/// <summary>
/// Aligns fragments observed Mz values
/// </summary>
/// <param name="result"></param>
/// <param name="allPSMs"></param>
public static void AlignProductsByDiff(Result result, PeptideSpectrumMatches allPSMs)
{
List <double> observedDiff = new List <double>();
List <double> observedMz = new List <double>();
//Precursors and Tracks
foreach (Precursor precursor in result.matchedPrecursors)//.ComputeAtFDR(result.dbOptions.maximumFalseDiscoveryRate, false))
{
PeptideSpectrumMatch psm = precursor.OptimizedBestPsm();
if (psm.Target)
{
foreach (ProductMatch fragment in psm.AllProductMatches)
{
observedMz.Add(fragment.obsMz);
observedDiff.Add(fragment.mass_diff);
}
}
}
PolynominalRegression pr = new PolynominalRegression(observedMz, observedDiff, 2);
foreach (PeptideSpectrumMatch psm in allPSMs)
{
foreach (ProductMatch match in psm.AllProductMatches)
{
match.obsMz += pr.Calculate(match.obsMz);
match.mass_diff = match.theoMz - match.obsMz;
}
psm.Initialize(result.dbOptions, psm.AllProductMatches);
foreach (MsMsPeak peak in psm.Query.spectrum.Peaks)
{
peak.MZ += pr.Calculate(peak.MZ);
}
}
}
/// <summary>
/// Aligns precursors observed Mz values
/// </summary>
/// <param name="result"></param>
/// <param name="allPSMs"></param>
public static void AlignPrecursorsByDiff(Result result, PeptideSpectrumMatches allPSMs)
{
List <double> observedDiff = new List <double>();
List <double> observedMz = new List <double>();
//Precursors and Tracks
foreach (Precursor precursor in result.matchedPrecursors)//.ComputeAtFDR(result.dbOptions.maximumFalseDiscoveryRate, false))
{
PeptideSpectrumMatch psm = precursor.OptimizedBestPsm();
if (psm.Target)
{
observedMz.Add(precursor.Track.MZ);
observedDiff.Add(Numerics.MZFromMass(psm.Peptide.MonoisotopicMass, precursor.Charge) - precursor.Track.MZ);
}
}
PolynominalRegression pr = new PolynominalRegression(observedMz, observedDiff, 2);
foreach (Query query in result.queries)
{
query.precursor.Track.MZ += pr.Calculate(query.precursor.Track.MZ);
query.precursor.Mass = Numerics.MassFromMZ(query.precursor.Track.MZ, query.precursor.Charge);
foreach (Precursor precursor in query.precursor.Isotopes)
{
precursor.Track.MZ += pr.Calculate(precursor.Track.MZ);
precursor.Mass = Numerics.MassFromMZ(precursor.Track.MZ, precursor.Charge);
}
foreach (Precursor precursor in query.precursor.OtherCharges)
{
precursor.Track.MZ += pr.Calculate(precursor.Track.MZ);
precursor.Mass = Numerics.MassFromMZ(precursor.Track.MZ, precursor.Charge);
}
query.spectrum.PrecursorMZ += pr.Calculate(query.spectrum.PrecursorMZ);
query.spectrum.PrecursorMass = Numerics.MassFromMZ(query.spectrum.PrecursorMZ, query.spectrum.PrecursorCharge);
}
foreach (PeptideSpectrumMatch psm in allPSMs)
{
psm.UpdatePrecursor(result.dbOptions);
}
}
private void Draw(int iterationCount, double[] yData, string methodName, GraphPane graphPane, Color color)
{
double[] xData = Enumerable.Range(0, iterationCount).Select(iter => (double)iter).ToArray();
if (cbPrecise.Checked)
{
graphPane.AddCurve(methodName,
xData,
yData,
color, ZedGraph.SymbolType.None);
}
if (cbApprox.Checked)
{
var regression = new PolynominalRegression(yData, (int)udApproxPolygonPow.Value);
var curve = graphPane.AddCurve(methodName + " (approx)",
xData,
xData.Select(x => regression.Calculate(x)).ToArray(),
color, ZedGraph.SymbolType.None);
curve.Line.Width = 3;
}
}
