private HalfLifeSettings GetHalfLifeSettingsFromUi(HalfLifeSettings value)
{
value.NewlySynthesizedTracerQuantity
= radioLabeledAminoAcid.Checked
? TracerQuantity.LabeledAminoAcid
: radioLabelDistribution.Checked
? TracerQuantity.PartialLabelDistribution
: radioUnlabeledPeptide.Checked
? TracerQuantity.UnlabeledPeptide : 0;
value.InitialPrecursorPool = HalfLifeSettings.TryParseDouble(tbxInitialPrecursorPool.Text, 0);
value.CurrentPrecursorPool = HalfLifeSettings.TryParseDouble(tbxCurrentPrecursorPool.Text, 0);
value.PrecursorPoolCalculation = radioFixedPrecursorPool.Checked
? PrecursorPoolCalculation.Fixed
: radioUseMedianPrecursorPool.Checked
? PrecursorPoolCalculation.MedianPerSample
: radioIndividualPrecursorPool.Checked
? PrecursorPoolCalculation.Individual
: 0;
value.MinimumAuc = HalfLifeSettings.TryParseDouble(tbxMinAuc.Text, 0);
value.MinimumDeconvolutionScore = HalfLifeSettings.TryParseDouble(tbxMinimumDeconvolutionScore.Text, 0);
value.MinimumTurnoverScore = HalfLifeSettings.TryParseDouble(tbxMinTurnoverScore.Text, 0);
value.EvviesFilter = (EvviesFilterEnum)comboEvviesFilter.SelectedIndex;
value.ForceThroughOrigin = cbxForceThroughOrigin.Checked;
value.SimpleLinearRegression = cbxSimpleLinearRegression.Checked;
return(value);
}
private bool IsIncluded(HalfLifeSettings halfLifeSettings, PeptideFileAnalysis peptideFileAnalysis)
{
if (!string.IsNullOrEmpty(Cohort))
{
if (Cohort != HalfLifeCalculator.GetCohort(peptideFileAnalysis.MsDataFile, GetHalfLifeSettings().BySample))
{
return(false);
}
}
if (peptideFileAnalysis.MsDataFile.TimePoint == null)
{
return(false);
}
if (IsTimePointExcluded(peptideFileAnalysis.MsDataFile.TimePoint.Value))
{
return(false);
}
if (halfLifeSettings.PrecursorPoolCalculation == PrecursorPoolCalculation.Individual)
{
if (null == peptideFileAnalysis.CalculatedPeaks || !peptideFileAnalysis.CalculatedPeaks.Turnover.HasValue)
{
return(false);
}
}
return(true);
}
public HalfLifeSettings GetHalfLifeSettings(HalfLifeSettings halfLifeSettings)
{
var tracerDef = GetTracerDefs().FirstOrDefault();
if (tracerDef != null)
{
halfLifeSettings.InitialPrecursorPool = tracerDef.InitialApe;
halfLifeSettings.CurrentPrecursorPool = tracerDef.FinalApe;
}
return(halfLifeSettings);
}
private void UpdateSettings(object sender, EventArgs e)
{
HalfLifeSettings = GetHalfLifeSettingsFromUi(HalfLifeSettings);
}
private HalfLifeCalculator UpdateGraph(List <PeptideFileAnalysis> peptideFileAnalyses, HalfLifeSettings halfLifeSettings, out HalfLifeCalculator.ResultData resultData)
{
var halfLifeCalculator = new HalfLifeCalculator(Workspace, halfLifeSettings);
var halfLife = resultData = halfLifeCalculator.CalculateHalfLife(peptideFileAnalyses);
_zedGraphControl.GraphPane.CurveList.Clear();
_zedGraphControl.GraphPane.GraphObjList.Clear();
_pointsCurve = null;
_peptideFileAnalysisPoints = null;
var xValues = new List <double>();
var yValues = new List <double>();
var fileAnalysisPoints = new List <PeptideFileAnalysis>();
var filteredFileAnalysisIds =
new HashSet <long>(resultData.FilteredRowDatas.Select(rd => rd.RawRowData.PeptideFileAnalysisId));
foreach (var peptideFileAnalysis in peptideFileAnalyses)
{
if (!filteredFileAnalysisIds.Contains(peptideFileAnalysis.Id))
{
continue;
}
double?value;
var processedRowData = halfLifeCalculator.ToRowData(peptideFileAnalysis);
if (!processedRowData.Turnover.HasValue)
{
continue;
}
if (LogPlot)
{
value = 2 - Math.Log10(100 - processedRowData.Turnover.Value * 100);
}
else
{
value = processedRowData.Turnover.Value * 100;
}
if (double.IsInfinity(value.Value) || double.IsNaN(value.Value))
{
continue;
}
Debug.Assert(peptideFileAnalysis.MsDataFile.TimePoint != null);
xValues.Add(peptideFileAnalysis.MsDataFile.TimePoint.Value);
yValues.Add(value.Value);
fileAnalysisPoints.Add(peptideFileAnalysis);
}
UpdateStatsGrid(xValues, yValues);
var pointsCurve = _zedGraphControl.GraphPane.AddCurve("Data Points", xValues.ToArray(), yValues.ToArray(), Color.Black);
pointsCurve.Line.IsVisible = false;
pointsCurve.Label.IsVisible = false;
Func <double, double> funcMiddle = x => halfLife.YIntercept + halfLife.RateConstant * x;
Func <double, double> funcMin = x => halfLife.YIntercept + (halfLife.RateConstant - halfLife.RateConstantError) * x;
Func <double, double> funcMax = x => halfLife.YIntercept + (halfLife.RateConstant + halfLife.RateConstantError) * x;
Func <double, double> funcConvertToDisplayedValue;
if (LogPlot)
{
_zedGraphControl.GraphPane.YAxis.Title.Text = "-Log(100% - % Newly Synthesized)";
funcConvertToDisplayedValue = x => - x / Math.Log(10);
}
else
{
_zedGraphControl.GraphPane.YAxis.Title.Text = "% Newly Synthesized";
funcConvertToDisplayedValue = x => (1 - Math.Exp(x)) * 100;
}
// ReSharper disable ImplicitlyCapturedClosure
AddFunction("Best Fit", x => funcConvertToDisplayedValue(funcMiddle(x)), Color.Black);
AddFunction("Minimum Bound", x => funcConvertToDisplayedValue(funcMin(x)), Color.LightBlue);
AddFunction("Maximum Bound", x => funcConvertToDisplayedValue(funcMax(x)), Color.LightGreen);
// ReSharper restore ImplicitlyCapturedClosure
_zedGraphControl.GraphPane.AxisChange();
_zedGraphControl.Invalidate();
_pointsCurve = pointsCurve;
_peptideFileAnalysisPoints = fileAnalysisPoints;
tbxRateConstant.Text = resultData.RateConstant.ToString("0.##E0") + "+/-" +
resultData.RateConstantError.ToString("0.##E0");
tbxHalfLife.Text = resultData.HalfLife.ToString("0.##") + "(" + resultData.MinHalfLife.ToString("0.##") + "-" +
resultData.MaxHalfLife.ToString("0.##") + ")";
if (resultData.RSquared.HasValue)
{
tbxCorrelationCoefficient.Text = Math.Sqrt(resultData.RSquared.Value).ToString(CultureInfo.InvariantCulture);
}
else
{
tbxCorrelationCoefficient.Text = "";
}
return(halfLifeCalculator);
}
public void SetHalfLifeSettings(HalfLifeSettings halfLifeSettings)
{
cbxBySample.Checked = halfLifeSettings.BySample;
halfLifeSettingsControl.HalfLifeSettings = halfLifeSettings;
UpdateRows(true);
}
