public PeakSet(DbPeptideFileAnalysis dbPeptideFileAnalysis, IEnumerable <Peak> peaks) : this()
{
TracerPercent = dbPeptideFileAnalysis.TracerPercent;
DeconvolutionScore = dbPeptideFileAnalysis.DeconvolutionScore;
PrecursorEnrichment = dbPeptideFileAnalysis.PrecursorEnrichment;
if (dbPeptideFileAnalysis.PrecursorEnrichmentFormula != null)
{
PrecursorEnrichmentFormula = TracerPercentFormula.Parse(dbPeptideFileAnalysis.PrecursorEnrichmentFormula);
}
Turnover = dbPeptideFileAnalysis.Turnover;
TurnoverScore = dbPeptideFileAnalysis.TurnoverScore;
IntegrationNote = IntegrationNote.Parse(dbPeptideFileAnalysis.IntegrationNote);
if (peaks != null)
{
_peaks = ImmutableList.ValueOf(peaks);
}
}
private void BtnGoOnClick(object sender, EventArgs e)
{
graphDetails.GraphPane.CurveList.Clear();
int pointCount = PointCount;
double precursorPool = PrecursorPool;
double turnover = Turnover;
int labelCount = LabelCount;
double noise = Noise;
var points = new PointPairList();
var tracerDef = Workspace.GetTracerDefs().FirstOrDefault(td => td.AminoAcidSymbol.HasValue);
if (tracerDef == null)
{
MessageBox.Show(
"The simulation cannot be run because there is no amino acid tracer defined in this workspace");
return;
}
Debug.Assert(tracerDef.AminoAcidSymbol.HasValue);
string peptide = new string(tracerDef.AminoAcidSymbol.Value, labelCount);
var turnoverCalculator = new TurnoverCalculator(Workspace, peptide);
var initialTracerPercents = TracerPercentFormula.Parse("").SetElementCount(tracerDef.Name, tracerDef.InitialApe);
var newTracerPercents = TracerPercentFormula.Parse("").SetElementCount(tracerDef.Name, precursorPool);
var initialDistribution = turnoverCalculator.GetDistribution(initialTracerPercents);
var newDistribution = turnoverCalculator.GetDistribution(newTracerPercents);
var currentMixture = Mix(initialDistribution, (100.0 - turnover) / 100, newDistribution, turnover / 100);
var keys = new List <TracerFormula>();
for (int i = 0; i <= labelCount; i++)
{
keys.Add(TracerFormula.Parse("").SetElementCount(tracerDef.Name, i));
}
var bestMatches = new List <IDictionary <TracerFormula, double> >();
var precursorEnrichments = new List <TracerPercentFormula>();
var observedResults = new List <IDictionary <TracerFormula, double> >();
while (points.Count < pointCount)
{
var noisyMixture = Perturb(keys, currentMixture, noise / 100);
double calcTurnover;
double calcTurnoverScore;
double calcPrecursorPool;
IDictionary <TracerFormula, double> bestMatch;
var calcMixture = turnoverCalculator.ComputePrecursorEnrichmentAndTurnover(noisyMixture, out calcTurnover, out calcTurnoverScore, out bestMatch);
if (calcMixture == null)
{
continue;
}
calcMixture.TryGetValue(tracerDef.Name, out calcPrecursorPool);
points.Add(new PointPair(calcTurnover * 100, calcPrecursorPool));
bestMatches.Add(bestMatch);
precursorEnrichments.Add(calcMixture);
observedResults.Add(noisyMixture);
}
graphResults.GraphPane.CurveList.Clear();
graphResults.GraphPane.GraphObjList.Clear();
var lineItem = graphResults.GraphPane.AddCurve(null, points, Color.Black);
lineItem.Line.IsVisible = false;
graphResults.GraphPane.XAxis.Title.Text = "% newly synthesized";
graphResults.GraphPane.YAxis.Title.Text = "Precursor pool";
graphResults.GraphPane.AxisChange();
graphResults.Invalidate();
dataGridView.Rows.Clear();
var row = dataGridView.Rows[dataGridView.Rows.Add()];
row.Cells[colQuantity.Index].Value = "% newly synthesized";
var statsTurnover = new Statistics(points.Select(p => p.X).ToArray());
row.Cells[colMean.Index].Value = statsTurnover.Mean();
row.Cells[colMedian.Index].Value = statsTurnover.Median();
row.Cells[colStdDev.Index].Value = statsTurnover.StdDev();
row = dataGridView.Rows[dataGridView.Rows.Add()];
var statsPrecursorPool = new Statistics(points.Select(p => p.Y).ToArray());
row.Cells[colQuantity.Index].Value = "Precursor Pool";
row.Cells[colMean.Index].Value = statsPrecursorPool.Mean();
row.Cells[colMedian.Index].Value = statsPrecursorPool.Median();
row.Cells[colStdDev.Index].Value = statsPrecursorPool.StdDev();
_precursorEnrichmentsByPoint = points.Select(p => p.Y).ToArray();
_bestMatches = bestMatches;
_observedResults = observedResults;
_scatterPlotCurve = lineItem;
_expected = currentMixture;
_turnovers = points.Select(p => p.X).ToArray();
_tracerFormulas = keys;
ShowResult(-1);
}
private void UpdateGraph()
{
if (_inUpdateGraph)
{
return;
}
try
{
_inUpdateGraph = true;
_msGraphControl.GraphPane.GraphObjList.Clear();
_msGraphControl.GraphPane.CurveList.Clear();
dataGridView1.Rows.Clear();
int charge;
try
{
charge = Convert.ToInt32(tbxCharge.Text);
tbxCharge.BackColor = Color.White;
}
catch
{
charge = 0;
tbxCharge.BackColor = Color.Red;
}
double massResolution;
try
{
massResolution = double.Parse(tbxMassResolution.Text);
tbxMassResolution.BackColor = Color.White;
}
catch
{
tbxMassResolution.BackColor = Color.Red;
massResolution = .01;
}
var sequence = tbxSequence.Text;
MassDistribution spectrum;
if (string.IsNullOrEmpty(sequence))
{
var formula = tbxFormula.Text;
var molecule = Molecule.Parse(formula);
if (molecule.Values.Sum() > 10000000)
{
tbxFormula.BackColor = Color.Red;
return;
}
try
{
spectrum = Workspace.GetAminoAcidFormulas().GetMassDistribution(molecule, charge);
tbxFormula.BackColor = Color.White;
}
catch
{
tbxFormula.BackColor = Color.Red;
return;
}
}
else
{
tbxFormula.Text = Workspace.GetAminoAcidFormulas().GetFormula(sequence).ToString();
var turnoverCalculator = new TurnoverCalculator(Workspace, sequence);
var aminoAcidFormulas = Workspace.GetAminoAcidFormulasWithTracers();
aminoAcidFormulas = aminoAcidFormulas.SetMassResolution(massResolution);
try
{
if (cbxTracerPercents.Checked)
{
var tracerPercentFormula = TracerPercentFormula.Parse(tbxTracerFormula.Text);
spectrum = turnoverCalculator.GetAminoAcidFormulas(tracerPercentFormula)
.GetMassDistribution(sequence, charge);
}
else
{
var tracerFormula = TracerFormula.Parse(tbxTracerFormula.Text);
spectrum = aminoAcidFormulas.GetMassDistribution(
turnoverCalculator.MoleculeFromTracerFormula(tracerFormula), charge);
double massShift = aminoAcidFormulas.GetMassShift(sequence);
if (charge > 0)
{
massShift /= charge;
}
spectrum = spectrum.OffsetAndDivide(massShift, 1);
}
tbxTracerFormula.BackColor = Color.White;
}
catch
{
tbxTracerFormula.BackColor = Color.Red;
spectrum = aminoAcidFormulas.GetMassDistribution(sequence, charge);
}
}
if (spectrum == null)
{
return;
}
var curveItem = _msGraphControl.AddGraphItem(_msGraphControl.GraphPane, new GraphItem
{
Title = "Intensity",
Color = Color.Black,
Points =
new PointPairList(
spectrum.Keys.
ToArray(),
spectrum.Values.
ToArray())
});
curveItem.Label.IsVisible = false;
_msGraphControl.AxisChange();
_msGraphControl.Invalidate();
var entries = spectrum.ToArray();
dataGridView1.Rows.Add(entries.Length);
for (int i = 0; i < entries.Count(); i++)
{
var row = dataGridView1.Rows[i];
row.Cells[colMass.Index].Value = entries[i].Key;
row.Cells[colIntensity.Index].Value = entries[i].Value;
}
}
finally
{
_inUpdateGraph = false;
}
}
