public void SetThreshold(double?value)
{
if (value.HasValue)
{
if (m_Threshold == null)
{
m_Threshold = new LineObj(Color.Red, 0, value.Value, 1, value.Value)
{
Location = { CoordinateFrame = CoordType.XChartFractionYScale },
IsClippedToChartRect = true
};
GraphObjList.Add(m_Threshold);
}
else
{
m_Threshold.Location.Y = value.Value;
}
}
else
{
GraphObjList.Remove(m_Threshold);
m_Threshold = null;
}
m_Parent.UpdateGraph();
}
private void AddAnnotations(Graphics g)
{
foreach (GraphObj obj in _pointAnnotations)
{
TextObj text = obj as TextObj;
if (text != null)
{
if (text.Location.CoordinateFrame == CoordType.ChartFraction &&
text.Location.AlignH == AlignH.Left && text.Location.AlignV == AlignV.Top)
{
GraphObjList.Add(text);
continue;
}
if (isXChartFractionObject(text) && (text.Location.X < XAxis.Scale.Min || text.Location.X > XAxis.Scale.Max))
{
continue;
}
var textRect = _labelBoundsCache.GetLabelBounds(text, this, g);
if (_overlapDetector == null || !_overlapDetector.Overlaps(textRect))
{
_manualLabels[text] = textRect;
}
}
else if (!GraphObjList.Contains(obj)) // always add non-text annotations
{
GraphObjList.Add(obj);
}
}
}
private void AddDotProductLabels(Graphics g, TransitionGroupDocNode nodeGroup, IList <double> sumAreas)
{
// Create temporary label to calculate positions
var pointSize = GetDotProductsPointSize(g);
bool visible = pointSize.HasValue;
bool visibleState = _dotpLabels.Count > 0;
if (visible == visibleState && (!visibleState || ((TextObj)_dotpLabels[0]).FontSpec.Size == pointSize))
{
return;
}
foreach (GraphObj pa in _dotpLabels)
{
GraphObjList.Remove(pa);
}
_dotpLabels.Clear();
if (visible)
{
// x shift of the dot product labels
var xShift = 1;
if (IsExpectedVisible)
{
// shift dot product labels over by 1 more, if library is visible
xShift++;
}
for (int i = 0; i < sumAreas.Count; i++)
{
string text = GetDotProductResultsText(nodeGroup, i);
if (string.IsNullOrEmpty(text))
{
continue;
}
TextObj textObj = new TextObj(text,
i + xShift, sumAreas[i],
CoordType.AxisXYScale,
AlignH.Center,
AlignV.Bottom)
{
IsClippedToChartRect = true,
ZOrder = ZOrder.F_BehindGrid,
};
textObj.FontSpec.Border.IsVisible = false;
textObj.FontSpec.Size = pointSize.Value;
_lableHeight = (int)textObj.FontSpec.GetHeight(CalcScaleFactor());
GraphObjList.Add(textObj);
_dotpLabels.Add(textObj);
}
}
}
public override void Draw(Graphics g)
{
GraphObjList.Clear();
if (_graphData != null)
{
// Force Axes to recalculate to ensure proper layout of labels
AxisChange(g);
// Reposition the regression label.
RectangleF rectChart = Chart.Rect;
PointF ptTop = rectChart.Location;
// Setup axes scales to enable the ReverseTransform method
XAxis.Scale.SetupScaleData(this, XAxis);
YAxis.Scale.SetupScaleData(this, YAxis);
float yNext = ptTop.Y;
double left = XAxis.Scale.ReverseTransform(ptTop.X + 8);
FontSpec fontSpec = GraphSummary.CreateFontSpec(COLOR_LINE_REGRESSION);
if (_labelRegression != null)
{
// Add regression text
double top = YAxis.Scale.ReverseTransform(yNext);
TextObj text = new TextObj(_labelRegression, left, top,
CoordType.AxisXYScale, AlignH.Left, AlignV.Top)
{
IsClippedToChartRect = true,
ZOrder = ZOrder.E_BehindCurves,
FontSpec = fontSpec,
};
// text.FontSpec.Size = 12;
GraphObjList.Add(text);
}
if (_labelRegressionCurrent != null)
{
// Add text for current regression
SizeF sizeLabel = fontSpec.MeasureString(g, _labelRegression, CalcScaleFactor());
yNext += sizeLabel.Height + 3;
double top = YAxis.Scale.ReverseTransform(yNext);
TextObj text = new TextObj(_labelRegressionCurrent, left, top,
CoordType.AxisXYScale, AlignH.Left, AlignV.Top)
{
IsClippedToChartRect = true,
ZOrder = ZOrder.E_BehindCurves,
FontSpec = GraphSummary.CreateFontSpec(COLOR_LINE_REGRESSION_CURRENT),
};
// text.FontSpec.Size = 12;
GraphObjList.Add(text);
}
}
base.Draw(g);
}
private void AddRetentionTimeAnnotation(MSGraphPane graphPane, Graphics g, GraphObjList annotations,
PointF ptTop, string title, GraphObjType graphObjType, Color color, ScaledRetentionTime retentionTime)
{
// ReSharper disable LocalizableElement
string label = string.Format("{0}\n{1:F01}", title, retentionTime.DisplayTime);
// ReSharper restore LocalizableElement
FontSpec fontLabel = CreateFontSpec(color, _fontSpec.Size);
SizeF sizeLabel = fontLabel.MeasureString(g, label, graphPane.CalcScaleFactor());
PointF realTopPoint = ptTop;
ptTop = new PointF(0, ptTop.Y + sizeLabel.Height + 15);
float chartHeightWithLabel = graphPane.Chart.Rect.Height + sizeLabel.Height + 15;
double intensityChartFraction = (ptTop.Y - realTopPoint.Y) / chartHeightWithLabel;
LineObj stick = new LineObj(color, retentionTime.DisplayTime, intensityChartFraction, retentionTime.DisplayTime, 1)
{
IsClippedToChartRect = true,
Location = { CoordinateFrame = CoordType.XScaleYChartFraction },
ZOrder = ZOrder.E_BehindCurves,
Line = { Width = 1 },
Tag = new GraphObjTag(this, graphObjType, retentionTime),
};
annotations.Add(stick);
ptTop = new PointF(0, ptTop.Y - 5);
intensityChartFraction = (ptTop.Y - realTopPoint.Y) / chartHeightWithLabel;
TextObj text = new TextObj(label, retentionTime.DisplayTime, intensityChartFraction,
CoordType.XScaleYChartFraction, AlignH.Center, AlignV.Bottom)
{
IsClippedToChartRect = true,
ZOrder = ZOrder.E_BehindCurves,
FontSpec = CreateFontSpec(color, _fontSpec.Size),
Tag = new GraphObjTag(this, graphObjType, retentionTime),
};
annotations.Add(text);
}
public void addEquity(Simulator simulator)
{
Bomb.when(Objects.hasContent(equity), () => "equity has content already: " + Objects.toShortString(equity));
equity.AddRange(simulator.equity(symbol));
var points = new PointPairList();
Objects.eachIt(simulator.equity(symbol), (i, value) => points.Add(i + 1, value));
var curve = AddCurve("equity", points, Color.Red);
curve.Symbol.IsVisible = false;
curve.IsOverrideOrdinal = true;
var zero = new LineObj(Color.Gray, 1, 0, bars.count(), 0)
{
Line = { Style = DashStyle.Dash }, Location = { CoordinateFrame = CoordType.AxisXYScale }
};
GraphObjList.Add(zero);
AxisChange();
var graphable = new EquityGraphable("equity", simulator.equity(symbol), simulator.dates(symbol));
graphables.Add(graphable);
var needsNewPoint = false;
bars.pushedDown += () => needsNewPoint = true;
bars.valueSet += bar => {
var value = simulator.pnl(symbol);
var todaysMarketPnl = Objects.sum(Objects.convert(simulator.positions(symbol), position => position.pnl(bars[1].close, bars[0].close)));
value += todaysMarketPnl;
graphable.add(bar.time, value);
QControl.runOnGuiThread(dispatchTo, () => {
var lastPoint = curve[curve.Points.Count - 1];
if (needsNewPoint)
{
curve.AddPoint(lastPoint.X + 1, value);
equity.Add(value);
}
else
{
lastPoint.Y = value;
equity[equity.Count - 1] = value;
}
BarSpudGraph.addEquityTo(Objects.first(parentTyped.dataTable().Rows), value);
needsNewPoint = false;
parentTyped.Invalidate();
});
};
}
public override void AddAnnotations(MSGraphPane graphPane, Graphics g, MSPointList pointList, GraphObjList annotations)
{
// ReSharper disable UseObjectOrCollectionInitializer
foreach (var rmi in SpectrumInfo.PeaksMatched)
{
if (!IsVisibleIon(rmi))
{
continue;
}
var matchedIon = rmi.MatchedIons.First(IsVisibleIon);
Color color;
switch (matchedIon.IonType)
{
default: color = COLOR_NONE; break;
case IonType.a: color = COLOR_A; break;
case IonType.x: color = COLOR_X; break;
case IonType.b: color = COLOR_B; break;
case IonType.y: color = COLOR_Y; break;
case IonType.c: color = COLOR_C; break;
case IonType.z: color = COLOR_Z; break;
case IonType.custom: color = (rmi.Rank > 0) ? COLOR_OTHER_IONS : COLOR_NONE; break; // Small molecule fragments - only color if ranked
case IonType.precursor: color = COLOR_PRECURSOR; break;
}
if (rmi.MatchedIons.Any(mfi => IsMatch(mfi.PredictedMz)))
{
color = COLOR_SELECTED;
}
double mz = rmi.ObservedMz;
var stick = new LineObj(color, mz, rmi.Intensity, mz, 0);
stick.IsClippedToChartRect = true;
stick.Location.CoordinateFrame = CoordType.AxisXYScale;
stick.Line.Width = LineWidth + 1;
annotations.Add(stick);
}
//ReSharper restore UseObjectOrCollectionInitializer
}
public override void AddAnnotations(MSGraphPane graphPane, Graphics g, MSPointList pointList, GraphObjList annotations)
{
// ReSharper disable UseObjectOrCollectionInitializer
foreach (var rmi in SpectrumInfo.PeaksMatched)
{
if (!IsVisibleIon(rmi))
{
continue;
}
IonType type = IsVisibleIon(rmi.IonType, rmi.Ordinal, rmi.Charge) ?
rmi.IonType : rmi.IonType2;
Color color;
switch (type)
{
default: color = COLOR_NONE; break;
case IonType.a: color = COLOR_A; break;
case IonType.x: color = COLOR_X; break;
case IonType.b: color = COLOR_B; break;
case IonType.y: color = COLOR_Y; break;
case IonType.c: color = COLOR_C; break;
case IonType.z: color = COLOR_Z; break;
// FUTURE: Add custom ions when LibraryRankedSpectrumInfo can support them
case IonType.precursor: color = COLOR_PRECURSOR; break;
}
if (IsMatch(rmi.PredictedMz))
{
color = COLOR_SELECTED;
}
double mz = rmi.ObservedMz;
var stick = new LineObj(color, mz, rmi.Intensity, mz, 0);
stick.IsClippedToChartRect = true;
stick.Location.CoordinateFrame = CoordType.AxisXYScale;
stick.Line.Width = LineWidth + 1;
annotations.Add(stick);
}
//ReSharper restore UseObjectOrCollectionInitializer
}
private void AddOriginalPeakAnnotation(ChromPeak bestPeak, GraphObjList annotations, GraphPane graphPane)
{
var start = ScaleRetentionTime(bestPeak.StartTime);
var end = ScaleRetentionTime(bestPeak.EndTime);
var width = end.DisplayTime - start.DisplayTime;
var height = graphPane.YAxis.Scale.Max;
var originalPeakShadingBox = new BoxObj(start.DisplayTime, graphPane.YAxis.Scale.Max, width, height)
{
Fill = new Fill(Color.FromArgb(30, COLOR_ORIGINAL_PEAK_SHADE)),
ZOrder = ZOrder.F_BehindGrid,
Border = new Border {
IsVisible = false
},
IsClippedToChartRect = true,
Tag = new GraphObjTag(this, GraphObjType.original_peak_shading, start, end)
};
annotations.Add(originalPeakShadingBox);
}
private void AddLabels(Graphics g)
{
if (_areaCVGraphData == null)
{
Title.Text = Resources.AreaCVHistogramGraphPane_AddLabels_Calculating____;
}
else if (!_areaCVGraphData.IsValid)
{
Title.Text = Resources.AreaCVHistogramGraphPane_AddLabels_Not_enough_data;
}
else
{
Title.Text = string.Empty;
var unit = _percentage ? @"%" : string.Empty;
var factor = _percentage ? 100.0 : 1.0;
var scaleFactor = CalcScaleFactor();
var fontHeight = GraphSummary.CreateFontSpec(Color.Black).GetHeight(scaleFactor);
var height = PaneHeightToYValue(fontHeight);
// Anchor labels at top of graph pane
var y = Math.Min(PaneHeightToYValue(Rect.Height - TitleGap * Title.FontSpec.GetHeight(scaleFactor) - fontHeight * _stickItems.Count), _areaCVGraphData.MaxFrequency + height);
var index = 0;
if (Settings.Default.AreaCVShowMedianCV)
{
_stickItems[index++].Points[1].Y = y;
string text = string.Format(Resources.AreaCVHistogramGraphPane_AddLabels_Median___0_,
HistogramHelper.FormatDouble(_areaCVGraphData.MedianCV * factor, _decimals) + unit);
GraphObjList.Add(AddLabel(text, _areaCVGraphData.MedianCV * factor, y, Color.Blue));
y += height;
}
if (Settings.Default.AreaCVShowCVCutoff)
{
_stickItems[index++].Points[1].Y = y;
string text = string.Format(Resources.AreaCVHistogramGraphPane_UpdateGraph_Below__0____1_,
Settings.Default.AreaCVCVCutoff + unit, HistogramHelper.FormatDouble(_areaCVGraphData.BelowCVCutoff * factor, _decimals) + unit);
GraphObjList.Add(AddLabel(text, Settings.Default.AreaCVCVCutoff, y, Color.Red));
}
}
}
void addCrosshair(float x, float y)
{
Bomb.unlessNull(xLine, () => "addCrosshair called twice without removeCrossHair");
Bomb.unlessNull(yLine, () => "addCrosshair called twice without removeCrossHair");
var chartPoint = point(x, y);
xLine = new LineObj(Color.Gray, chartPoint.X, 0, chartPoint.X, 1)
{
Location = { CoordinateFrame = CoordType.XScaleYChartFraction }
};
yLine = new LineObj(Color.Gray, 0, chartPoint.Y, 1, chartPoint.Y)
{
Location = { CoordinateFrame = CoordType.XChartFractionYScale }
};
Objects.each(Objects.list(xLine, yLine), line => {
line.ZOrder = ZOrder.E_BehindCurves;
line.Line.Style = DashStyle.Dash;
});
GraphObjList.Add(xLine);
GraphObjList.Add(yLine);
}
private void AddSelection(int selectedReplicateIndex, double maxRetentionTime, double minRetentionTime)
{
bool selectLines = CurveList.Any(c => c is LineItem);
if (selectLines)
{
GraphObjList.Add(new LineObj(Color.Black, selectedReplicateIndex + 1, 0, selectedReplicateIndex + 1,
maxRetentionTime)
{
IsClippedToChartRect = true,
Line = new Line {
Width = 2, Color = Color.Black, Style = DashStyle.Dash
}
});
}
else
{
GraphObjList.Add(new BoxObj(selectedReplicateIndex + .5, maxRetentionTime, 1,
maxRetentionTime - minRetentionTime, Color.Black, Color.Empty)
{
IsClippedToChartRect = true,
});
}
}
public override void AddAnnotations(MSGraphPane graphPane, Graphics g, MSPointList pointList, GraphObjList annotations)
{
// ReSharper disable UseObjectOrCollectionInitializer
foreach (var rmi in SpectrumInfo.PeaksMatched)
{
if (!IsVisibleIon(rmi))
{
continue;
}
var matchedIon = rmi.MatchedIons.First(IsVisibleIon);
Color color;
switch (matchedIon.IonType)
{
default: color = COLOR_NONE; break;
case IonType.a: color = COLOR_A; break;
case IonType.x: color = COLOR_X; break;
case IonType.b: color = COLOR_B; break;
case IonType.y: color = COLOR_Y; break;
case IonType.c: color = COLOR_C; break;
case IonType.z: color = COLOR_Z; break;
case IonType.custom: color = (rmi.Rank > 0) ? COLOR_OTHER_IONS : COLOR_NONE; break; // Small molecule fragments - only color if ranked
case IonType.precursor: color = COLOR_PRECURSOR; break;
}
if (Invert)
{
color = InvertColor(color);
}
if (rmi.MatchedIons.Any(mfi => IsMatch(mfi.PredictedMz)))
{
color = COLOR_SELECTED;
}
double mz = rmi.ObservedMz;
var intensity = Invert ? -rmi.Intensity : rmi.Intensity;
var stick = new LineObj(color, mz, intensity, mz, 0);
stick.IsClippedToChartRect = true;
stick.Location.CoordinateFrame = CoordType.AxisXYScale;
stick.Line.Width = LineWidth + 1;
annotations.Add(stick);
}
//ReSharper restore UseObjectOrCollectionInitializer
if (ShowScores && SpectrumInfo.Score.HasValue)
{
var text = new TextObj(
string.Format(LocalizationHelper.CurrentCulture, Resources.AbstractSpectrumGraphItem_AddAnnotations_, SpectrumInfo.Score),
0.01, 0, CoordType.ChartFraction, AlignH.Left, AlignV.Top)
{
IsClippedToChartRect = true,
ZOrder = ZOrder.E_BehindCurves,
FontSpec = GraphSummary.CreateFontSpec(Color.Black),
};
annotations.Add(text);
}
}
public override void AddPreCurveAnnotations(MSGraphPane graphPane, Graphics g,
MSPointList pointList, GraphObjList annotations)
{
if (Chromatogram == null)
{
return;
}
// Give priority to showing the best peak text object above all other annotations
if (DragInfo != null || (!HideBest && TransitionChromInfo != null) || CurveAnnotation != null)
{
// Show text and arrow for the best peak
double intensityBest = 0;
if (_bestPeakTimeIndex != -1)
{
ScaledRetentionTime timeBest = new ScaledRetentionTime(_measuredTimes[_bestPeakTimeIndex], _displayTimes[_bestPeakTimeIndex]);
float xBest = graphPane.XAxis.Scale.Transform(timeBest.DisplayTime);
intensityBest = _intensities[_bestPeakTimeIndex];
float yBest = graphPane.YAxis.Scale.Transform(intensityBest);
if (GraphChromatogram.ShowRT != ShowRTChrom.none || DragInfo != null)
{
// Best peak gets its own label to avoid curve overlap detection
double intensityLabel = graphPane.YAxis.Scale.ReverseTransform(yBest - 5);
float? massError = Settings.Default.ShowMassError && TransitionChromInfo != null
? TransitionChromInfo.MassError
: null;
double dotProduct = _dotProducts != null ? _bestProduct : 0;
TextObj text;
if (CurveAnnotation != null)
{
// Darken peptide name a little so light colors stand out against the white background.
var color = FontSpec.FontColor;
if (!GraphInfo.IsSelected)
{
color = Color.FromArgb(color.R * 7 / 10, color.G * 7 / 10, color.B * 7 / 10);
}
var fontSpec = new FontSpec(FontSpec)
{
FontColor = color, Angle = 90
};
if (GraphInfo.IsSelected)
{
fontSpec = new FontSpec(fontSpec)
{
IsBold = true, Size = fontSpec.Size + 2, IsAntiAlias = true
}
}
;
// Display peptide name label using vertical text.
text = new TextObj(CurveAnnotation, timeBest.DisplayTime, intensityLabel,
CoordType.AxisXYScale, AlignH.Left, AlignV.Center)
{
ZOrder = ZOrder.A_InFront,
IsClippedToChartRect = true,
FontSpec = fontSpec,
Tag = new GraphObjTag(this, GraphObjType.best_peak, timeBest),
};
}
else
{
string label = FormatTimeLabel(timeBest.DisplayTime, massError, dotProduct);
text = new TextObj(label, timeBest.DisplayTime, intensityLabel,
CoordType.AxisXYScale, AlignH.Center, AlignV.Bottom)
{
ZOrder = ZOrder.A_InFront,
IsClippedToChartRect = true,
FontSpec = FontSpec,
Tag = new GraphObjTag(this, GraphObjType.best_peak, timeBest),
};
}
annotations.Add(text);
}
// If showing multiple peptides, skip the best peak arrow indicator.
if (CurveAnnotation == null)
{
// Show the best peak arrow indicator
double timeArrow = graphPane.XAxis.Scale.ReverseTransform(xBest - 4);
double intensityArrow = graphPane.YAxis.Scale.ReverseTransform(yBest - 2);
ArrowObj arrow = new ArrowObj(COLOR_BEST_PEAK, 12f,
timeArrow, intensityArrow, timeArrow, intensityArrow)
{
Location = { CoordinateFrame = CoordType.AxisXYScale },
IsArrowHead = true,
IsClippedToChartRect = true,
ZOrder = ZOrder.A_InFront
};
annotations.Add(arrow);
}
}
// Show the best peak boundary lines
if (CurveAnnotation == null)
{
double startTime = 0, endTime = 0;
if (DragInfo != null)
{
startTime = DragInfo.StartTime.MeasuredTime;
endTime = DragInfo.EndTime.MeasuredTime;
}
else if (TransitionChromInfo != null)
{
var tranPeakInfo = TransitionChromInfo;
startTime = tranPeakInfo.StartRetentionTime;
endTime = tranPeakInfo.EndRetentionTime;
}
AddPeakBoundaries(graphPane, annotations, true,
ScaleRetentionTime(startTime), ScaleRetentionTime(endTime), intensityBest);
}
if (Chromatogram.BestPeakIndex >= 0)
{
// Only shade peak when user modified. Otherwise, shading can be added when an entire
// precursor was force integrated because of another precursor (e.g. heavy) since that
// leads to an empty peak, which will not match the best peak.
if (Settings.Default.ShowOriginalPeak && TransitionChromInfo != null && TransitionChromInfo.IsUserModified)
{
var bestPeak = Chromatogram.GetPeak(Chromatogram.BestPeakIndex);
if (bestPeak.StartTime != TransitionChromInfo.StartRetentionTime ||
bestPeak.EndTime != TransitionChromInfo.EndRetentionTime)
{
AddOriginalPeakAnnotation(bestPeak, annotations, graphPane);
}
}
}
}
if (_displayRawTimes.HasValue)
{
AddPeakRawTimes(graphPane, annotations,
ScaleRetentionTime(_displayRawTimes.Value.StartBound),
ScaleRetentionTime(_displayRawTimes.Value.EndBound),
Chromatogram);
}
}
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();
}
/// <summary>
/// We know which labels are overlapping the data points, but we need to make sure the labels that will be
/// displayed can fit in the scale using the Min/MaxGrace properties and adjusting the label fractions if appropriate:
/// TextObjs with CoordType.AxisXYScale coordinates will move proportionally with Min/MaxGrace, but ChartFraction
/// coordinates will not.
/// </summary>
protected void autoScaleForManualLabels(Graphics g)
{
Axis yAxis = YAxis;
bool maxAuto = yAxis.Scale.MaxAuto;
try
{
if (maxAuto)
{
AxisChange(g);
}
double yMaxRequired = 0;
foreach (var kvp in _manualLabels)
{
TextObj text = kvp.Key;
if (text.Location.X < XAxis.Scale.Min || text.Location.X > XAxis.Scale.Max)
{
continue;
}
if (!YAxis.Scale.IsLog && !IsYChartFractionObject(text))
{
double axisHeight = YAxis.Scale.Max - YAxis.Scale.Min;
PointF[] pts = text.FontSpec.GetBox(g, text.Text, 0, 0, text.Location.AlignH, text.Location.AlignV, 1.0f,
new SizeF());
float pixelShift = 0;
var rectPeak = _labelBoundsCache.GetLabelBounds(text, this, g);
foreach (var id in _manualLabels.Keys.Where(IsYChartFractionObject))
{
var rectID = _labelBoundsCache.GetLabelBounds(id, this, g);
// If the rectangles overlap
if (Math.Min(rectID.Right, rectPeak.Right) - Math.Max(rectID.Left, rectPeak.Left) > 0 &&
Math.Min(rectID.Bottom, rectPeak.Bottom) - Math.Max(rectID.Top, rectPeak.Top) > 0)
{
pixelShift = Math.Max(rectID.Height + 7, pixelShift); // 7 pixel gap between labels
}
}
double y2Pos = yAxis.Scale.ReverseTransform(pts[2].Y);
double labelHeight =
Math.Abs(yAxis.Scale.ReverseTransform(pts[0].Y - pixelShift) - y2Pos);
// If separating the labels takes too much space, just revert to showing them aligned
if (labelHeight >= axisHeight / 2)
{
labelHeight = Math.Abs(yAxis.Scale.ReverseTransform(pts[0].Y) - y2Pos);
}
if (labelHeight < axisHeight / 2)
{
// Ensure that the YAxis will have enough space to show the label.
// Only do this if the labelHeight is going to take up less than half the space on the graph, because
// otherwise the graph will be shrunk too much to have any useful information.
// When calculating the scaling required, take into account that the height of the label
// itself will not shrink when we shrink the YAxis.
var labelYMaxRequired = (text.Location.Y - labelHeight * YAxis.Scale.Min / axisHeight) /
(1 - labelHeight / axisHeight);
yMaxRequired = Math.Max(yMaxRequired, labelYMaxRequired);
}
}
if (!GraphObjList.Any(
o =>
(o is TextObj) && ((TextObj)o).Location == text.Location &&
((TextObj)o).Text == text.Text))
{
if (_pointAnnotations.Contains(text))
{
GraphObjList.Add(text);
}
}
}
if (maxAuto && yMaxRequired > 0)
{
yAxis.Scale.Max = Math.Max(yAxis.Scale.Max, yMaxRequired);
}
}
finally
{
// Reset the value of MaxAuto since it may have been changed to false when Scale.Max was changed.
yAxis.Scale.MaxAuto = maxAuto;
}
}
private void drawLabels(Graphics g)
{
foreach (GraphObj pa in _pointAnnotations)
{
GraphObjList.Remove(pa);
}
_pointAnnotations.Clear();
_manualLabels.Clear();
Axis xAxis = XAxis;
Axis yAxis = YAxis;
yAxis.Scale.MinAuto = false;
if (LockYAxisAtZero)
{
yAxis.Scale.Min = 0;
}
// ensure that the chart rectangle is the right size
AxisChange(g);
// then setup axes scales to enable the Transform method
xAxis.Scale.SetupScaleData(this, xAxis);
yAxis.Scale.SetupScaleData(this, yAxis);
if (Chart.Rect.Width < 1 || Chart.Rect.Height < 1)
{
return;
}
_overlapDetector = AllowLabelOverlap ? null : new OverlapDetector();
Region chartRegion = new Region(Chart.Rect);
Region clipRegion = new Region();
clipRegion.MakeEmpty();
var previousClip = g.Clip.Clone();
g.SetClip(Rect, CombineMode.Replace);
g.SetClip(chartRegion, CombineMode.Exclude);
/*Bitmap clipBmp = new Bitmap(Convert.ToInt32(Chart.Rect.Width), Convert.ToInt32(Chart.Rect.Height));
* Graphics clipG = Graphics.FromImage(clipBmp);
* clipG.Clear(Color.White);
* clipG.FillRegion(new SolidBrush(Color.Black), g.Clip);
* clipBmp.Save("C:\\clip.bmp");*/
// some dummy labels for very fast clipping
string baseLabel = "0"; // Not L10N
foreach (CurveItem item in CurveList)
{
IMSGraphItemInfo info = item.Tag as IMSGraphItemInfo;
if (info != null)
{
PointAnnotation annotation = info.AnnotatePoint(new PointPair(0, 0));
if (annotation != null &&
annotation.Label != null &&
annotation.Label.Length > baseLabel.Length)
{
baseLabel = annotation.Label;
}
}
}
TextObj baseTextObj = new TextObj(baseLabel, 0, 0);
baseTextObj.FontSpec.Border.IsVisible = false;
baseTextObj.FontSpec.Fill.IsVisible = false;
PointF[] pts = baseTextObj.FontSpec.GetBox(g, baseLabel, 0, 0,
AlignH.Center, AlignV.Bottom, 1.0f, new SizeF());
float baseLabelWidth = pts[1].X - pts[0].X;
float baseLabelHeight = pts[2].Y - pts[0].Y;
baseLabelWidth = (float)xAxis.Scale.ReverseTransform(xAxis.Scale.Transform(0) + baseLabelWidth);
baseLabelHeight = (float)yAxis.Scale.ReverseTransform(yAxis.Scale.Transform(0) - baseLabelHeight);
float labelLengthToWidthRatio = baseLabelWidth / baseLabel.Length;
float xAxisPixel = yAxis.Scale.Transform(0);
double xMin = xAxis.Scale.Min;
double xMax = xAxis.Scale.Max;
double yMin = yAxis.Scale.Min;
double yMax = yAxis.Scale.Max;
// add manual annotations with TextObj priority over curve annotations
foreach (CurveItem item in CurveList)
{
var info = item.Tag as IMSGraphItemExtended;
MSPointList points = item.Points as MSPointList;
if (info == null || points == null)
{
continue;
}
info.AddPreCurveAnnotations(this, g, points, _pointAnnotations);
AddAnnotations(g);
}
// add automatic labels for MSGraphItems
foreach (CurveItem item in CurveList)
{
IMSGraphItemInfo info = item.Tag as IMSGraphItemInfo;
MSPointList points = item.Points as MSPointList;
if (info == null || points == null)
{
continue;
}
if (info.ToString().Length == 0)
{
continue;
}
PointPairList fullList = points.FullList;
List <int> maxIndexList = points.ScaledMaxIndexList;
var annotationsPrioritized = new Dictionary <PointAnnotation, int>();
for (int i = 0; i < maxIndexList.Count; ++i)
{
if (maxIndexList[i] < 0)
{
continue;
}
PointPair pt = fullList[maxIndexList[i]];
if (pt.X < xMin || pt.Y > yMax || pt.Y < yMin)
{
continue;
}
if (pt.X > xMax)
{
break;
}
float yPixel = yAxis.Scale.Transform(pt.Y);
// labelled points must be at least 3 pixels off the X axis
if (xAxisPixel - yPixel < 3)
{
continue;
}
PointAnnotation annotation = info.AnnotatePoint(pt);
if (annotation != null)
{
annotationsPrioritized.Add(annotation, i);
}
}
// Give the higher ranked point priority
foreach (var annotation in annotationsPrioritized.Keys.OrderBy(a => a.ZOrder ?? int.MaxValue))
{
if (annotation.ExtraAnnotation != null)
{
GraphObjList.Add(annotation.ExtraAnnotation);
_pointAnnotations.Add(annotation.ExtraAnnotation);
}
if (string.IsNullOrEmpty(annotation.Label))
{
continue;
}
float pointLabelWidth = labelLengthToWidthRatio * annotation.Label.Split('\n').Max(o => o.Length);
var i = annotationsPrioritized[annotation];
PointPair pt = fullList[maxIndexList[i]];
float yPixel = yAxis.Scale.Transform(pt.Y);
double labelY = yAxis.Scale.ReverseTransform(yPixel - 5);
if (!AllowCurveOverlap)
{
// do fast check for overlap against all MSGraphItems
bool overlap = false;
foreach (CurveItem item2 in CurveList)
{
MSPointList points2 = item2.Points as MSPointList;
if (points2 != null)
{
int nearestMaxIndex = points2.GetNearestMaxIndexToBin(i);
if (nearestMaxIndex < 0)
{
continue;
}
RectangleF r = new RectangleF((float)pt.X - pointLabelWidth / 2,
(float)labelY - baseLabelHeight,
pointLabelWidth,
baseLabelHeight);
overlap = detectLabelCurveOverlap(this, points2.FullList, nearestMaxIndex, item2 is StickItem, r);
if (overlap)
{
break;
}
}
}
if (overlap)
{
continue;
}
}
TextObj text = new TextObj(annotation.Label, pt.X, labelY,
CoordType.AxisXYScale, AlignH.Center, AlignV.Bottom)
{
ZOrder = ZOrder.A_InFront,
FontSpec = annotation.FontSpec,
IsClippedToChartRect = true
};
var textRect = _labelBoundsCache.GetLabelBounds(text, this, g);
bool overlap2 = _overlapDetector != null && _overlapDetector.Overlaps(textRect);
_manualLabels[text] = textRect;
if (!overlap2)
{
_pointAnnotations.Add(text);
AddAnnotations(g);
}
}
}
// add manual annotations
foreach (CurveItem item in CurveList)
{
IMSGraphItemInfo info = item.Tag as IMSGraphItemInfo;
MSPointList points = item.Points as MSPointList;
if (info == null || points == null)
{
continue;
}
info.AddAnnotations(this, g, points, _pointAnnotations);
AddAnnotations(g);
}
autoScaleForManualLabels(g);
g.Clip = previousClip;
}
private void drawLabels(Graphics g)
{
foreach (GraphObj pa in _pointAnnotations)
{
GraphObjList.Remove(pa);
}
_pointAnnotations.Clear();
Axis xAxis = XAxis;
Axis yAxis = YAxis;
yAxis.Scale.MinAuto = false;
yAxis.Scale.Min = 0;
// setup axes scales to enable the Transform method
xAxis.Scale.SetupScaleData(this, xAxis);
yAxis.Scale.SetupScaleData(this, yAxis);
if (Chart.Rect.Width < 1 || Chart.Rect.Height < 1)
{
return;
}
Region textBoundsRegion;
Region chartRegion = new Region(Chart.Rect);
Region clipRegion = new Region();
clipRegion.MakeEmpty();
g.SetClip(Rect, CombineMode.Replace);
g.SetClip(chartRegion, CombineMode.Exclude);
/*Bitmap clipBmp = new Bitmap(Convert.ToInt32(Chart.Rect.Width), Convert.ToInt32(Chart.Rect.Height));
* Graphics clipG = Graphics.FromImage(clipBmp);
* clipG.Clear(Color.White);
* clipG.FillRegion(new SolidBrush(Color.Black), g.Clip);
* clipBmp.Save("C:\\clip.bmp");*/
// some dummy labels for very fast clipping
string baseLabel = "0";
foreach (CurveItem item in CurveList)
{
IMSGraphItemInfo info = item.Tag as IMSGraphItemInfo;
if (info != null)
{
PointAnnotation annotation = info.AnnotatePoint(new PointPair(0, 0));
if (annotation != null &&
annotation.Label != null &&
annotation.Label.Length > baseLabel.Length)
{
baseLabel = annotation.Label;
}
}
}
TextObj baseTextObj = new TextObj(baseLabel, 0, 0);
baseTextObj.FontSpec.Border.IsVisible = false;
baseTextObj.FontSpec.Fill.IsVisible = false;
PointF[] pts = baseTextObj.FontSpec.GetBox(g, baseLabel, 0, 0,
AlignH.Center, AlignV.Bottom, 1.0f, new SizeF());
float baseLabelWidth = (float)Math.Round(pts[1].X - pts[0].X);
float baseLabelHeight = (float)Math.Round(pts[2].Y - pts[0].Y);
baseLabelWidth = (float)xAxis.Scale.ReverseTransform(xAxis.Scale.Transform(0) + baseLabelWidth);
baseLabelHeight = (float)yAxis.Scale.ReverseTransform(yAxis.Scale.Transform(0) - baseLabelHeight);
float labelLengthToWidthRatio = baseLabelWidth / baseLabel.Length;
float xAxisPixel = yAxis.Scale.Transform(0);
double xMin = xAxis.Scale.Min;
double xMax = xAxis.Scale.Max;
double yMin = yAxis.Scale.Min;
double yMax = yAxis.Scale.Max;
// add automatic labels for MSGraphItems
foreach (CurveItem item in CurveList)
{
IMSGraphItemInfo info = item.Tag as IMSGraphItemInfo;
MSPointList points = item.Points as MSPointList;
if (info == null || points == null)
{
continue;
}
if (info.ToString().Length == 0)
{
continue;
}
PointPairList fullList = points.FullList;
List <int> maxIndexList = points.ScaledMaxIndexList;
for (int i = 0; i < maxIndexList.Count; ++i)
{
if (maxIndexList[i] < 0)
{
continue;
}
PointPair pt = fullList[maxIndexList[i]];
if (pt.X < xMin || pt.Y > yMax || pt.Y < yMin)
{
continue;
}
if (pt.X > xMax)
{
break;
}
float yPixel = yAxis.Scale.Transform(pt.Y);
// labelled points must be at least 3 pixels off the X axis
if (xAxisPixel - yPixel < 3)
{
continue;
}
PointAnnotation annotation = info.AnnotatePoint(pt);
if (annotation == null)
{
continue;
}
if (annotation.ExtraAnnotation != null)
{
GraphObjList.Add(annotation.ExtraAnnotation);
_pointAnnotations.Add(annotation.ExtraAnnotation);
}
if (string.IsNullOrEmpty(annotation.Label))
{
continue;
}
float pointLabelWidth = labelLengthToWidthRatio * annotation.Label.Length;
double labelY = yAxis.Scale.ReverseTransform(yPixel - 5);
if (!AllowCurveOverlap)
{
// do fast check for overlap against all MSGraphItems
bool overlap = false;
foreach (CurveItem item2 in CurveList)
{
MSPointList points2 = item2.Points as MSPointList;
if (points2 != null)
{
int nearestMaxIndex = points2.GetNearestMaxIndexToBin(i);
if (nearestMaxIndex < 0)
{
continue;
}
RectangleF r = new RectangleF((float)pt.X - pointLabelWidth / 2,
(float)labelY - baseLabelHeight,
pointLabelWidth,
baseLabelHeight);
overlap = detectLabelCurveOverlap(this, points2.FullList, nearestMaxIndex, item2 is StickItem, r);
if (overlap)
{
break;
}
}
}
if (overlap)
{
continue;
}
}
TextObj text = new TextObj(annotation.Label, pt.X, labelY,
CoordType.AxisXYScale, AlignH.Center, AlignV.Bottom)
{
ZOrder = ZOrder.A_InFront,
FontSpec = annotation.FontSpec
};
//text.IsClippedToChartRect = true;
if (!detectLabelOverlap(this, g, text, out textBoundsRegion, item.Points, maxIndexList[i], item is StickItem))
{
GraphObjList.Add(text);
_pointAnnotations.Add(text);
clipRegion.Union(textBoundsRegion);
g.SetClip(clipRegion, CombineMode.Replace);
}
}
}
// add manual annotations
foreach (CurveItem item in CurveList)
{
IMSGraphItemInfo info = item.Tag as IMSGraphItemInfo;
MSPointList points = item.Points as MSPointList;
if (info == null || points == null)
{
continue;
}
info.AddAnnotations(this, g, points, _pointAnnotations);
foreach (GraphObj obj in _pointAnnotations)
{
if (!GraphObjList.Contains(obj))
{
TextObj text = obj as TextObj;
if (text != null)
{
if (detectLabelOverlap(this, g, text, out textBoundsRegion, item.Points, -1, item is StickItem))
{
continue;
}
clipRegion.Union(textBoundsRegion);
g.SetClip(clipRegion, CombineMode.Replace);
}
GraphObjList.Add(obj);
}
}
/*GraphObjList objsToRemove = new GraphObjList();
* foreach( GraphObj obj in GraphObjList )
* if( !pointAnnotations_.Contains( obj ) )
* objsToRemove.Add( obj );
* foreach( GraphObj obj in objsToRemove )
* GraphObjList.Remove( obj );*/
}
}
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 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)
{
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 AddAnnotations(MSGraphPane graphPane, Graphics g,
MSPointList pointList, GraphObjList annotations)
{
if (Chromatogram == null)
{
return;
}
// Calculate maximum y for potential retention time indicators
PointF ptTop = new PointF(0, graphPane.Chart.Rect.Top);
if (GraphChromatogram.ShowRT != ShowRTChrom.none)
{
if (RetentionMsMs != null)
{
foreach (double retentionTime in RetentionMsMs)
{
Color color = COLOR_MSMSID_TIME;
if (SelectedRetentionMsMs.HasValue && Equals((float)retentionTime, (float)SelectedRetentionMsMs))
{
color = ColorSelected;
}
AddRetentionTimeAnnotation(graphPane, g, annotations, ptTop,
Resources.ChromGraphItem_AddAnnotations_ID, GraphObjType.ms_ms_id, color,
ScaleRetentionTime(retentionTime));
}
}
if (MidasRetentionMsMs != null)
{
foreach (var retentionTime in MidasRetentionMsMs)
{
var color = SelectedRetentionMsMs.HasValue && Equals((float)retentionTime, (float)SelectedRetentionMsMs)
? ColorSelected
: COLOR_MSMSID_TIME;
AddRetentionTimeAnnotation(graphPane, g, annotations, ptTop, string.Empty, GraphObjType.midas_spectrum, color, ScaleRetentionTime(retentionTime));
}
}
if (AlignedRetentionMsMs != null)
{
foreach (var time in AlignedRetentionMsMs)
{
var scaledTime = ScaleRetentionTime(time);
var line = new LineObj(COLOR_ALIGNED_MSMSID_TIME, scaledTime.DisplayTime, 0,
scaledTime.DisplayTime, 1)
{
ZOrder = ZOrder.F_BehindGrid,
Location = { CoordinateFrame = CoordType.XScaleYChartFraction },
IsClippedToChartRect = true,
Tag = new GraphObjTag(this, GraphObjType.aligned_ms_id, scaledTime),
};
annotations.Add(line);
}
}
if (UnalignedRetentionMsMs != null)
{
foreach (var time in UnalignedRetentionMsMs)
{
var scaledTime = ScaleRetentionTime(time);
var line = new LineObj(COLOR_UNALIGNED_MSMSID_TIME, scaledTime.DisplayTime, 0,
scaledTime.DisplayTime, 1)
{
ZOrder = ZOrder.F_BehindGrid,
Location = { CoordinateFrame = CoordType.XScaleYChartFraction },
IsClippedToChartRect = true,
Tag = new GraphObjTag(this, GraphObjType.unaligned_ms_id, scaledTime),
};
annotations.Add(line);
}
}
}
// Draw retention time indicator, if set
if (RetentionPrediction.HasValue)
{
double time = RetentionPrediction.Value;
// Create temporary label to calculate positions
if (GraphChromatogram.ShowRT != ShowRTChrom.none)
{
AddRetentionTimeAnnotation(graphPane,
g,
annotations,
ptTop,
Resources.ChromGraphItem_AddAnnotations_Predicted,
GraphObjType.predicted_rt_window,
COLOR_RETENTION_TIME,
ScaleRetentionTime(time));
}
// Draw background for retention time window
if (RetentionWindow > 0)
{
double x1 = ScaleRetentionTime(time - RetentionWindow / 2).DisplayTime;
double x2 = ScaleRetentionTime(time + RetentionWindow / 2).DisplayTime;
BoxObj box = new BoxObj(x1, 0, x2 - x1, 1,
COLOR_RETENTION_WINDOW, COLOR_RETENTION_WINDOW)
{
Location = { CoordinateFrame = CoordType.XScaleYChartFraction },
IsClippedToChartRect = true,
ZOrder = ZOrder.F_BehindGrid
};
annotations.Add(box);
}
}
if (RetentionExplicit != null && GraphChromatogram.ShowRT != ShowRTChrom.none)
{
// Create temporary label to calculate positions
AddRetentionTimeAnnotation(graphPane,
g,
annotations,
ptTop,
Resources.ChromGraphItem_AddAnnotations_Explicit,
GraphObjType.predicted_rt_window,
COLOR_RETENTION_TIME,
ScaleRetentionTime(RetentionExplicit.RetentionTime));
}
for (int i = 0, len = Chromatogram.NumPeaks; i < len; i++)
{
if (_arrayLabelIndexes[i] == -1)
{
continue;
}
double maxIntensity = _intensities[_arrayLabelIndexes[i]];
// Show peak extent indicators, if they are far enough apart
ChromPeak peak = Chromatogram.GetPeak(i);
AddPeakBoundaries(graphPane, annotations, false,
ScaleRetentionTime(peak.StartTime), ScaleRetentionTime(peak.EndTime), maxIntensity);
}
}
public void doPlot(IEnumerable <Position> positions)
{
clear();
var closed = O.accept(positions, position => position.isClosed());
var pnls = O.sort(O.convert(closed, toValue));
var min = O.first(pnls);
var max = O.last(pnls);
var range = max - min;
var bucketCount = Math.Max(Math.Min(150, pnls.Count / 5), 1);
var blockSize = Math.Max(1, range / bucketCount);
if (blockSize == 1)
{
bucketCount = (int)range + 1;
}
var buckets = O.array(O.nCopies(bucketCount, 0.0));
O.each(pnls, pnl => {
var bucket = (int)((pnl - min) / blockSize);
if (bucket == bucketCount)
{
bucket--;
}
buckets[bucket]++;
});
var bucketStarts = O.array(O.convert(buckets, (i, unused) => i * blockSize + min));
var pnlCount = O.count(pnls);
var lowerQuartile = pnls[pnlCount / 4];
var upperQuartile = pnls[3 * pnlCount / 4];
var median = pnls[pnlCount / 2];
var mean = O.average(pnls);
var sd = O.populationStandardDeviation(pnls);
var colors = O.array(O.convert(bucketStarts, (i, bucket) => {
var isLow = bucket < median;
var isBright = bucket <= lowerQuartile || bucket >= upperQuartile;
if (isLow)
{
return(isBright ? (2.0 / 3.0) : 0.0);
}
return(isBright ? 1.0 : (1.0 / 3.0));
}));
var points = new PointPairList(bucketStarts, buckets, colors);
addBars("pnls", O.array(Color.DarkRed, Color.FromArgb(0, 18, 110), Color.Red, Color.FromArgb(0, 60, 255)), points);
GraphObjList.Add(new LineObj(Color.Lime, 0, 0, 0, 1)
{
Location = { CoordinateFrame = CoordType.XScaleYChartFraction },
Line = { Style = DashStyle.Dot, Width = 2 }
});
GraphObjList.Add(new TextObj(O.join("\n", O.list(
"min = " + O.prettyNumber(min),
"25% = " + O.prettyNumber(lowerQuartile),
"50% = " + O.prettyNumber(median),
"75% = " + O.prettyNumber(upperQuartile),
"max = " + O.prettyNumber(max), "",
"mean = " + O.prettyNumber(mean),
"sd(pop) = " + O.prettyNumber(sd)
)), 0.9, 0.12, CoordType.ChartFraction)
{
FontSpec = { StringAlignment = StringAlignment.Near }
});
BarSettings.MinClusterGap = 0;
XAxis.Scale.MinGrace = 0;
XAxis.Scale.MaxGrace = 0;
}
public override void UpdateGraph(bool selectionChanged)
{
GraphObjList.Clear();
CurveList.Clear();
Legend.IsVisible = false;
if (!DetectionPlotData.GetDataCache().TryGet(
GraphSummary.DocumentUIContainer.DocumentUI, Settings.QValueCutoff, this.DataCallback,
out _detectionData))
{
return;
}
AddLabels();
BarSettings.Type = BarType.SortedOverlay;
BarSettings.MinClusterGap = 0.3f;
Legend.IsVisible = Settings.ShowLegend;
var emptySymbol = new Symbol(SymbolType.None, Color.Transparent);
//draw bars
var counts = TargetData.TargetsCount;
var countPoints = new PointPairList(Enumerable.Range(0, _detectionData.ReplicateCount)
.Select(i => new PointPair(i, counts[i] / YScale)).ToList());
CurveList.Insert(0, MakeBarItem(countPoints, Color.FromArgb(180, 220, 255)));
//draw cumulative curve
counts = TargetData.TargetsCumulative;
var cumulativePoints = new PointPairList(Enumerable.Range(0, _detectionData.ReplicateCount)
.Select(i => new PointPair(i, counts[i] / YScale)).ToList());
CurveList.Insert(1,
new LineItem(Resources.DetectionPlotPane_CumulativeLine_Name)
{
Points = cumulativePoints,
Symbol = emptySymbol,
Line = new Line()
{
Color = Color.Coral, Width = 2
}
});
//draw inclusive curve
counts = TargetData.TargetsAll;
var allPoints = new PointPairList(Enumerable.Range(0, _detectionData.ReplicateCount)
.Select(i => new PointPair(i, counts[i] / YScale)).ToList());
CurveList.Insert(2,
new LineItem(Resources.DetectionPlotPane_AllRunsLine_Name)
{
Symbol = emptySymbol,
Points = allPoints,
Line = new Line()
{
Color = Color.Black, Width = 2
}
});
//axes formatting
XAxis.Scale.Max = _detectionData.ReplicateCount + 1;
YAxis.Scale.Max = _detectionData.GetTargetData(Settings.TargetType).MaxCount / YScale * 1.15;
if (Settings.ShowAtLeastN)
{
double lineY = TargetData.getCountForMinReplicates(Settings.RepCount);
var atLeastLine = new Line()
{
Width = 1, Color = Color.Blue, Style = DashStyle.Dash
};
var dummyPoints = new PointPairList(new[] { new PointPair(0, 0) });
var line = new LineObj(Color.Blue, 0, lineY / YScale, XAxis.Scale.Max, lineY / YScale)
{
IsClippedToChartRect = true,
Line = atLeastLine
};
GraphObjList.Add(line);
//This is a placeholder to make sure the line shows in the legend.
CurveList.Insert(3,
new LineItem(String.Format(CultureInfo.CurrentCulture,
Resources.DetectionPlotPane_AtLeastLine_Name,
Settings.RepCount, _detectionData.ReplicateCount, lineY))
{
Symbol = emptySymbol,
Points = dummyPoints,
Line = atLeastLine
});
}
if (Settings.ShowSelection)
{
var selectedIndex = GraphSummary.StateProvider.SelectedResultsIndex;
var lineLength = TargetData.TargetsCount[selectedIndex] / YScale + YAxis.Scale.Max * 0.05;
GraphObjList.Add(
new LineObj(Color.Black, selectedIndex + 1, 0, selectedIndex + 1, lineLength)
{
IsClippedToChartRect = true,
Line = new Line()
{
Width = 1, Color = Color.Black, Style = DashStyle.Dash
}
});
}
if (Settings.ShowMean)
{
var stats = new Statistics(TargetData.TargetsCount.Select((x) => (double)x));
var labelText = String.Format(CultureInfo.CurrentCulture,
TextUtil.LineSeparate(new[]
{
Resources.DetectionPlotPane_Label_Mean,
Resources.DetectionPlotPane_Label_Stddev
}
),
stats.Mean(), stats.StdDev());
GraphObjList.Add(new TextObj(labelText, 0.1, YAxis.Scale.Max,
CoordType.AxisXYScale, AlignH.Left, AlignV.Top)
{
IsClippedToChartRect = true,
ZOrder = ZOrder.E_BehindCurves,
FontSpec = GraphSummary.CreateFontSpec(Color.Black),
});
}
}
/// <summary>
/// Highlight the interiorPos position of selected planets or averages.
/// </summary>
/// <param name="sender"></param>
/// <param name="e"></param>
private void timer1_Tick(object sender, EventArgs e)
{
if (currentIndicators.Count != 0)
{
foreach (GraphObj obj in currentIndicators)
{
zedLongTerm.GraphPane.GraphObjList.Remove(obj);
}
currentIndicators.Clear();
}
#region Draw the line to highlight interiorPos planet positions
DateTimeOffset now = DateTimeOffset.UtcNow;
string timeString = DateTimeOffset.Now.ToString("MM-dd HH:mm");
now = new DateTimeOffset(now.Year, now.Month, now.Day, now.Hour, now.Minute, 0, TimeSpan.Zero);
double x = now.DateTime.ToOADate();
LineObj nowIndicator = new LineObj(x, zedLongTerm.GraphPane.YAxis.Scale.Min - 10, x, zedLongTerm.GraphPane.YAxis.Scale.Max + 10);
nowIndicator.Line.Style = System.Drawing.Drawing2D.DashStyle.Dash;
nowIndicator.Line.Color = Color.Gray;
currentIndicators.Add(nowIndicator);
#region With the lable of local time under the line
TextObj timeIndicator = new TextObj(timeString, x, 0, CoordType.AxisXYScale);
timeIndicator.Location.AlignH = AlignH.Center;
timeIndicator.Location.AlignV = AlignV.Top;
timeIndicator.FontSpec.Fill.Color = Color.Yellow;
timeIndicator.FontSpec.Fill.IsVisible = true;
timeIndicator.FontSpec.Border.IsVisible = true;
timeIndicator.FontSpec.Size = 6f;
currentIndicators.Add(timeIndicator);
#endregion
if (checkBoxReadings.Checked)
{
for (int i = 0; i < CurrentEphemeris.Luminaries.Count; i++)
{
CheckBox cb = panelStars.Controls[i] as CheckBox;
Position pos = null;
if (cb != null && cb.Checked)
{
PlanetId id = CurrentEphemeris.Luminaries[i];
string label = null;
double y = 180;
if (id < PlanetId.SE_FICT_OFFSET)
{
pos = CurrentEphemeris[now, id];
y = pos.Longitude;
label = string.Format("{0}: {1} ({2})", Planet.Glyphs[id], pos.Longitude.ToString("F1"), Rectascension.AstroStringOf(pos.Longitude));
}
else if (OrbitsDict[PositionValueIndex.Longitude].ContainsKey(id))
{
int todayIndex = (int)Math.Floor(x - since.DateTime.ToOADate());
double y1 = OrbitsDict[PositionValueIndex.Longitude][id][todayIndex];
double y2 = OrbitsDict[PositionValueIndex.Longitude][id][todayIndex + 1];
y = y1 + (y2 - y1) / (x - since.DateTime.ToOADate());
label = string.Format("{0}: {1:F1} ({2})", Planet.Glyphs[id], y, Rectascension.AstroStringOf(y));
}
TextObj posText = lableOf(label, x, y);
posText.Location.AlignV = y < 180 ? AlignV.Bottom : AlignV.Top;
currentIndicators.Add(posText);
}
}
}
#endregion
foreach (GraphObj obj in currentIndicators)
{
zedLongTerm.GraphPane.GraphObjList.Add(obj);
}
zedLongTerm.Invalidate();
}
public void add(List <Position> positions, List <Trade> trades, Simulator simulator)
{
Action <Trade, double> addTrade = (trade, x) => {
var y = trade.price;
var color = trade.direction.longShort(Color.Green, Color.Red);
var line = AddCurve("", new PointPairList {
{ x, y }
}, color, SymbolType.Circle);
line.Symbol.Fill = new Fill(color);
line.Label.IsVisible = false;
line.Line.IsVisible = false;
line.IsOverrideOrdinal = true;
var arrow = new ArrowObj(x, trade.direction.longShort(0.93, 0.07), x, trade.direction.longShort(0.89, 0.11))
{
Location = { CoordinateFrame = CoordType.XScaleYChartFraction },
ZOrder = ZOrder.A_InFront
};
GraphObjList.Add(arrow);
var dottedLine = new LineObj(Color.LightGray, x, 0.11, x, 0.89)
{
ZOrder = ZOrder.E_BehindCurves,
Line = { Style = DashStyle.Dot },
Location = { CoordinateFrame = CoordType.XScaleYChartFraction }
};
GraphObjList.Add(dottedLine);
var text = new TextObj(
trade.description + "\n" + trade.size + "@" + trade.price.ToString("n4"),
x, trade.direction.longShort(0.935, 0.065),
CoordType.XScaleYChartFraction,
AlignH.Center,
trade.direction.longShort(AlignV.Top, AlignV.Bottom)
)
{
FontSpec = { Size = 8, Border = { IsVisible = false } }
};
if (Objects.username().Equals("rsheftel"))
{
text.FontSpec.FontColor = Color.Fuchsia;
text.FontSpec.Size = 11;
}
GraphObjList.Add(text);
};
Objects.each(trades, trade => addTrade(trade, dateParent.index(trade.time)));
Action <Position> addPositionMaybe = position => {
if (!position.isClosed())
{
return;
}
var pnl = position.pnl(true, simulator.runInNativeCurrency());
var color = pnl > 0 ? Color.Green : (pnl < 0 ? Color.Red : Color.Black);
var line = AddCurve("", new PointPairList {
{ dateParent.index(position.entry().time), position.entry().price }, { dateParent.index(position.exitTrade().time), position.exitTrade().price }
}, color);
line.Symbol.IsVisible = false;
line.Line.Style = DashStyle.Dot;
line.Line.Width = 2;
line.Label.IsVisible = false;
line.IsOverrideOrdinal = true;
};
Objects.each(positions, addPositionMaybe);
simulator.addNewTradeListener((position, trade) => {
if (!position.symbol.Equals(symbol))
{
return;
}
addTrade(trade, bars.count());
addPositionMaybe(position);
});
}
