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);
}
}
}
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;
//draw bars
var countPoints = new PointPairList(Enumerable.Range(0, _detectionData.ReplicateCount)
.Select(i => new PointPair(i, TargetData.Histogram[i] / YScale)).ToList());
CurveList.Insert(0, MakeBarItem(countPoints, Color.FromArgb(180, 220, 255)));
//axes formatting
XAxis.Scale.Max = _detectionData.ReplicateCount + 1;
YAxis.Scale.Max = TargetData.Histogram.Max() / YScale * 1.15;
}
public MSGraphPane(MSGraphPane other)
: base(other)
{
_currentItemType = other._currentItemType;
_pointAnnotations = new GraphObjList();
_manualLabels = new Dictionary <TextObj, RectangleF>();
_labelBoundsCache = other._labelBoundsCache;
}
/// <summary>
/// 设置memo
/// </summary>
/// <param name="gl"></param>
public void SetTextObj(GraphObjList gl)
{
zed1.GraphPane.GraphObjList = gl;
foreach (var a in zed1.GraphPane.GraphObjList)
{
((TextObj)a).FontSpec.FontColor = Color.Black;
}
}
public override void Draw(Graphics g)
{
GraphObjList.Clear();
// Force Axes to recalculate to ensure proper layout of labels
AxisChange(g);
base.Draw(g);
}
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);
}
public override void Draw(Graphics g)
{
GraphObjList.Clear();
YAxis.Scale.Min = 0.0;
AxisChange(g);
AddLabels(g);
base.Draw(g);
}
public void removeCrosshair()
{
if (xLine == null)
{
return;
}
GraphObjList.Remove(xLine);
GraphObjList.Remove(yLine);
xLine = null;
yLine = null;
}
private void SetMappedItem(string itemID)
{
if (m_MappedItem == itemID)
{
return;
}
GraphObjList.Clear();
CurveItem item = GetCurve(m_MappedItem);
if (item != null)
{
item.IsVisible = true;
}
m_MappedItem = itemID;
item = CurveList[itemID];
if (item != null)
{
item.IsVisible = false;
List <GraphObj> objects = new List <GraphObj>();
for (int index = 0; index < item.Points.Count; index++)
{
PointPair point = item[index];
LineObj line = new LineObj(Color.Gray, point.X, 0, point.X, 1);
line.Tag = point.Y;
line.Location.CoordinateFrame = CoordType.XScaleYChartFraction;
line.ZOrder = ZOrder.E_BehindCurves;
TextObj text = new TextObj(point.Y.ToString(), point.X, 1);
text.Location.CoordinateFrame = CoordType.XScaleYChartFraction;
text.IsClippedToChartRect = false;
text.FontSpec.Border.IsVisible = false;
text.Location.AlignV = AlignV.Bottom;
text.Location.AlignH = AlignH.Right;
text.FontSpec.Angle = -90;
text.FontSpec.Fill.IsVisible = false;
objects.Add(line);
objects.Add(text);
}
GraphObjList.AddRange(objects);
}
m_HasChanged = true;
m_Parent.UpdateGraph();
}
public override void Draw(Graphics g)
{
GraphObjList.Clear();
var data = Data;
if (data != null && RTGraphController.PlotType == PlotTypeRT.correlation)
{
// Force Axes to recalculate to ensure proper layout of labels
AxisChange(g);
data.AddLabels(this, g);
}
base.Draw(g);
}
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 MSGraphPane()
{
Title.IsVisible = false;
Chart.Border.IsVisible = false;
Y2Axis.IsVisible = false;
X2Axis.IsVisible = false;
XAxis.MajorTic.IsOpposite = false;
YAxis.MajorTic.IsOpposite = false;
XAxis.MinorTic.IsOpposite = false;
YAxis.MinorTic.IsOpposite = false;
IsFontsScaled = false;
YAxis.Scale.MaxGrace = 0.1;
_currentItemType = MSGraphItemType.unknown;
_pointAnnotations = new GraphObjList();
}
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);
}
public override void Draw(Graphics g)
{
GraphObjList.Clear();
YAxis.Scale.Min = 0.0;
AxisChange(g);
foreach (var l in _lineItems)
{
if (l != null)
{
l[0].X = XAxis.Scale.Min;
l[1].X = XAxis.Scale.Max;
}
}
base.Draw(g);
}
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));
}
}
}
public MSGraphPane(LabelBoundsCache labelBoundsCache = null)
{
Title.IsVisible = false;
Chart.Border.IsVisible = false;
Y2Axis.IsVisible = false;
X2Axis.IsVisible = false;
XAxis.MajorTic.IsOpposite = false;
YAxis.MajorTic.IsOpposite = false;
XAxis.MinorTic.IsOpposite = false;
YAxis.MinorTic.IsOpposite = false;
IsFontsScaled = false;
YAxis.Scale.MaxGrace = 0.1;
YAxis.MajorGrid.IsZeroLine = false; // Hide the y=0 line
LockYAxisAtZero = true;
_currentItemType = MSGraphItemType.unknown;
_pointAnnotations = new GraphObjList();
_manualLabels = new Dictionary <TextObj, RectangleF>();
_labelBoundsCache = labelBoundsCache ?? new LabelBoundsCache();
}
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 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);
}
/// <summary>
/// Get all annotation label text, for testing purposes
/// </summary>
public IEnumerable <string> GetAnnotationLabelStrings()
{
foreach (CurveItem item in CurveList)
{
var info = item.Tag as IMSGraphItemExtended;
if (info == null || string.IsNullOrEmpty(info.ToString()))
{
continue;
}
var points = item.Points as MSPointList;
if (points == null)
{
continue;
}
var listAnnotations = new GraphObjList();
info.AddPreCurveAnnotations(this, null, points, listAnnotations);
foreach (var annotation in listAnnotations)
{
var textObj = annotation as TextObj;
if (textObj != null)
{
yield return(textObj.Text);
}
}
foreach (var pt in points.FullList)
{
var annotation = info.AnnotatePoint(pt);
if (annotation != null)
{
yield return(annotation.Label);
}
}
}
}
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 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 abstract void AddPreCurveAnnotations(MSGraphPane graphPane, Graphics g,
MSPointList pointList, GraphObjList annotations);
public override void AddPreCurveAnnotations(MSGraphPane graphPane, Graphics g, MSPointList pointList, GraphObjList annotations)
{
// Do nothing
}
public override void UpdateGraph(bool selectionChanged)
{
Clear();
TransitionGroupDocNode selectedGroup = null;
PeptideGroupDocNode selectedProtein = null;
var selectedTreeNode = GraphSummary.StateProvider.SelectedNode as SrmTreeNode;
if (selectedTreeNode != null)
{
if (selectedTreeNode is TransitionTreeNode)
{
selectedGroup = (TransitionGroupDocNode)selectedTreeNode.SrmParent.Model;
}
else if (selectedTreeNode is TransitionGroupTreeNode)
{
selectedGroup = (TransitionGroupDocNode)selectedTreeNode.Model;
}
else
{
var node = selectedTreeNode as PeptideTreeNode;
if (node != null)
{
var nodePep = node.DocNode;
selectedGroup = nodePep.TransitionGroups.FirstOrDefault();
}
}
var proteinTreeNode = selectedTreeNode.GetNodeOfType <PeptideGroupTreeNode>();
if (proteinTreeNode != null)
{
selectedProtein = proteinTreeNode.DocNode;
}
}
SrmDocument document = GraphSummary.DocumentUIContainer.DocumentUI;
var displayType = GraphChromatogram.GetDisplayType(document, selectedTreeNode);
_graphData = CreateGraphData(document, selectedProtein, selectedGroup, displayType);
int iColor = 0;
int colorOffset = 0;
if (selectedGroup != null && displayType == DisplayTypeChrom.products)
{
// If we are only displaying product ions, we want to use an offset in the colors array
// so that we do not re-use colors that would be used for any precursor ions.
colorOffset =
GraphChromatogram.GetDisplayTransitions(selectedGroup, DisplayTypeChrom.precursors).Count();
}
foreach (var pointPairList in _graphData.PointPairLists)
{
Color color = displayType == DisplayTypeChrom.total
? COLORS_GROUPS[iColor++ % COLORS_GROUPS.Count]
: COLORS_TRANSITION[(iColor++ + colorOffset) % COLORS_TRANSITION.Count];
BarItem curveItem;
if (HiLowMiddleErrorBarItem.IsHiLoMiddleErrorList(pointPairList))
{
curveItem = new HiLowMiddleErrorBarItem(string.Empty, pointPairList, color, Color.Black);
}
else
{
curveItem = new MeanErrorBarItem(string.Empty, pointPairList, color, Color.Black);
}
curveItem.Bar.Border.IsVisible = false;
curveItem.Bar.Fill.Brush = new SolidBrush(color);
CurveList.Add(curveItem);
}
if (ShowSelection && SelectedIndex != -1)
{
double yValue = _graphData.SelectedMaxY;
double yMin = _graphData.SelectedMinY;
double height = yValue - yMin;
GraphObjList.Add(new BoxObj(SelectedIndex + .5, yValue, 0.99,
height, Color.Black, Color.Empty)
{
IsClippedToChartRect = true,
});
}
UpdateAxes();
}
public void Clear()
{
Data = null;
CurveList.Clear();
GraphObjList.Clear();
}
/// <summary>
/// Constructor for deserializing objects
/// </summary>
/// <param name="info">A <see c_ref="SerializationInfo"/> instance that defines the serialized data
/// </param>
/// <param name="context">A <see c_ref="StreamingContext"/> instance that contains the serialized data
/// </param>
protected PaneBase( SerializationInfo info, StreamingContext context )
{
// The schema value is just a file version parameter. You can use it to make future versions
// backwards compatible as new member variables are added to classes
int sch = info.GetInt32( "schema" );
_rect = (RectangleF) info.GetValue( "rect", typeof(RectangleF) );
_legend = (Legend) info.GetValue( "legend", typeof(Legend) );
_title = (GapLabel) info.GetValue( "title", typeof(GapLabel) );
//this.isShowTitle = info.GetBoolean( "isShowTitle" );
_isFontsScaled = info.GetBoolean( "isFontsScaled" );
_isPenWidthScaled = info.GetBoolean( "isPenWidthScaled" );
//this.fontSpec = (FontSpec) info.GetValue( "fontSpec" , typeof(FontSpec) );
_titleGap = info.GetSingle( "titleGap" );
_fill = (Fill) info.GetValue( "fill", typeof(Fill) );
_border = (Border) info.GetValue( "border", typeof(Border) );
_baseDimension = info.GetSingle( "baseDimension" );
_margin = (Margin)info.GetValue( "margin", typeof( Margin ) );
_graphObjList = (GraphObjList) info.GetValue( "graphObjList", typeof(GraphObjList) );
_tag = info.GetValue( "tag", typeof(object) );
}
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);
}
}
/// <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;
}
}
/// <summary>
/// Default constructor for the <see c_ref="PaneBase"/> class. Specifies the <see c_ref="Title"/> of
/// the <see c_ref="PaneBase"/>, and the size of the <see c_ref="Rect"/>.
/// </summary>
public PaneBase( string title, RectangleF paneRect )
{
_rect = paneRect;
_legend = new Legend();
_baseDimension = Default.BaseDimension;
_margin = new Margin();
_titleGap = Default.TitleGap;
_isFontsScaled = Default.IsFontsScaled;
_isPenWidthScaled = Default.IsPenWidthScaled;
_fill = new Fill( Default.FillColor );
_border = new Border( Default.IsBorderVisible, Default.BorderColor,
Default.BorderPenWidth );
_title = new GapLabel( title, Default.FontFamily,
Default.FontSize, Default.FontColor, Default.FontBold,
Default.FontItalic, Default.FontUnderline );
_title._fontSpec.Fill.IsVisible = false;
_title._fontSpec.Border.IsVisible = false;
_graphObjList = new GraphObjList();
_tag = null;
}
public void AddAnnotations(MSGraphPane graphPane, Graphics g, MSPointList pointList, GraphObjList annotations)
{
}
/// <summary>
/// The Copy Constructor
/// </summary>
/// <param name="rhs">The <see c_ref="PaneBase"/> object from which to copy</param>
public PaneBase( PaneBase rhs )
{
// copy over all the value types
_isFontsScaled = rhs._isFontsScaled;
_isPenWidthScaled = rhs._isPenWidthScaled;
_titleGap = rhs._titleGap;
_baseDimension = rhs._baseDimension;
_margin = rhs._margin.Clone();
_rect = rhs._rect;
// Copy the reference types by cloning
_fill = rhs._fill.Clone();
_border = rhs._border.Clone();
_title = rhs._title.Clone();
_legend = rhs.Legend.Clone();
_title = rhs._title.Clone();
_graphObjList = rhs._graphObjList.Clone();
if ( rhs._tag is ICloneable )
_tag = ((ICloneable) rhs._tag).Clone();
else
_tag = rhs._tag;
}
