private IEnumerable <ChromGraphItem> GetChromGraphItems(MSGraphPane msGraphPane)
{
return(msGraphPane.CurveList
.Where(curve => !string.IsNullOrEmpty(curve.Label.Text))
.Select(curve => curve.Tag)
.OfType <ChromGraphItem>());
}
/// <summary>
/// Resets the all of the properties of a graph pane that might have changed
/// (or initialize the properties of a newly created pane) so that it's ready
/// to be used by a different set of graphs.
/// </summary>
public virtual void ApplySettingsToGraphPane(MSGraphPane graphPane)
{
graphPane.Legend.IsVisible = ShowLegend;
graphPane.Title.IsVisible = true;
graphPane.Title.Text = null;
graphPane.AllowLabelOverlap = AllowLabelOverlap;
}
/// <summary>
/// Resets the all of the properties of a graph pane that might have changed
/// (or initialize the properties of a newly created pane) so that it's ready
/// to be used by a different set of graphs.
/// </summary>
public virtual void ApplySettingsToGraphPane(MSGraphPane graphPane)
{
graphPane.Legend.IsVisible = ShowLegend;
graphPane.Title.IsVisible = true;
graphPane.Title.Text = null;
graphPane.AllowLabelOverlap = true; // Always allow labels to overlap - they're transparent so it's OK to do so
}
private int GetChromatogramCount(MSGraphPane msGraphPane)
{
int count = 0;
RunUI(() => count = GetChromGraphItems(msGraphPane).Count());
return(count);
}
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 MSGraphPane InsertMsGraphPane(MSGraphControl graphControl, int iInsert)
{
var pane = new MSGraphPane
{
Border = { IsVisible = false },
AllowCurveOverlap = true,
};
ApplySettingsToGraphPane(pane);
var primaryPane = graphControl.GraphPane;
pane.CurrentItemType = primaryPane.CurrentItemType;
pane.ZoomStack.AddRange(primaryPane.ZoomStack);
var zoomState = new ZoomState(primaryPane, ZoomState.StateType.Zoom);
zoomState.ApplyState(pane);
pane.YAxis.Title.Text = primaryPane.YAxis.Title.Text;
pane.XAxis.Title.Text = primaryPane.XAxis.Title.Text;
graphControl.MasterPane.PaneList.Insert(iInsert, pane);
return(pane);
}
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);
}
bool msGraphControl_MouseMoveEvent(ZedGraphControl sender, MouseEventArgs e)
{
MSGraphPane hoverPane = sender.MasterPane.FindPane(e.Location) as MSGraphPane;
if (hoverPane == null)
{
return(false);
}
CurveItem nearestCurve;
int nearestIndex;
//change the cursor if the mouse is sufficiently close to a point
if (hoverPane.FindNearestPoint(e.Location, out nearestCurve, out nearestIndex))
{
msGraphControl.Cursor = Cursors.Cross;
}
else
{
msGraphControl.Cursor = Cursors.Default;
}
return(false);
}
bool msGraphControl_MouseDownEvent(ZedGraphControl sender, MouseEventArgs e)
{
// keep track of MSGraphItem nearest the last left click
Point pos = MousePosition;
focusedPane = sender.MasterPane.FindPane(e.Location) as MSGraphPane;
if (focusedPane == null)
{
return(false);
}
CurveItem nearestCurve; int nearestIndex;
focusedPane.FindNearestPoint(e.Location, out nearestCurve, out nearestIndex);
if (nearestCurve == null)
{
setFocusedItem(sender.MasterPane[0].CurveList[0]);
}
else
{
setFocusedItem(nearestCurve);
}
return(false);
}
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 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 void AddAnnotations(MSGraphPane graphPane, Graphics g, MSPointList pointList, GraphObjList annotations)
{
}
protected override void OnShown(EventArgs e)
{
var dgv = source.SpectrumListForm.GridView;
var ionMobilityColumn = dgv.Columns["IonMobility"];
if (ionMobilityColumn == null || !ionMobilityColumn.Visible)
{
throw new InvalidOperationException("cannot show heatmap if SpectrumListForm doesn't have an IonMobility column");
}
var scanTimeColumn = dgv.Columns["ScanTime"];
var ticColumn = dgv.Columns["TotalIonCurrent"];
var msLevelColumn = dgv.Columns["MsLevel"];
var dataPointsColumn = dgv.Columns["DataPoints"];
var idColumn = dgv.Columns["Id"];
var mainSpectrumList = source.Source.MSDataFile.run.spectrumList;
if (scanTimeColumn == null || ticColumn == null || msLevelColumn == null || dataPointsColumn == null)
{
throw new InvalidOperationException("scan time, TIC, ms level, and data points columns should never be null");
}
// build map of ms levels, to scan times, to scan indices
for (int i = 0; i < dgv.RowCount; ++i)
{
int msLevel = (int)dgv[msLevelColumn.Index, i].Value - 1;
while (heatmapGraphPaneByMsLevel.Count <= msLevel)
{
heatmapBoundsByMsLevel.Add(new BoundingBox {
MinX = Double.MaxValue, MaxX = Double.MinValue, MinY = Double.MaxValue, MaxY = Double.MinValue
});
heatmapGraphPaneByMsLevel.Add(new HeatMapGraphPane()
{
ShowHeatMap = true,
MinDotRadius = 4,
MaxDotRadius = 13,
//XAxis = {Title = {Text = "Scan Time"}},
XAxis = { Title = { Text = "m/z" } },
YAxis = { Title = { Text = "Ion Mobility" } },
Legend = { IsVisible = false },
Title = { Text = String.Format("Ion Mobility Heatmap (ms{0})", msLevel + 1), IsVisible = true },
LockYAxisAtZero = false
});
ionMobilityBinsByMsLevelAndScanTime.Add(new Map <double, List <MobilityBin> >());
}
int dataPoints = Convert.ToInt32(dgv[dataPointsColumn.Index, i].Value);
if (dataPoints == 0)
{
continue;
}
double scanTime = (double)dgv[scanTimeColumn.Index, i].Value;
double ionMobility = (double)dgv[ionMobilityColumn.Index, i].Value;
if (ionMobility == 0)
{
var s = mainSpectrumList.spectrum(i, true);
var mobilityArray = s.getArrayByCVID(pwiz.CLI.cv.CVID.MS_mean_drift_time_array);
if (mobilityArray == null)
{
mobilityArray = s.getArrayByCVID(pwiz.CLI.cv.CVID.MS_mean_inverse_reduced_ion_mobility_array);
if (mobilityArray == null)
{
continue;
}
}
var mobilityBins = mobilityArray.data;
foreach (double bin in mobilityBins)
{
ionMobilityBinsByMsLevelAndScanTime[msLevel][scanTime].Add(new MobilityBin(bin, i));
}
}
else
{
ionMobilityBinsByMsLevelAndScanTime[msLevel][scanTime].Add(new MobilityBin(ionMobility, i));
}
//double intensity = (double) dgv[ticColumn.Index, i].Value;
}
var g = msGraphControl.CreateGraphics();
msGraphControl.MasterPane.PaneList.Clear();
int numColumns = ionMobilityBinsByMsLevelAndScanTime.Count(o => !o.IsNullOrEmpty()); // skip empty MS levels (e.g. files with only MS2)
var rowCounts = new int[2] {
numColumns, numColumns
};
msGraphControl.MasterPane.SetLayout(g, true, rowCounts, new float[2] {
0.25f, 0.75f
});
// first row is control chromatograms
for (int i = 0; i < heatmapGraphPaneByMsLevel.Count; ++i)
{
if (ionMobilityBinsByMsLevelAndScanTime[i].IsNullOrEmpty())
{
ticChromatogramByMsLevel.Add(null);
continue; // skip empty MS levels (e.g. files with only MS2)
}
var chromatogramPane = new MSGraphPane()
{
Legend = { IsVisible = false },
Title = { Text = String.Format("TIC Chromatogram (ms{0})", i + 1), IsVisible = true },
Tag = i
};
msGraphControl.MasterPane.Add(chromatogramPane);
ticChromatogramByMsLevel.Add(new ChromatogramControl(source, i + 1, chromatogramPane));
msGraphControl.AddGraphItem(chromatogramPane, ticChromatogramByMsLevel[i], true);
}
// second row is heatmaps
for (int i = 0; i < heatmapGraphPaneByMsLevel.Count; ++i)
{
if (ionMobilityBinsByMsLevelAndScanTime[i].IsNullOrEmpty())
{
continue; // skip empty MS levels (e.g. files with only MS2)
}
var heatmapGraphPane = heatmapGraphPaneByMsLevel[i];
msGraphControl.MasterPane.Add(heatmapGraphPane);
heatmapGraphPane.GraphObjList.Add(new TextObj("Click on a chromatogram point to generate an IMS heatmap...", 0.5, 0.5, CoordType.ChartFraction)
{
FontSpec = new FontSpec {
Border = new Border {
IsVisible = false
}, IsBold = true, Size = 16
}
});
var bounds = heatmapBoundsByMsLevel[i];
setScale(heatmapGraphPane.XAxis.Scale, 0, 2000);
setScale(heatmapGraphPane.YAxis.Scale, 0, 100);
heatmapGraphPane.AxisChange(g);
heatmapGraphPane.SetScale(g);
}
//msGraphControl.PerformAutoScale();
msGraphControl.MasterPane.DoLayout(g);
msGraphControl.Refresh();
base.OnShown(e);
}
protected override void OnShown(EventArgs e)
{
var dgv = Source.SpectrumListForm.GridView;
var ionMobilityColumn = dgv.Columns["IonMobility"];
//if (ionMobilityColumn == null || !ionMobilityColumn.Visible)
// throw new InvalidOperationException("cannot show heatmap if SpectrumListForm doesn't have an IonMobility column");
var scanTimeColumn = dgv.Columns["ScanTime"];
var ticColumn = dgv.Columns["TotalIonCurrent"];
var msLevelColumn = dgv.Columns["MsLevel"];
var isolationMzColumn = dgv.Columns["PrecursorInfo"];
var dataPointsColumn = dgv.Columns["DataPoints"];
var indexColumn = dgv.Columns["Index"];
var idColumn = dgv.Columns["Id"];
var mainSpectrumList = Source.Source.MSDataFile.run.spectrumList;
if (scanTimeColumn == null || ticColumn == null || msLevelColumn == null || dataPointsColumn == null)
{
throw new InvalidOperationException("scan time, TIC, ms level, and data points columns should never be null");
}
// build map of ms levels, to scan times, to scan indices;
// group keys are ms level and scan time, aggregated values are isolation m/z and spectrum index
var ionMobilityRows = GetIonMobilityRows().GroupBy(r => new Tuple <int, double>((int)r.Cells[msLevelColumn.Index].Value, (double)r.Cells[scanTimeColumn.Index].Value),
r => new Tuple <double, int>(ToDoubleOrDefault(r.Cells[isolationMzColumn.Index].Value), r.Index));
foreach (var group in ionMobilityRows)
{
int msLevel = group.Key.Item1 - 1;
while (heatmapGraphPaneByMsLevel.Count <= msLevel)
{
heatmapGraphPaneByMsLevel.Add(new HeatMapGraphPane()
{
ShowHeatMap = true,
MinDotRadius = 4,
MaxDotRadius = 13,
//XAxis = {Title = {Text = "Scan Time"}},
XAxis = { Title = { Text = "m/z" } },
YAxis = { Title = { Text = "Ion Mobility" } },
Legend = { IsVisible = false },
Title = { Text = String.Format("Ion Mobility Heatmap (ms{0})", msLevel + 1), IsVisible = true },
LockYAxisAtZero = false
});
ionMobilityBinsByMsLevelAndScanTime.Add(new Map <double, MobilityData>());
}
double scanTime = group.Key.Item2;
ionMobilityBinsByMsLevelAndScanTime[msLevel][scanTime] = new MobilityData(mainSpectrumList, scanTime,
(int)group.Min(o => o.Item2),
(int)group.Max(o => o.Item2));
if (msLevel + 1 == 2)
{
isolationMzByScanTime[scanTime] = group.Select(o => o.Item1.ToString()).ToList();
}
//double intensity = (double) dgv[ticColumn.Index, i].Value;
}
var g = msGraphControl.CreateGraphics();
msGraphControl.MasterPane.PaneList.Clear();
int numColumns = ionMobilityBinsByMsLevelAndScanTime.Count(o => !o.IsNullOrEmpty()); // skip empty MS levels (e.g. files with only MS2)
var rowCounts = new int[2] {
numColumns, numColumns
};
msGraphControl.MasterPane.SetLayout(g, true, rowCounts, new float[2] {
0.25f, 0.75f
});
heatmapPointsCache = new MemoryCache <MobilityData, Tuple <List <Point3D>, BoundingBox> >(ionMobilityBinsByMsLevelAndScanTime.Count);
// first row is control chromatograms
for (int i = 0; i < heatmapGraphPaneByMsLevel.Count; ++i)
{
if (ionMobilityBinsByMsLevelAndScanTime[i].IsNullOrEmpty())
{
ticChromatogramByMsLevel.Add(null);
continue; // skip empty MS levels (e.g. files with only MS2)
}
var chromatogramPane = new MSGraphPane()
{
Legend = { IsVisible = false },
Title = { Text = String.Format("TIC Chromatogram (ms{0})", i + 1), IsVisible = true },
Tag = i
};
msGraphControl.MasterPane.Add(chromatogramPane);
ticChromatogramByMsLevel.Add(new ChromatogramControl(Source, i + 1, chromatogramPane));
msGraphControl.AddGraphItem(chromatogramPane, ticChromatogramByMsLevel[i], true);
}
// second row is heatmaps
for (int i = 0; i < heatmapGraphPaneByMsLevel.Count; ++i)
{
if (ionMobilityBinsByMsLevelAndScanTime[i].IsNullOrEmpty())
{
continue; // skip empty MS levels (e.g. files with only MS2)
}
var heatmapGraphPane = heatmapGraphPaneByMsLevel[i];
msGraphControl.MasterPane.Add(heatmapGraphPane);
heatmapGraphPane.GraphObjList.Add(new TextObj("Click on a chromatogram point to generate an IMS heatmap...", 0.5, 0.5, CoordType.ChartFraction)
{
FontSpec = new FontSpec {
Border = new Border {
IsVisible = false
}, IsBold = true, Size = 16
}
});
setScale(heatmapGraphPane.XAxis.Scale, 0, 2000);
setScale(heatmapGraphPane.YAxis.Scale, 0, 100);
heatmapGraphPane.AxisChange(g);
heatmapGraphPane.SetScale(g);
}
//msGraphControl.PerformAutoScale();
msGraphControl.MasterPane.DoLayout(g);
msGraphControl.Refresh();
base.OnShown(e);
}
public override void Refresh()
{
MasterPane mp = msGraphControl.MasterPane;
mp.Border.IsVisible = false;
//pane.Chart.Border.IsVisible = false;
if (mp.PaneList.Count != paneList.Count)
{
mp.PaneList.Clear();
foreach (Pane logicalPane in paneList)
{
MSGraphPane pane = new MSGraphPane();
pane.Border.IsVisible = false;
pane.IsFontsScaled = false;
pane.YAxis.ScaleFormatEvent += YAxis_ScaleFormatEvent;
mp.Add(pane);
}
//mp.SetLayout( msGraphControl.CreateGraphics(), paneLayout );
}
else
{
for (int i = 0; i < paneList.Count; ++i)
{
MSGraphPane pane = mp.PaneList[i] as MSGraphPane;
pane.Border.IsVisible = false;
pane.CurveList.Clear();
pane.GraphObjList.Clear();
}
}
for (int i = 0; i < paneList.Count; ++i)
{
Pane logicalPane = paneList[i];
MSGraphPane pane = mp.PaneList[i] as MSGraphPane;
pane.IsFontsScaled = false;
pane.Border.IsVisible = false;
bool needSourceNamePrefix = logicalPane.Select(o => o.Source).Distinct().Count() > 1;
int maxAutoLegendItems = needSourceNamePrefix ? 5 : 10;
foreach (GraphItem item in logicalPane.Take(logicalPane.Count - 1))
{
//item.AddSourceToId = needSourceNamePrefix;
msGraphControl.AddGraphItem(pane, item, false);
}
//logicalPane.Last().AddSourceToId = needSourceNamePrefix;
msGraphControl.AddGraphItem(pane, logicalPane.Last(), true);
if (mp.PaneList.Count > 1)
{
if (msGraphControl.IsSynchronizeXAxes && i < paneList.Count - 1)
{
pane.XAxis.Title.IsVisible = false;
pane.XAxis.Scale.IsVisible = false;
pane.Margin.Bottom = 0;
//pane.Margin.Top = 0;
}
else
{
//pane.Margin.Top = 0;
pane.XAxis.Title.IsVisible = true;
pane.XAxis.Scale.IsVisible = true;
}
pane.YAxis.Title.IsVisible = true;
pane.YAxis.Scale.IsVisible = true;
pane.YAxis.Title.Text = String.Join(", ", logicalPane.Select(o => o.Title)) + "\n" + pane.YAxis.Title.Text.Split('\n').Last();
pane.YAxis.Scale.SetupScaleData(pane, pane.YAxis);
}
else
{
pane.XAxis.IsVisible = true;
pane.XAxis.Title.IsVisible = true;
pane.XAxis.Scale.IsVisible = true;
pane.YAxis.Title.IsVisible = true;
pane.YAxis.Scale.IsVisible = true;
}
if (logicalPane.Count == 1)
{
pane.Legend.IsVisible = false;
}
else
{
pane.Legend.IsVisible = ShowPaneLegends ?? (logicalPane.Count < maxAutoLegendItems);
pane.Legend.Position = ZedGraph.LegendPos.TopCenter;
ZedGraph.ColorSymbolRotator rotator = new ColorSymbolRotator();
foreach (CurveItem item in pane.CurveList)
{
item.Color = rotator.NextColor;
}
}
if (paneList.Count > 0 && paneList[0].Count > 0)
{
this.Text = paneList[0][0].Id;
if (paneList[0][0].IsMassSpectrum)
{
this.TabText = (paneList[0][0] as MassSpectrum).AbbreviatedId;
}
else
{
this.TabText = this.Text;
}
}
if (pane.XAxis.Scale.MaxAuto)
{
using (Graphics g = msGraphControl.CreateGraphics())
{
if (msGraphControl.IsSynchronizeXAxes || msGraphControl.IsSynchronizeYAxes)
{
foreach (GraphPane p in msGraphControl.MasterPane.PaneList)
{
p.XAxis.ResetAutoScale(p, g);
p.X2Axis.ResetAutoScale(p, g);
foreach (YAxis axis in p.YAxisList)
{
axis.ResetAutoScale(p, g);
}
foreach (Y2Axis axis in p.Y2AxisList)
{
axis.ResetAutoScale(p, g);
}
}
}
else
{
pane.XAxis.ResetAutoScale(pane, g);
pane.X2Axis.ResetAutoScale(pane, g);
foreach (YAxis axis in pane.YAxisList)
{
axis.ResetAutoScale(pane, g);
}
foreach (Y2Axis axis in pane.Y2AxisList)
{
axis.ResetAutoScale(pane, g);
}
}
}
//msGraphControl.RestoreScale(pane);
}
else
{
pane.AxisChange();
}
}
mp.SetLayout(msGraphControl.CreateGraphics(), paneLayout);
/*if( isOverlay )
* {
* pane.Legend.IsVisible = true;
* pane.Legend.Position = ZedGraph.LegendPos.TopCenter;
* for( int i = 0; i < pane.CurveList.Count; ++i )
* {
* pane.CurveList[i].Color = overlayColors[i];
* ( pane.CurveList[i] as ZedGraph.LineItem ).Line.Width = 2;
* }
* } else
* {
* pane.Legend.IsVisible = false;
* currentGraphItem = chromatogram;
* }*/
//msGraphControl.RestoreScale( pane );
//msGraphControl.ZoomOutAll( pane );
/*bool isScaleAuto = !pane.IsZoomed;
*
* if( isScaleAuto )
* pointList.SetScale( bins, pointList[0].X, pointList[pointList.Count - 1].X );
* else
* pointList.SetScale( bins, pane.XAxis.Scale.Min, pane.XAxis.Scale.Max );*/
// String.Format( "{0} - {1}", currentDataSource.Name, chromatogram.Id )
if (mp.PaneList.Count > 0 &&
(focusedPane == null ||
!mp.PaneList.Contains(focusedPane)))
{
focusedPane = mp.PaneList[0] as MSGraphPane;
}
if (mp.PaneList.Count > 0 &&
mp.PaneList[0].CurveList.Count > 0 &&
(focusedItem == null ||
//!focusedPane.CurveList.Contains( focusedItem ) ) ) // somehow focusedItem.Tag can be the same as one of focusedPane.CurveList's Tags, but Contains returns false
!focusedPane.CurveList.Any(o => o.Tag == focusedItem.Tag)))
{
setFocusedItem(mp.PaneList[0].CurveList[0]);
}
msGraphControl.Refresh();
}
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 Refresh()
{
MasterPane mp = msGraphControl.MasterPane;
mp.Border.IsVisible = false;
//pane.Chart.Border.IsVisible = false;
if (mp.PaneList.Count != paneList.Count)
{
mp.PaneList.Clear();
foreach (Pane logicalPane in paneList)
{
MSGraphPane pane = new MSGraphPane();
pane.Border.IsVisible = false;
pane.IsFontsScaled = false;
mp.Add(pane);
}
//mp.SetLayout( msGraphControl.CreateGraphics(), paneLayout );
}
else
{
for (int i = 0; i < paneList.Count; ++i)
{
MSGraphPane pane = mp.PaneList[i] as MSGraphPane;
pane.Border.IsVisible = false;
pane.CurveList.Clear();
pane.GraphObjList.Clear();
}
}
for (int i = 0; i < paneList.Count; ++i)
{
Pane logicalPane = paneList[i];
MSGraphPane pane = mp.PaneList[i] as MSGraphPane;
pane.IsFontsScaled = false;
pane.Border.IsVisible = false;
foreach (GraphItem item in logicalPane)
{
msGraphControl.AddGraphItem(pane, item);
}
if (mp.PaneList.Count > 1)
{
//if( i < paneList.Count - 1 )
{
pane.XAxis.Title.IsVisible = false;
pane.XAxis.Scale.IsVisible = false;
pane.Margin.Bottom = 0;
pane.Margin.Top = 2;
}/* else
* {
* pane.XAxis.Title.IsVisible = true;
* pane.XAxis.Scale.IsVisible = true;
* }*/
pane.YAxis.Title.IsVisible = false;
pane.YAxis.Scale.IsVisible = false;
pane.YAxis.Scale.SetupScaleData(pane, pane.YAxis);
}
else
{
pane.XAxis.IsVisible = true;
pane.XAxis.Title.IsVisible = true;
pane.XAxis.Scale.IsVisible = true;
pane.YAxis.Title.IsVisible = true;
pane.YAxis.Scale.IsVisible = true;
}
if (logicalPane.Count == 1)
{
pane.Legend.IsVisible = false;
}
else
{
pane.Legend.IsVisible = true;
pane.Legend.Position = ZedGraph.LegendPos.TopCenter;
ZedGraph.ColorSymbolRotator rotator = new ColorSymbolRotator();
foreach (CurveItem item in pane.CurveList)
{
item.Color = rotator.NextColor;
}
}
if (paneList.Count > 0 && paneList[0].Count > 0)
{
this.Text = paneList[0][0].Id;
if (paneList[0][0].IsMassSpectrum)
{
this.TabText = pwiz.CLI.msdata.id.abbreviate(paneList[0][0].Id);
}
else
{
this.TabText = this.Text;
}
}
if (pane.XAxis.Scale.MaxAuto)
{
msGraphControl.RestoreScale(pane);
}
else
{
pane.AxisChange();
}
}
mp.SetLayout(msGraphControl.CreateGraphics(), paneLayout);
/*if( isOverlay )
* {
* pane.Legend.IsVisible = true;
* pane.Legend.Position = ZedGraph.LegendPos.TopCenter;
* for( int i = 0; i < pane.CurveList.Count; ++i )
* {
* pane.CurveList[i].Color = overlayColors[i];
* ( pane.CurveList[i] as ZedGraph.LineItem ).Line.Width = 2;
* }
* } else
* {
* pane.Legend.IsVisible = false;
* currentGraphItem = chromatogram;
* }*/
//msGraphControl.RestoreScale( pane );
//msGraphControl.ZoomOutAll( pane );
/*bool isScaleAuto = !pane.IsZoomed;
*
* if( isScaleAuto )
* pointList.SetScale( bins, pointList[0].X, pointList[pointList.Count - 1].X );
* else
* pointList.SetScale( bins, pane.XAxis.Scale.Min, pane.XAxis.Scale.Max );*/
// String.Format( "{0} - {1}", currentDataSource.Name, chromatogram.Id )
if (mp.PaneList.Count > 0 &&
(focusedPane == null ||
!mp.PaneList.Contains(focusedPane)))
{
focusedPane = mp.PaneList[0] as MSGraphPane;
}
if (mp.PaneList.Count > 0 &&
mp.PaneList[0].CurveList.Count > 0 &&
(focusedItem == null ||
!focusedPane.CurveList.Contains(focusedItem)))
{
setFocusedItem(mp.PaneList[0].CurveList[0]);
}
msGraphControl.Refresh();
}
