);
EmptyGraph(document);
CanShowMassErrorLegend = 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
displayType = DisplayTypeChrom.all;
}
var replicateGroupOp = ReplicateGroupOp.FromCurrentSettings(document.Settings);
GraphData graphData = new MassErrorGraphData(document,
identityPath,
displayType,
replicateGroupOp,
PaneKey);
CanShowMassErrorLegend = graphData.DocNodes.Count != 0;
InitFromData(graphData);
int selectedReplicateIndex = SelectedIndex;
double minRetentionTime = double.MaxValue;
double maxRetentionTime = double.MinValue;
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 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;
// ReSharper disable ExpressionIsAlwaysNull
var nodeGroup = docNode as TransitionGroupDocNode;
if (parentNode is PeptideDocNode)
{
int iColorGroup = GetColorIndex(nodeGroup, countLabelTypes, ref charge, ref iCharge);
color = COLORS_GROUPS[iColorGroup % COLORS_GROUPS.Count];
}
else if (displayType == DisplayTypeChrom.total)
{
color = COLORS_GROUPS[iColor % COLORS_GROUPS.Count];
}
else if (docNode.Equals(selectedNode) && step == 0)
{
color = ChromGraphItem.ColorSelected;
}
else
{
color = COLORS_TRANSITION[(iColor + colorOffset) % COLORS_TRANSITION.Count];
}
// ReSharper restore ExpressionIsAlwaysNull
iColor++;
string label = graphData.DocNodeLabels[i];
if (step != 0)
{
label = string.Format(Resources.RTReplicateGraphPane_UpdateGraph_Step__0__, step);
}
BarItem 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.Y);
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)
{
maxRetentionTime = Math.Max(maxRetentionTime, 0);
minRetentionTime = Math.Min(minRetentionTime, 0);
GraphObjList.Add(new BoxObj(selectedReplicateIndex + .5, maxRetentionTime, 1,
maxRetentionTime - minRetentionTime, Color.Black, Color.Empty)
{
IsClippedToChartRect = true,
});
}
XAxis.Scale.MinAuto = XAxis.Scale.MaxAuto = selectionChanged;
YAxis.Scale.MinAuto = YAxis.Scale.MaxAuto = true;
if (Settings.Default.MinMassError != 0)
{
YAxis.Scale.Min = Settings.Default.MinMassError;
}
if (Settings.Default.MaxMassError != 0)
{
YAxis.Scale.Max = Settings.Default.MaxMassError;
}
Legend.IsVisible = Settings.Default.ShowMassErrorLegend;
AxisChange();
}
