public override Value Evaluate(FSharpList<Value> args)
{
CurveList curves = new CurveList();
var input = (args[0] as Value.List).Item;
foreach (Value v in input)
{
Curve c = ((Value.Container)v).Item as Curve;
curves.Add(c);
}
_surface = Surface.by_patch(curves);
return Value.NewContainer(_surface);
}
// Revision: JCarpenter 10/06
/// <summary>
/// Find any objects that exist within the specified (screen) rectangle. This method will search through all of the graph objects, such as
/// <see cref="Axis"/>, <see cref="Legend"/>, <see cref="PaneBase.Title"/>,
/// <see cref="GraphObj"/>, and <see cref="CurveItem"/>. and see if the objects' bounding boxes are within the specified (screen) rectangle This method
/// returns true if any are found.
/// </summary>
/// <param name="rectF">
/// The rect F.
/// </param>
/// <param name="g">
/// The g.
/// </param>
/// <param name="containedObjs">
/// The contained Objs.
/// </param>
/// <returns>
/// The <see cref="bool"/>.
/// </returns>
public bool FindContainedObjects(RectangleF rectF, Graphics g, out CurveList containedObjs)
{
containedObjs = new CurveList();
foreach (CurveItem ci in this.CurveList)
{
for (int i = 0; i < ci.Points.Count; i++)
{
if (ci.Points[i].X > rectF.Left && ci.Points[i].X < rectF.Right && ci.Points[i].Y > rectF.Bottom && ci.Points[i].Y < rectF.Top)
{
containedObjs.Add(ci);
}
}
}
return containedObjs.Count > 0;
}
/// <summary>
/// Find the data point that lies closest to the specified mouse (screen) point for the specified curve.
/// </summary>
/// <remarks>
/// This method will search only through the points for the specified curve to determine which point is nearest the mouse point. It will only consider
/// points that are within
/// <see cref="Default.NearestTol"/> pixels of the screen point.
/// </remarks>
/// <param name="mousePt">
/// The screen point, in pixel coordinates.
/// </param>
/// <param name="targetCurve">
/// A <see cref="CurveItem"/> object containing the data points to be searched.
/// </param>
/// <param name="nearestCurve">
/// A reference to the <see cref="CurveItem"/>
/// instance that contains the closest point. nearestCurve will be null if no data points are available.
/// </param>
/// <param name="iNearest">
/// The index number of the closest point. The actual data vpoint will then be <see cref="CurveItem.Points">CurveItem.Points[iNearest]</see>
/// . iNearest will be -1 if no data points are available.
/// </param>
/// <returns>
/// true if a point was found and that point lies within
/// <see cref="Default.NearestTol"/> pixels of the screen point, false otherwise.
/// </returns>
public bool FindNearestPoint(PointF mousePt, CurveItem targetCurve, out CurveItem nearestCurve, out int iNearest)
{
CurveList targetCurveList = new CurveList();
targetCurveList.Add(targetCurve);
return this.FindNearestPoint(mousePt, targetCurveList, out nearestCurve, out iNearest);
}
/// <summary>
/// Forces a update of the scatter plot.
/// </summary>
///
public void UpdateGraph()
{
zedGraphControl.GraphPane.Title.Text = scatterplot.Title;
zedGraphControl.GraphPane.XAxis.Title.Text = Scatterplot.XAxisTitle;
zedGraphControl.GraphPane.YAxis.Title.Text = Scatterplot.YAxisTitle;
classes.Clear();
if (scatterplot.Classes != null)
{
if (scatterplot.Classes.Count == 0)
{
zedGraphControl.GraphPane.Legend.IsVisible = false;
// Create space for unlabelled data
PointPairList list = new PointPairList(scatterplot.XAxis, scatterplot.YAxis);
LineItem item = new LineItem(String.Empty, list, Color.Black, SymbolType.Default);
item.Line.IsVisible = LinesVisible;
item.Symbol.Border.IsVisible = false;
item.Symbol.Fill = new Fill(Color.Black);
if (SymbolSize == 0)
{
item.Symbol.IsVisible = false;
}
else
{
item.Symbol.Size = SymbolSize;
}
classes.Add(item);
}
else
{
zedGraphControl.GraphPane.Legend.IsVisible = true;
var colors = new ColorSequenceCollection(scatterplot.Classes.Count);
// Create a curve item for each of the labels
for (int i = 0; i < scatterplot.Classes.Count; i++)
{
// retrieve the x,y pairs for the label
double[] x = scatterplot.Classes[i].XAxis;
double[] y = scatterplot.Classes[i].YAxis;
PointPairList list = new PointPairList(x, y);
LineItem item = new LineItem(scatterplot.Classes[i].Text,
list, colors[i], SymbolType.Default);
item.Line.IsVisible = LinesVisible;
item.Symbol.Border.IsVisible = false;
item.Symbol.Fill = new Fill(colors[i]);
if (SymbolSize == 0)
{
item.Symbol.IsVisible = false;
}
else
{
item.Symbol.Size = SymbolSize;
}
classes.Add(item);
}
}
zedGraphControl.AxisChange();
zedGraphControl.Invalidate();
if (!ScaleTight)
{
zedGraphControl.ZoomPane(zedGraphControl.GraphPane, 1.1, PointF.Empty, false);
}
else
{
zedGraphControl.RestoreScale(zedGraphControl.GraphPane);
}
}
}
private void DisplayCalibrationCurve()
{
CalibrationCurveOptions options = Settings.Default.CalibrationCurveOptions;
zedGraphControl.GraphPane.YAxis.Type = zedGraphControl.GraphPane.XAxis.Type
= options.LogPlot ? AxisType.Log : AxisType.Linear;
zedGraphControl.GraphPane.Legend.IsVisible = options.ShowLegend;
_scatterPlots = null;
CalibrationCurve = null;
SrmDocument document = DocumentUiContainer.DocumentUI;
if (!document.Settings.HasResults)
{
zedGraphControl.GraphPane.Title.Text =
QuantificationStrings.CalibrationForm_DisplayCalibrationCurve_No_results_available;
return;
}
PeptideDocNode peptide = null;
PeptideGroupDocNode peptideGroup = null;
SequenceTree sequenceTree = _skylineWindow.SequenceTree;
if (null != sequenceTree)
{
PeptideTreeNode peptideTreeNode = sequenceTree.GetNodeOfType <PeptideTreeNode>();
if (null != peptideTreeNode)
{
peptide = peptideTreeNode.DocNode;
}
PeptideGroupTreeNode peptideGroupTreeNode = sequenceTree.GetNodeOfType <PeptideGroupTreeNode>();
if (null != peptideGroupTreeNode)
{
peptideGroup = peptideGroupTreeNode.DocNode;
}
}
if (null == peptide)
{
zedGraphControl.GraphPane.Title.Text =
QuantificationStrings
.CalibrationForm_DisplayCalibrationCurve_Select_a_peptide_to_see_its_calibration_curve;
return;
}
PeptideQuantifier peptideQuantifier = PeptideQuantifier.GetPeptideQuantifier(document.Settings, peptideGroup,
peptide);
CalibrationCurveFitter curveFitter = new CalibrationCurveFitter(peptideQuantifier, document.Settings);
if (peptideQuantifier.QuantificationSettings.RegressionFit == RegressionFit.NONE)
{
if (string.IsNullOrEmpty(
peptideQuantifier.QuantificationSettings.NormalizationMethod.IsotopeLabelTypeName))
{
zedGraphControl.GraphPane.Title.Text =
QuantificationStrings.CalibrationForm_DisplayCalibrationCurve_Use_the_Quantification_tab_on_the_Peptide_Settings_dialog_to_control_the_conversion_of_peak_areas_to_concentrations_;
}
else
{
if (!peptide.InternalStandardConcentration.HasValue)
{
zedGraphControl.GraphPane.Title.Text =
string.Format(QuantificationStrings.CalibrationForm_DisplayCalibrationCurve_To_convert_peak_area_ratios_to_concentrations__specify_the_internal_standard_concentration_for__0__, peptide);
}
else
{
zedGraphControl.GraphPane.Title.Text = null;
}
}
}
else
{
if (curveFitter.GetStandardConcentrations().Any())
{
zedGraphControl.GraphPane.Title.Text = null;
}
else
{
zedGraphControl.GraphPane.Title.Text = QuantificationStrings.CalibrationForm_DisplayCalibrationCurve_To_fit_a_calibration_curve__set_the_Sample_Type_of_some_replicates_to_Standard__and_specify_their_concentration_;
}
}
zedGraphControl.GraphPane.XAxis.Title.Text = curveFitter.GetXAxisTitle();
zedGraphControl.GraphPane.YAxis.Title.Text = curveFitter.GetYAxisTitle();
CalibrationCurve = curveFitter.GetCalibrationCurve();
double minX = double.MaxValue, maxX = double.MinValue;
_scatterPlots = new CurveList();
foreach (var sampleType in SampleType.ListSampleTypes())
{
if (!Options.DisplaySampleType(sampleType))
{
continue;
}
PointPairList pointPairList = new PointPairList();
for (int iReplicate = 0;
iReplicate < document.Settings.MeasuredResults.Chromatograms.Count;
iReplicate++)
{
ChromatogramSet chromatogramSet = document.Settings.MeasuredResults.Chromatograms[iReplicate];
if (!Equals(sampleType, chromatogramSet.SampleType))
{
continue;
}
double?y = curveFitter.GetYValue(iReplicate);
double?x = curveFitter.GetSpecifiedXValue(iReplicate)
?? curveFitter.GetCalculatedXValue(CalibrationCurve, iReplicate);
if (y.HasValue && x.HasValue)
{
PointPair point = new PointPair(x.Value, y.Value)
{
Tag = iReplicate
};
pointPairList.Add(point);
if (!Options.LogPlot || x.Value > 0)
{
minX = Math.Min(minX, x.Value);
}
maxX = Math.Max(maxX, x.Value);
}
}
if (pointPairList.Any())
{
var lineItem = zedGraphControl.GraphPane.AddCurve(sampleType.ToString(), pointPairList,
sampleType.Color, sampleType.SymbolType);
lineItem.Line.IsVisible = false;
lineItem.Symbol.Fill = new Fill(sampleType.Color);
_scatterPlots.Add(lineItem);
}
}
List <string> labelLines = new List <String>();
RegressionFit regressionFit = document.Settings.PeptideSettings.Quantification.RegressionFit;
if (regressionFit != RegressionFit.NONE)
{
if (minX <= maxX)
{
int interpolatedLinePointCount = 100;
if (!options.LogPlot)
{
if (regressionFit == RegressionFit.LINEAR_THROUGH_ZERO)
{
minX = Math.Min(0, minX);
}
if (regressionFit != RegressionFit.QUADRATIC)
{
interpolatedLinePointCount = 2;
}
}
LineItem interpolatedLine = CreateInterpolatedLine(CalibrationCurve, minX, maxX,
interpolatedLinePointCount, Options.LogPlot);
if (null != interpolatedLine)
{
zedGraphControl.GraphPane.CurveList.Add(interpolatedLine);
}
}
labelLines.Add(CalibrationCurve.ToString());
if (CalibrationCurve.RSquared.HasValue)
{
labelLines.Add(QuantificationStrings.CalibrationForm_DisplayCalibrationCurve_ +
CalibrationCurve.RSquared.Value.ToString("0.####")); // Not L10N
}
if (!Equals(curveFitter.QuantificationSettings.RegressionWeighting, RegressionWeighting.NONE))
{
labelLines.Add(string.Format("{0}: {1}", // Not L10N
QuantificationStrings.Weighting, curveFitter.QuantificationSettings.RegressionWeighting));
}
}
if (options.ShowSelection)
{
double?ySelected = curveFitter.GetYValue(_skylineWindow.SelectedResultsIndex);
double?xSelected = curveFitter.GetCalculatedXValue(CalibrationCurve, _skylineWindow.SelectedResultsIndex);
if (xSelected.HasValue && ySelected.HasValue)
{
ArrowObj arrow = new ArrowObj(xSelected.Value, ySelected.Value, xSelected.Value,
ySelected.Value)
{
Line = { Color = GraphSummary.ColorSelected }
};
zedGraphControl.GraphPane.GraphObjList.Insert(0, arrow);
}
var quantificationResult = curveFitter.GetQuantificationResult(_skylineWindow.SelectedResultsIndex);
if (quantificationResult.CalculatedConcentration.HasValue)
{
labelLines.Add(string.Format("{0} = {1}", // Not L10N
QuantificationStrings.Calculated_Concentration, quantificationResult));
}
else if (!quantificationResult.NormalizedArea.HasValue)
{
labelLines.Add(QuantificationStrings.CalibrationForm_DisplayCalibrationCurve_The_selected_replicate_has_missing_or_truncated_transitions);
}
}
if (labelLines.Any())
{
TextObj text = new TextObj(TextUtil.LineSeparate(labelLines), .01, 0,
CoordType.ChartFraction, AlignH.Left, AlignV.Top)
{
IsClippedToChartRect = true,
ZOrder = ZOrder.E_BehindCurves,
FontSpec = GraphSummary.CreateFontSpec(Color.Black),
};
zedGraphControl.GraphPane.GraphObjList.Add(text);
}
}
public override void UpdateGraph(bool selectionChanged)
{
if (!GraphSummary.DocumentUIContainer.DocumentUI.Settings.HasResults)
{
_areaCVGraphData = null;
return;
}
var settings = new AreaCVGraphData.AreaCVGraphSettings(GraphSummary.Type);
_document = GraphSummary.DocumentUIContainer.DocumentUI;
var factor = AreaGraphController.GetAreaCVFactorToDecimal();
BarSettings.Type = BarType.SortedOverlay;
BarSettings.ClusterScaleWidth = Settings.Default.AreaCVHistogramBinWidth;
BarSettings.MinClusterGap = 0.0f;
_percentage = !Settings.Default.AreaCVShowDecimals;
_decimals = _percentage ? 1 : 3;
GraphObjList.Clear();
CurveList.Clear();
_stickItems.Clear();
var gotData = _cache.TryGet(_document, settings, DataCallback, out _areaCVGraphData);
if (!gotData || !_areaCVGraphData.IsValid)
{
return;
}
var fontHeight = GraphSummary.CreateFontSpec(Color.Black).GetHeight(CalcScaleFactor());
var height = PaneHeightToYValue(fontHeight);
var heightFactor = 1;
if (Settings.Default.AreaCVShowMedianCV)
{
var stick = AddStickItem(_areaCVGraphData.MedianCV * factor, _areaCVGraphData.MedianCV * factor, 0.0, _areaCVGraphData.MaxFrequency + heightFactor++ *height, Color.Blue);
CurveList.Add(stick);
_stickItems.Add(stick);
}
if (Settings.Default.AreaCVShowCVCutoff)
{
var stick = AddStickItem(Settings.Default.AreaCVCVCutoff, Settings.Default.AreaCVCVCutoff, 0.0, _areaCVGraphData.MaxFrequency + heightFactor++ *height, Color.Red);
CurveList.Add(stick);
_stickItems.Add(stick);
}
var selected = HistogramHelper.GetSelectedPeptides(GraphSummary).NodePeps.OrderBy(p => p.Id.GlobalIndex).ToList();
var comparer = Comparer <PeptideDocNode> .Create((a, b) => a.Id.GlobalIndex.CompareTo(b.Id.GlobalIndex));
var selectedPoints = new PointPairList();
var selectedPoints2 = new PointPairList();
var otherPoints = new PointPairList();
foreach (var d in _areaCVGraphData.Data)
{
int frequency;
var x = d.CV * factor + Settings.Default.AreaCVHistogramBinWidth / 2.0f;
var pt = new PointPair(x, d.Frequency)
{
Tag = d
};
if (Settings.Default.ShowReplicateSelection &&
(frequency = d.PeptideAnnotationPairs.Count(pair => selected.BinarySearch(pair.Peptide, comparer) >= 0)) > 0)
{
selectedPoints.Add(pt);
selectedPoints2.Add(new PointPair(x, frequency)
{
Tag = d
});
}
else
{
otherPoints.Add(pt);
}
}
CurveList.Insert(0, MakeBarItem(selectedPoints2, Color.Red));
CurveList.Insert(1, MakeBarItem(selectedPoints, Color.FromArgb(Color.Red.ToArgb() & 0x7FFFFFFF)));
CurveList.Insert(2, MakeBarItem(otherPoints, Color.FromArgb(180, 220, 255)));
XAxis.Title.Text = Resources.AreaCVHistogramGraphPane_UpdateGraph_CV + (_percentage ? " (%)" : string.Empty); // Not L10N
YAxis.Title.Text = Resources.AreaCVHistogramGraphPane_UpdateGraph_Frequency;
XAxis.Scale.Min = YAxis.Scale.Min = 0;
XAxis.Scale.MinAuto = XAxis.Scale.MaxAuto = YAxis.Scale.MinAuto = YAxis.Scale.MaxAuto = false;
if (!double.IsNaN(Settings.Default.AreaCVMaxCV))
{
XAxis.Scale.Max = Settings.Default.AreaCVMaxCV;
}
else
{
XAxis.Scale.Max = _areaCVGraphData.MaxCV * factor + Settings.Default.AreaCVHistogramBinWidth;
}
if (!double.IsNaN(Settings.Default.AreaCVMaxFrequency))
{
YAxis.Scale.Max = Settings.Default.AreaCVMaxFrequency;
}
else
{
YAxis.Scale.Max = _areaCVGraphData.MaxFrequency + heightFactor * height;
}
AxisChange();
}
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;
ReplicateGroupOp replicateGroupOp;
if (rtValue == RTPeptideValue.All)
{
replicateGroupOp = ReplicateGroupOp.FromCurrentSettings(document.Settings, GraphValues.AggregateOp.MEAN);
}
else
{
replicateGroupOp = 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(document.Settings, 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 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();
}
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 override Result RunCommand(RhinoDoc doc, RunMode mode)
{
var gc = new GetObject();
gc.SetCommandPrompt("Select some FANCY curves");
gc.GeometryFilter = ObjectType.Curve;
gc.GetMultiple(1, 0);
if (gc.CommandResult() != Result.Success)
{
return(gc.CommandResult());
}
int linecount = 0;
int arccount = 0;
int circlecount = 0;
int polylinecount = 0;
//create a collection of curves
// var curves = new List<Curve>(gc.ObjectCount); OR
var curves = new CurveList();
for (var i = 0; i < gc.ObjectCount; i++)
{
var curve = gc.Object(i).Curve();
if (null != curve)
{
curves.Add(curve);
}
// ADD THE CURVE TO THE CURVES LIST, expanding dynamically through the loop
LineCurve line_curve = curve as LineCurve; //check if curve is a line, 'as' is simplest form of casting
if (line_curve != null) // so long as the selection is not null, the our curve is a line
{
linecount++; // then we can increase our linecount
}
PolylineCurve polyline_curve = curve as PolylineCurve;
if (polyline_curve != null)
{
polylinecount++;
}
ArcCurve arc_curve = curve as ArcCurve;
if (arc_curve != null)
{
if (arc_curve.IsCircle())
{
circlecount++;
}
else
{
arccount++;
}
}
curve.Domain = new Interval(0, 1);
//this will force all curves to have the Domain from 0 to 1
doc.Objects.AddPoint(curve.PointAtStart);
doc.Objects.AddPoint(curve.PointAtEnd);
doc.Objects.AddPoint(curve.PointAt(0.75));
//add points along the domain...
var format = string.Format("F{0}", doc.DistanceDisplayPrecision);
string crvinfo = string.Format("The curve {0} has the length {1} and domain: {2} to {3}. Degree {4}. Points at 0,0.75 and 1 of domain.",
i,
curve.GetLength().ToString(format),
curve.Domain.T0.ToString(format),
curve.Domain.T1.ToString(format),
curve.Degree.ToString(format));
RhinoApp.WriteLine(crvinfo);
}
doc.Views.Redraw();
string s = string.Format("{0} line(s), {1} polyline(s), {2} circle(s), {3} arc(s) and {4} curve(s) selected in total",
linecount.ToString(), polylinecount.ToString(), circlecount.ToString(), arccount.ToString(), curves.Count.ToString());
RhinoApp.WriteLine(s);
return(Result.Success);
}