public GraphObjTag(ChromGraphItem chromGraphItem, GraphObjType graphObjType, ScaledRetentionTime start, ScaledRetentionTime end)
{
ChromGraphItem = chromGraphItem;
GraphObjType = graphObjType;
StartTime = start;
EndTime = end;
}
private void ZoomXAxis(double min, double max)
{
foreach (var graphPaneKeyItem in ListPrimaryGraphItems())
{
ScaledRetentionTime scaledMin = graphPaneKeyItem.Value.ScaleRetentionTime(min);
ScaledRetentionTime scaledMax = graphPaneKeyItem.Value.ScaleRetentionTime(max);
var graphPane = _displayState.GetGraphPane(GraphControl, graphPaneKeyItem.Key);
var axis = graphPane.XAxis;
axis.Scale.Min = scaledMin.DisplayTime;
axis.Scale.MinAuto = false;
axis.Scale.Max = scaledMax.DisplayTime;
axis.Scale.MaxAuto = false;
}
}
private void AddPeakRawTimes(GraphPane graphPane, ICollection <GraphObj> annotations,
ScaledRetentionTime startTime, ScaledRetentionTime endTime, ChromatogramInfo info)
{
var hasTimes = info.RawTimes != null && info.RawTimes.Any(); // has measured points
var scaledHeight = graphPane.YAxis.Scale.Max / 20; // 5% of graph pane height
var rawtimes = new List <double>();
if (hasTimes)
{
rawtimes.AddRange(GetRawTimes(startTime, endTime, info));
if (rawtimes.Count == 0)
{
return;
}
foreach (var time in rawtimes)
{
LineObj stick = new LineObj(time, scaledHeight, time, 0)
{
IsClippedToChartRect = true,
Location = { CoordinateFrame = CoordType.AxisXYScale },
ZOrder = ZOrder.A_InFront,
Line = { Width = 1, Style = DashStyle.Dash, Color = ColorSelected },
Tag = new GraphObjTag(this, GraphObjType.raw_time, new ScaledRetentionTime(time)),
};
annotations.Add(stick);
}
}
var countTxt = hasTimes ? " " + rawtimes.Count : " ?"; // Not L10N
var isBold = !hasTimes; // Question mark if no times exist is visually clearer if bold
TextObj pointCount = new TextObj(countTxt, endTime.DisplayTime, scaledHeight) // Not L10N
{
FontSpec = new FontSpec(FontSpec.Family, FontSpec.Size, ColorSelected, isBold, false, false)
{
Border = new Border {
IsVisible = false
},
Fill = new Fill()
},
Location =
{
AlignH = AlignH.Left,
AlignV = AlignV.Bottom
}
};
annotations.Add(pointCount);
}
private IEnumerable <double> GetRawTimes(ScaledRetentionTime startTime, ScaledRetentionTime endTime, ChromatogramInfo info)
{
double end = endTime.DisplayTime;
double start = startTime.DisplayTime;
var times = info.RawTimes;
if (times != null)
{
for (int j = 0; j < times.Count; j++)
{
if (start > times[j])
{
continue;
}
if (end < times[j])
{
break;
}
yield return(times[j]);
}
}
}
private void AddPeakBoundaries(GraphPane graphPane, ICollection <GraphObj> annotations,
bool best, ScaledRetentionTime startTime, ScaledRetentionTime endTime, double maxIntensity)
{
// Only show boundaries for dragging when boundaries turned off
if (!Settings.Default.ShowPeakBoundaries && (!best || DragInfo == null))
{
return;
}
float xStart = graphPane.XAxis.Scale.Transform(startTime.DisplayTime);
float xEnd = graphPane.XAxis.Scale.Transform(endTime.DisplayTime);
// Hide boundaries, if they are too close together
if (xEnd - xStart <= MIN_BOUNDARY_DISPLAY_WIDTH)
{
// But not if they are currently part of a drag operation.
if (DragInfo == null)
{
return;
}
}
// Make sure the best borders are visible
if (best)
{
float yMax = graphPane.YAxis.Scale.Transform(maxIntensity);
float yZero = graphPane.YAxis.Scale.Transform(0);
if (yZero - yMax < MIN_BEST_BOUNDARY_HEIGHT)
{
maxIntensity = graphPane.YAxis.Scale.ReverseTransform(yZero - MIN_BEST_BOUNDARY_HEIGHT);
}
}
// Summary graphs show only the best peak boundaries
else if (_isSummary)
{
return;
}
Color colorBoundaries = (best ? COLOR_BOUNDARIES_BEST : COLOR_BOUNDARIES);
GraphObjType graphObjType = best ? GraphObjType.best_peak : GraphObjType.peak;
// Make sure to get maximum intensity within the peak range,
// as this is not guaranteed to be the center of the peak
LineObj stickStart = new LineObj(colorBoundaries, startTime.DisplayTime, maxIntensity, startTime.DisplayTime, 0)
{
IsClippedToChartRect = true,
Location = { CoordinateFrame = CoordType.AxisXYScale },
ZOrder = ZOrder.B_BehindLegend,
Line = { Width = 1, Style = DashStyle.Dash },
Tag = new GraphObjTag(this, graphObjType, startTime),
};
annotations.Add(stickStart);
LineObj stickEnd = new LineObj(colorBoundaries, endTime.DisplayTime, maxIntensity, endTime.DisplayTime, 0)
{
IsClippedToChartRect = true,
Location = { CoordinateFrame = CoordType.AxisXYScale },
ZOrder = ZOrder.B_BehindLegend,
Line = { Width = 1, Style = DashStyle.Dash },
Tag = new GraphObjTag(this, graphObjType, endTime),
};
annotations.Add(stickEnd);
}
private void AddRetentionTimeAnnotation(MSGraphPane graphPane, Graphics g, GraphObjList annotations,
PointF ptTop, string title, GraphObjType graphObjType, Color color, ScaledRetentionTime retentionTime)
{
string label = string.Format("{0}\n{1:F01}", title, retentionTime.DisplayTime); // Not L10N
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 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 GraphObjTag(ChromGraphItem chromGraphItem, GraphObjType graphObjType, ScaledRetentionTime retentionTime)
{
ChromGraphItem = chromGraphItem;
GraphObjType = graphObjType;
RetentionTime = retentionTime;
}
