public RunToRunRegressionToolbar(GraphSummary graphSummary) :
base(graphSummary)
{
InitializeComponent();
toolStrip1_Resize(null, null);
}
public RTScheduleGraphPane(GraphSummary graphSummary)
: base(graphSummary)
{
XAxis.Title.Text = Resources.RTScheduleGraphPane_RTScheduleGraphPane_Scheduled_Time;
YAxis.Scale.MinAuto = false;
YAxis.Scale.Min = 0;
}
protected SummaryReplicateGraphPane(GraphSummary graphSummary)
: base(graphSummary)
{
XAxis.Title.Text = Resources.SummaryReplicateGraphPane_SummaryReplicateGraphPane_Replicate;
XAxis.Type = AxisType.Text;
IsRepeatRemovalAllowed = true;
}
public bool ShowDelete(Point mousePt)
{
var regressionGraphPane = GraphSummary.GraphPaneFromPoint(mousePt) as RTLinearRegressionGraphPane;
return(regressionGraphPane != null &&
regressionGraphPane.AllowDeletePoint(new PointF(mousePt.X, mousePt.Y)));
}
public void OnRatioIndexChanged()
{
if (GraphSummary.GraphPanes.OfType <AreaReplicateGraphPane>().Any() /* || !Settings.Default.AreaAverageReplicates */)
{
GraphSummary.UpdateUI();
}
}
public void OnActiveLibraryChanged()
{
if (GraphSummary.GraphPanes.OfType <AreaReplicateGraphPane>().Any())
{
GraphSummary.UpdateUI();
}
}
public void OnUpdateGraph()
{
switch (GraphSummary.Type)
{
case GraphTypeSummary.replicate:
case GraphTypeSummary.peptide:
GraphSummary.DoUpdateGraph(this, GraphSummary.Type);
break;
case GraphTypeSummary.histogram:
if (!(GraphSummary.GraphPanes.FirstOrDefault() is MassErrorHistogramGraphPane))
{
GraphSummary.GraphPanes = new[] { new MassErrorHistogramGraphPane(GraphSummary) }
}
;
break;
case GraphTypeSummary.histogram2d:
if (!(GraphSummary.GraphPanes.FirstOrDefault() is MassErrorHistogram2DGraphPane))
{
GraphSummary.GraphPanes = new[] { new MassErrorHistogram2DGraphPane(GraphSummary) }
}
;
break;
}
}
public void OnNormalizeOptionChanged()
{
if (GraphSummary.GraphPanes.OfType <MassErrorReplicateGraphPane>().Any() /* || !Settings.Default.AreaAverageReplicates */)
{
GraphSummary.UpdateUI();
}
}
public RTLinearRegressionGraphPane(GraphSummary graphSummary)
: base(graphSummary)
{
XAxis.Title.Text = Resources.RTLinearRegressionGraphPane_RTLinearRegressionGraphPane_Score;
Settings.Default.RTScoreCalculatorList.ListChanged += RTScoreCalculatorList_ListChanged;
}
public bool HandleKeyDownEvent(object sender, KeyEventArgs e)
{
switch (e.KeyCode)
{
// case Keys.D3:
// if (e.Alt)
// GraphSummary.Hide();
// break;
case Keys.F7:
if (!e.Alt && !(e.Shift && e.Control))
{
if (e.Control)
{
Settings.Default.AreaGraphType = GraphTypeArea.peptide.ToString();
}
else
{
Settings.Default.AreaGraphType = GraphTypeArea.replicate.ToString();
}
GraphSummary.UpdateUI();
}
break;
}
return(false);
}
public RTScheduleGraphPane(GraphSummary graphSummary)
: base(graphSummary)
{
XAxis.Title.Text = Resources.RTScheduleGraphPane_RTScheduleGraphPane_Scheduled_Time;
YAxis.Scale.MinAuto = false;
YAxis.Scale.Min = 0;
}
public AreaCVHistogram2DGraphPane(GraphSummary graphSummary)
: base(graphSummary)
{
_areaCVGraphData = null;
_lineItems = new LineItem[2];
_cache = new AreaCVGraphData.AreaCVGraphDataCache();
}
public bool HandleKeyDownEvent(object sender, KeyEventArgs e)
{
switch (e.KeyCode)
{
// case Keys.D2:
// if (e.Alt)
// {
// GraphSummary.Hide();
// return true;
// }
// break;
case Keys.F8:
if (!e.Alt && !(e.Shift && e.Control))
{
if (e.Shift)
{
GraphType = GraphTypeRT.regression;
}
else if (e.Control)
{
GraphType = GraphTypeRT.peptide;
}
else
{
GraphType = GraphTypeRT.replicate;
}
GraphSummary.UpdateUI();
return(true);
}
break;
}
return(false);
}
public void OnResultsIndexChanged()
{
if (GraphSummary.GraphPanes.OfType <AreaReplicateGraphPane>().Any() /* || !Settings.Default.AreaAverageReplicates */ ||
RTLinearRegressionGraphPane.ShowReplicate == ReplicateDisplay.single)
{
GraphSummary.UpdateUI();
}
}
public void OnResultsIndexChanged()
{
if (GraphSummary.GraphPanes.FirstOrDefault() is RTReplicateGraphPane ||
RTLinearRegressionGraphPane.ShowReplicate == ReplicateDisplay.single)
{
GraphSummary.UpdateUI();
}
}
public DetectionsToolbar(GraphSummary graphSummary) : base(graphSummary)
{
InitializeComponent();
_timer = new Timer {
Interval = 100
};
_timer.Tick += Timer_OnTick;
}
private TextObj AddLabel(string text, double x, double y, Color color)
{
return(new TextObj(text, x, y, CoordType.AxisXYScale, AlignH.Center, AlignV.Bottom)
{
FontSpec = GraphSummary.CreateFontSpec(color),
IsClippedToChartRect = true
});
}
public void OnActiveLibraryChanged()
{
var fod = GraphSummary.GraphPanes.FirstOrDefault() as IUpdateGraphPaneController;
if (fod != null && fod.UpdateUIOnLibraryChanged())
{
GraphSummary.UpdateUI();
}
}
public void OnResultsIndexChanged()
{
var fod = GraphSummary.GraphPanes.FirstOrDefault() as IUpdateGraphPaneController;
if (fod != null && fod.UpdateUIOnIndexChanged())
{
GraphSummary.UpdateUI();
}
}
public RTScheduleGraphPane(GraphSummary graphSummary, bool isExportMethodDlg = false)
: base(graphSummary)
{
_exportMethodDlg = isExportMethodDlg;
XAxis.Title.Text = Resources.RTScheduleGraphPane_RTScheduleGraphPane_Scheduled_Time;
YAxis.Scale.MinAuto = false;
YAxis.Scale.Min = 0;
}
public void SetSelectedFile(string file)
{
var group = _replicateGroups?.FirstOrDefault(g => (g.FileInfo != null && g.FileInfo.FilePath.GetFileName() == file) || (g.FileInfo == null && file == null));
if (group != null)
{
SelectedGroup = group;
GraphSummary.UpdateUI();
}
}
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);
}
protected SummaryPeptideGraphPane(GraphSummary graphSummary, PaneKey paneKey)
: base(graphSummary)
{
PaneKey = paneKey;
string xAxisTitle = Resources.SummaryPeptideGraphPane_SummaryPeptideGraphPane_Peptide;
if (null != paneKey.IsotopeLabelType && !paneKey.IsotopeLabelType.IsLight)
{
xAxisTitle += " (" + paneKey.IsotopeLabelType + ")"; // Not L10N
}
XAxis.Title.Text = xAxisTitle;
XAxis.Type = AxisType.Text;
}
protected SummaryPeptideGraphPane(GraphSummary graphSummary, PaneKey paneKey)
: base(graphSummary)
{
PaneKey = paneKey;
string xAxisTitle = Resources.SummaryPeptideGraphPane_SummaryPeptideGraphPane_Peptide;
if (null != paneKey.IsotopeLabelType && !paneKey.IsotopeLabelType.IsLight)
{
xAxisTitle += @" (" + paneKey.IsotopeLabelType + @")";
}
XAxis.Title.Text = xAxisTitle;
XAxis.Type = AxisType.Text;
}
public AreaCVToolbar(GraphSummary graphSummary) :
base(graphSummary)
{
InitializeComponent();
toolStripNumericDetections.NumericUpDownControl.ValueChanged += NumericUpDownControl_ValueChanged;
toolStripComboGroup.SelectedIndexChanged += toolStripComboGroup_SelectedIndexChanged;
_timer = new Timer
{
Interval = 100
};
_timer.Tick += timer_Tick;
}
private void RTScoreCalculatorList_ListChanged(object sender, EventArgs e)
{
// Avoid updating on every minor change to the list.
if (_pendingUpdate)
{
return;
}
// Wait for the UI thread to become available again, and then update
if (GraphSummary.IsHandleCreated)
{
GraphSummary.BeginInvoke(new Action(DelayedUpdate));
_pendingUpdate = true;
}
}
protected SummaryPeptideGraphPane(GraphSummary graphSummary, PaneKey paneKey)
: base(graphSummary)
{
PaneKey = paneKey;
string xAxisTitle =
Helpers.PeptideToMoleculeTextMapper.Translate(Resources.SummaryPeptideGraphPane_SummaryPeptideGraphPane_Peptide,
graphSummary.DocumentUIContainer.DocumentUI.DocumentType);
if (null != paneKey.IsotopeLabelType && !paneKey.IsotopeLabelType.IsLight)
{
xAxisTitle += @" (" + paneKey.IsotopeLabelType + @")";
}
XAxis.Title.Text = xAxisTitle;
XAxis.Type = AxisType.Text;
}
protected void ChangeSelectedIndex(int iResult)
{
if (iResult < 0)
{
return;
}
var document = GraphSummary.DocumentUIContainer.DocumentUI;
if (!document.Settings.HasResults || iResult >= document.Settings.MeasuredResults.Chromatograms.Count)
{
return;
}
GraphSummary.StateProvider.SelectedResultsIndex = iResult;
GraphSummary.Focus();
}
protected DetectionsPlotPane(GraphSummary graphSummary) : base(graphSummary)
{
MaxRepCount = graphSummary.DocumentUIContainer.DocumentUI.MeasuredResults.Chromatograms.Count;
Settings.RepCount = MaxRepCount / 2;
if (GraphSummary.Toolbar is DetectionsToolbar toolbar)
{
toolbar.UpdateUI();
}
XAxis.Scale.Min = YAxis.Scale.Min = 0;
XAxis.Scale.MinAuto = XAxis.Scale.MaxAuto = YAxis.Scale.MinAuto = YAxis.Scale.MaxAuto = false;
ToolTip = new ToolTipImplementation(this);
DetectionPlotData.GetDataCache().ReportProgress += UpdateProgressHandler;
DetectionPlotData.GetDataCache().StatusChange += UpdateStatusHandler;
}
public void OnUpdateGraph()
{
// CONSIDER: Need a better guarantee that this ratio index matches the
// one in the sequence tree, but at least this will keep the UI
// from crashing with IndexOutOfBoundsException.
var settings = GraphSummary.DocumentUIContainer.DocumentUI.Settings;
GraphSummary.NormalizeOption = NormalizeOption.Constrain(settings, GraphSummary.NormalizeOption);
var pane = GraphSummary.GraphPanes.FirstOrDefault();
switch (GraphSummary.Type)
{
case GraphTypeSummary.replicate:
case GraphTypeSummary.peptide:
GraphSummary.DoUpdateGraph(this, GraphSummary.Type);
break;
case GraphTypeSummary.histogram:
if (!(pane is AreaCVHistogramGraphPane))
{
GraphSummary.GraphPanes = new[] { new AreaCVHistogramGraphPane(GraphSummary) }
}
;
break;
case GraphTypeSummary.histogram2d:
if (!(pane is AreaCVHistogram2DGraphPane))
{
GraphSummary.GraphPanes = new[] { new AreaCVHistogram2DGraphPane(GraphSummary) }
}
;
break;
}
if (!ReferenceEquals(GraphSummary.GraphPanes.FirstOrDefault(), pane))
{
var disposable = pane as IDisposable;
if (disposable != null)
{
disposable.Dispose();
}
}
}
protected SummaryGraphPane(GraphSummary graphSummary)
{
GraphSummary = graphSummary;
PaneKey = PaneKey.DEFAULT;
Border.IsVisible = false;
Title.IsVisible = true;
Chart.Border.IsVisible = false;
XAxis.Scale.MaxAuto = true;
YAxis.Scale.MaxAuto = true;
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;
}
protected SummaryGraphPane(GraphSummary graphSummary)
{
GraphSummary = graphSummary;
PaneKey = PaneKey.DEFAULT;
Border.IsVisible = false;
Title.IsVisible = true;
Chart.Border.IsVisible = false;
XAxis.Scale.MaxAuto = true;
YAxis.Scale.MaxAuto = true;
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;
}
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 AreaReplicateGraphPane(GraphSummary graphSummary, PaneKey paneKey)
: base(graphSummary)
{
PaneKey = paneKey;
}
protected SummaryBarGraphPaneBase(GraphSummary graphSummary)
: base(graphSummary)
{
_axisLabelScaler = new AxisLabelScaler(this);
}
public RTLinearRegressionGraphPane(GraphSummary graphSummary)
: base(graphSummary)
{
XAxis.Title.Text = Resources.RTLinearRegressionGraphPane_RTLinearRegressionGraphPane_Score;
Settings.Default.RTScoreCalculatorList.ListChanged += RTScoreCalculatorList_ListChanged;
}
private GraphSummary CreateGraphPeakArea()
{
_graphPeakArea = new GraphSummary(this, new AreaGraphController())
{
TabText = Resources.SkylineWindow_CreateGraphPeakArea_Peak_Areas,
ResultsIndex = SelectedResultsIndex
};
_graphPeakArea.FormClosed += graphPeakArea_FormClosed;
_graphPeakArea.VisibleChanged += graphPeakArea_VisibleChanged;
return _graphPeakArea;
}
void GraphSummary.IStateProvider.BuildGraphMenu(ZedGraphControl zedGraphControl, ContextMenuStrip menuStrip, Point mousePt,
GraphSummary.IController controller)
{
var graphController = controller as RTGraphController;
if (graphController != null)
BuildRTGraphMenu(menuStrip, mousePt, graphController);
else if (controller is AreaGraphController)
BuildAreaGraphMenu(menuStrip);
CopyEmfToolStripMenuItem.AddToContextMenu(zedGraphControl, menuStrip);
}
private void graphRetentionTime_FormClosed(object sender, FormClosedEventArgs e)
{
// Update settings and menu check
Settings.Default.ShowRetentionTimeGraph = false;
_graphRetentionTime = null;
}
private void graphPeakArea_FormClosed(object sender, FormClosedEventArgs e)
{
// Update settings and menu check
Settings.Default.ShowPeakAreaGraph = false;
_graphPeakArea = null;
}
private void DestroyGraphRetentionTime()
{
if (_graphRetentionTime != null)
{
_graphRetentionTime.FormClosed -= graphRetentionTime_FormClosed;
_graphRetentionTime.VisibleChanged -= graphRetentionTime_VisibleChanged;
_graphRetentionTime.HideOnClose = false;
_graphRetentionTime.Close();
_graphRetentionTime = null;
}
}
private void DestroyGraphPeakArea()
{
if (_graphPeakArea != null)
{
_graphPeakArea.FormClosed -= graphPeakArea_FormClosed;
_graphPeakArea.VisibleChanged -= graphPeakArea_VisibleChanged;
_graphPeakArea.HideOnClose = false;
_graphPeakArea.Close();
_graphPeakArea = null;
}
}
private GraphSummary CreateGraphRetentionTime()
{
_graphRetentionTime = new GraphSummary(this, new RTGraphController())
{
TabText = Resources.SkylineWindow_CreateGraphRetentionTime_Retention_Times,
ResultsIndex = SelectedResultsIndex
};
_graphRetentionTime.FormClosed += graphRetentionTime_FormClosed;
_graphRetentionTime.VisibleChanged += graphRetentionTime_VisibleChanged;
return _graphRetentionTime;
}
public RTPeptideGraphPane(GraphSummary graphSummary)
: base(graphSummary, PaneKey.DEFAULT)
{
}
public AreaPeptideGraphPane(GraphSummary graphSummary, PaneKey paneKey)
: base(graphSummary, paneKey)
{
}
public void ShowGraphRetentionTime(bool show)
{
if (show)
{
if (_graphRetentionTime != null && !Program.SkylineOffscreen)
{
_graphRetentionTime.Activate();
}
else
{
_graphRetentionTime = _graphRetentionTime ?? CreateGraphRetentionTime();
// Choose a position to float the window
var rectFloat = GetFloatingRectangleForNewWindow();
_graphRetentionTime.Show(dockPanel, rectFloat);
}
}
else if (_graphRetentionTime != null)
{
// Save current setting for showing spectra
show = Settings.Default.ShowRetentionTimeGraph;
// Close the spectrum graph window
_graphRetentionTime.Hide();
// Restore setting and menuitem from saved value
Settings.Default.ShowRetentionTimeGraph = show;
}
}