public void UpdateGrid()
{
double monoisotopicMass =
Workspace.GetAminoAcidFormulas().GetMonoisotopicMass(PeptideAnalysis.Peptide.Sequence);
var masses = PeptideAnalysis.GetTurnoverCalculator().GetMzs(0);
if (MassColumn == null)
{
MassColumn = new DataGridViewTextBoxColumn
{
HeaderText = "Mass",
Name = "colMass",
Width = 60,
ReadOnly = true,
};
Columns.Add(MassColumn);
}
if (ExcludedColumn == null)
{
ExcludedColumn = new DataGridViewCheckBoxColumn
{
HeaderText = "Excluded",
Name = "colExcluded",
Width = 50,
SortMode = DataGridViewColumnSortMode.NotSortable,
};
Columns.Add(ExcludedColumn);
}
if (Rows.Count != PeptideAnalysis.GetMassCount())
{
Rows.Clear();
Rows.Add(PeptideAnalysis.GetMassCount());
for (int iRow = 0; iRow < Rows.Count; iRow++)
{
Rows[iRow].Tag = iRow;
}
}
for (int iRow = 0; iRow < Rows.Count; iRow++)
{
var row = Rows[iRow];
var iMass = (int)row.Tag;
double massDifference = masses[iMass].Center - monoisotopicMass;
var label = massDifference.ToString("0.#");
if (label[0] != '-')
{
label = "+" + label;
}
label = "M" + label;
row.Cells[MassColumn.Index].Value = label;
row.Cells[MassColumn.Index].ToolTipText = "Mass:" + masses[iMass];
row.Cells[MassColumn.Index].Style.BackColor = TracerChromatogramForm.GetColor(iRow, Rows.Count);
row.Cells[ExcludedColumn.Index].Value = ExcludedMasses.IsMassExcluded(iMass);
}
}
private void UpdateGraph()
{
zedGraphControl.GraphPane.CurveList.Clear();
zedGraphControl.GraphPane.GraphObjList.Clear();
zedGraphControl.GraphPane.Title.IsVisible = false;
MsDataFile normalizeTo = null;
var fileAnalyses = new List <PeptideFileAnalysis>();
for (int iRow = 0; iRow < dataGridView.Rows.Count; iRow++)
{
fileAnalyses.Add((PeptideFileAnalysis)dataGridView.Rows[iRow].Tag);
}
if (fileAnalyses.Count == 0)
{
return;
}
if (_normalizeRetentionTimes)
{
normalizeTo = fileAnalyses[0].MsDataFile;
}
var tracerFormulas = PeptideAnalysis.GetTurnoverCalculator().ListTracerFormulas();
var pointPairLists = tracerFormulas.Select(tf => new PointPairList()).ToArray();
for (int iFileAnalysis = 0; iFileAnalysis < fileAnalyses.Count; iFileAnalysis++)
{
var fileAnalysis = fileAnalyses[iFileAnalysis];
var peaks = fileAnalysis.CalculatedPeaks;
if (peaks == null)
{
continue;
}
for (int iTracerFormula = 0; iTracerFormula < tracerFormulas.Count; iTracerFormula++)
{
var pointPairList = pointPairLists[iTracerFormula];
var peak = peaks.GetPeak(tracerFormulas[iTracerFormula]);
if (peak == null)
{
pointPairList.Add(new PointPair(iFileAnalysis + 1, PointPairBase.Missing, PointPairBase.Missing));
}
else
{
if (normalizeTo == null)
{
pointPairList.Add(new PointPair(iFileAnalysis + 1, peak.Value.EndTime, peak.Value.StartTime));
}
else
{
var alignment = fileAnalysis.MsDataFile.GetRetentionTimeAlignment(normalizeTo);
if (alignment.IsInvalid)
{
pointPairList.Add(new PointPair(iFileAnalysis + 1, PointPairBase.Missing, PointPairBase.Missing));
}
else
{
pointPairList.Add(new PointPair(iFileAnalysis + 1, alignment.GetTargetTime(peak.Value.EndTime), alignment.GetTargetTime(peak.Value.StartTime), fileAnalysis));
}
}
}
}
}
zedGraphControl.GraphPane.XAxis.Type = AxisType.Text;
zedGraphControl.GraphPane.XAxis.Scale.TextLabels =
fileAnalyses.Select(fileAnalysis => fileAnalysis.MsDataFile.ToString()).ToArray();
zedGraphControl.GraphPane.XAxis.Title.Text = "Data File";
zedGraphControl.GraphPane.YAxis.Title.Text = normalizeTo == null ? "Retention Time" : "Normalized Retention Time";
for (int iTracerFormula = 0; iTracerFormula < tracerFormulas.Count; iTracerFormula++)
{
zedGraphControl.GraphPane.AddHiLowBar(tracerFormulas[iTracerFormula].ToDisplayString(),
pointPairLists[iTracerFormula],
TracerChromatogramForm.GetColor(iTracerFormula,
tracerFormulas.Count));
}
zedGraphControl.GraphPane.AxisChange();
zedGraphControl.Invalidate();
}
public void Recalc()
{
zedGraphControl.GraphPane.CurveList.Clear();
zedGraphControl.GraphPane.GraphObjList.Clear();
PeptideAnalysis.EnsurePeaksCalculated();
IDictionary <TracerFormula, double> bestMatch;
var peaks = PeptideFileAnalysis.CalculatedPeaks;
var peaksDict = peaks.ToDictionary();
var peaksDictList = peaksDict.ToList();
double turnover;
double turnoverScore;
var precursorEnrichment = PeptideAnalysis.GetTurnoverCalculator().ComputePrecursorEnrichmentAndTurnover(peaksDict, out turnover, out turnoverScore, out bestMatch);
dataGridViewPrecursorPool.Rows.Clear();
if (precursorEnrichment == null)
{
tbxTurnover.Text = "";
tbxTurnoverScore.Text = "";
dataGridViewPrecursorPool.Rows.Clear();
}
else
{
tbxTurnover.Text = turnover.ToString("0.##%");
tbxTurnoverScore.Text = turnoverScore.ToString("0.####");
var tracerDefs = Workspace.GetTracerDefs();
if (dataGridViewPrecursorPool.Rows.Count != tracerDefs.Count)
{
dataGridViewPrecursorPool.Rows.Clear();
dataGridViewPrecursorPool.Rows.Add(tracerDefs.Count);
}
for (int i = 0; i < tracerDefs.Count; i++)
{
var tracerDef = tracerDefs[i];
var row = dataGridViewPrecursorPool.Rows[i];
row.Cells[colTracer.Index].Value = tracerDef.Name;
row.Cells[colPercent.Index].Value = precursorEnrichment.GetElementCount(tracerDef.Name);
}
}
var observedDistribution = new PointPairList();
var matchedDistribution = new PointPairList();
var labels = new List <string>();
for (int i = 0; i < peaksDictList.Count(); i++)
{
var tracerFormula = peaksDictList[i].Key;
labels.Add(tracerFormula.ToDisplayString());
observedDistribution.Add(i, peaksDictList[i].Value);
if (bestMatch == null)
{
matchedDistribution.Add(i, 1.0);
}
else
{
matchedDistribution.Add(i, bestMatch[tracerFormula]);
}
}
zedGraphControl.GraphPane.AddBar("Observed", observedDistribution, Color.Black);
zedGraphControl.GraphPane.AddBar("Predicted", matchedDistribution, Color.Blue);
zedGraphControl.GraphPane.XAxis.Type = AxisType.Text;
zedGraphControl.GraphPane.XAxis.Scale.TextLabels = labels.ToArray();
zedGraphControl.AxisChange();
}