public void PlotAnotatedSpectrum(MSLight msExperimental, double ppm, string peptide)
{
//Predict the spectrum
//Find PTMs
List <ModificationItem> mods = SpectraPredictor.GetVMods(peptide);
SpectralPredictionParameters spp = new SpectralPredictionParameters(false, true, false, false, true, false, true, true, 2, true, mods);
SpectraPredictor sp = new SpectraPredictor(spp);
List <PredictedIon> theoreticalSpectrum = sp.PredictPeaks(peptide, 2, 1950, msExperimental, 500);
DataGridResultTable.ItemsSource = theoreticalSpectrum;
SpectrumEye1.Plot(msExperimental.Ions, msExperimental.Ions[0].MZ, msExperimental.Ions.Last().MZ, ppm, theoreticalSpectrum);
}
private void buttonPlot_Click(object sender, RoutedEventArgs e)
{
Plot();
//Evaluate the spectrum quality
PatternTools.SpectraPrediction.SpectralPredictionParameters spm = new SpectralPredictionParameters(
true,
true,
true,
true,
true,
true,
false,
false,
1,
true,
Modifications
);
PatternTools.SpectraPrediction.SpectraPredictor sp = new SpectraPredictor(spm);
List <PredictedIon> theoretical = sp.PredictPeaks(textBoxSequence.Text, ChargeState, TheoreticalMH);
List <Ion> filteredList = myMS.FindAll(a => a.Intensity > double.Parse(textBoxRelativeIntensityThreshold.Text));
List <SpectralMatchEvaluator.TheTests> evaluationTests = new List <SpectralMatchEvaluator.TheTests>()
{
SpectralMatchEvaluator.TheTests.AllTests
};
PatternTools.SpectralMatchEvaluator.SpectrumComparisonResult spectrumEvaluationResult =
PatternTools.SpectralMatchEvaluator.Compare.Do(
evaluationTests,
theoretical,
filteredList,
double.Parse(textBoxPPM.Text),
textBoxSequence.Text.Length,
RelativeIntensityThreshold
);
PatternTools.SpectralMatchEvaluator.Compare.PrintResults(spectrumEvaluationResult);
}
/// <summary>
///
/// </summary>
/// <param name="experimentalIons">List of Ions</param>
/// <param name="sMZ">Start M/Z</param>
/// <param name="fMZ">Finish M/Z</param>
/// <param name="PPM">ppm</param>
/// <param name="tIons">TheoreticalIons</param>
public void Plot(List <Ion> experimentalIons, double sMZ, double fMZ, double PPM, List <PredictedIon> tIons = null)
{
if (tIons != null)
{
//Get a B Series
List <PredictedIon> bions = tIons.FindAll(a => a.Series == IonSeries.B && a.Number > -1);
bions.Sort((a, b) => a.Number.CompareTo(b.Number));
string peptide = string.Join("", bions.FindAll(b => b.Charge == 1).Select(a => a.FinalAA));
List <Tuple <string, string, string> > anotations = new List <Tuple <string, string, string> >();
List <string> splitPeptide = SpectraPredictor.SplitPeptide(peptide);
for (int i = 0; i < splitPeptide.Count; i++)
{
string a = "";
string b = "";
if (tIons.Exists(x => x.MZ >= sMZ && x.MZ <= fMZ && x.Number == i + 1 && x.Matched && (x.Series == IonSeries.X || x.Series == IonSeries.Y || x.Series == IonSeries.Z)))
{
a = "y1";
}
if (tIons.Exists(x => x.MZ >= sMZ && x.MZ <= fMZ && x.Number == i + 1 && x.Matched && (x.Series == IonSeries.A || x.Series == IonSeries.B || x.Series == IonSeries.C)))
{
b = "b2";
}
anotations.Add(new Tuple <string, string, string>(splitPeptide[i], a, b));
}
MySequenceAnotation.Plot(anotations);
}
ZoomInProcess = false;
CanvasPeakDisplay.Children.Clear();
startMZ = sMZ;
finishMZ = fMZ;
ppm = PPM;
theoreticalSpectrum = tIons;
//Lets keep the original spectrum
if (OriginalIons == null)
{
OriginalIons = experimentalIons;
}
IonsInDisplay = experimentalIons.FindAll(a => a.MZ >= startMZ && a.MZ <= finishMZ);
if (IonsInDisplay.Count == 0)
{
//Return to the original spectrum
PlotOriginal();
}
double maxIntensity = IonsInDisplay.Max(a => a.Intensity);
List <Tuple <double, double> > addedPositions = new List <Tuple <double, double> >(); //Used for printing labels in the peaks
double minimumHorizonalPixelsBetweenLable = 10;
IonsInDisplay.Sort((a, b) => b.Intensity.CompareTo(a.Intensity));
foreach (Ion i in IonsInDisplay)
{
Line peak = new Line();
peak.Stroke = System.Windows.Media.Brushes.Black;
peak.StrokeThickness = 1;
double relativeIntensity = Math.Round(i.Intensity / maxIntensity, 3);
peak.ToolTip = "M/Z: " + i.MZ + "\n";
peak.ToolTip += "Intensity: " + i.Intensity + "\n";
peak.ToolTip += "Relative Intensity: " + relativeIntensity + "\n";
Tuple <double, double> p = ConvertMZToPixel(i, maxIntensity, startMZ, finishMZ);
peak.X1 = 0;
peak.X2 = 0;
peak.Y1 = 0;
peak.Y2 = p.Item2;
//Verify if there is a theoretical ion within the ppm tolerance - choose color
int matching = -1;
if (!object.Equals(theoreticalSpectrum, null))
{
matching = theoreticalSpectrum.FindIndex(a => Math.Abs(PatternTools.pTools.PPM(a.MZ, i.MZ)) < ppm);
if (matching >= 0)
{
peak.StrokeThickness = 2;
if (theoreticalSpectrum[matching].Series == IonSeries.A || theoreticalSpectrum[matching].Series == IonSeries.B || theoreticalSpectrum[matching].Series == IonSeries.C)
{
peak.Stroke = System.Windows.Media.Brushes.Red;
}
if (theoreticalSpectrum[matching].Series == IonSeries.X || theoreticalSpectrum[matching].Series == IonSeries.Y || theoreticalSpectrum[matching].Series == IonSeries.Z)
{
peak.Stroke = System.Windows.Media.Brushes.Blue;
}
if (theoreticalSpectrum[matching].FinalAA.Contains("-NH3") || theoreticalSpectrum[matching].FinalAA.Contains("-H20"))
{
peak.Stroke = System.Windows.Media.Brushes.Green;
}
peak.ToolTip += "Z : " + theoreticalSpectrum[matching].Charge + "\n";
peak.ToolTip += "Series: " + theoreticalSpectrum[matching].Series + theoreticalSpectrum[matching].Number.ToString() + "\n";
peak.ToolTip += "Sequence Item: " + theoreticalSpectrum[matching].FinalAA;
}
}
Canvas.SetLeft(peak, p.Item1);
Canvas.SetBottom(peak, 0);
CanvasPeakDisplay.Children.Add(peak);
if (relativeIntensity > 0.02)
{
TextBlock tb = new TextBlock();
tb.HorizontalAlignment = HorizontalAlignment.Center;
tb.FontSize = 10;
tb.Text = Math.Round(i.MZ, 3).ToString();
if (matching > -1)
{
tb.Text += "\n" + theoreticalSpectrum[matching].Series + theoreticalSpectrum[matching].Number.ToString();
}
tb.Measure(new Size(Double.PositiveInfinity, Double.PositiveInfinity));
Rect measureRect = new Rect(tb.DesiredSize);
double addedPos = p.Item1 - measureRect.Width / 2;
Tuple <double, double> thisRange = new Tuple <double, double>(p.Item1 - measureRect.Width / 2, p.Item1 + measureRect.Width / 2);
if (!addedPositions.Exists(
a =>
(Math.Abs(a.Item1 - thisRange.Item1) < minimumHorizonalPixelsBetweenLable)
||
(Math.Abs(a.Item2 - thisRange.Item2) < minimumHorizonalPixelsBetweenLable)
||
((thisRange.Item1 > a.Item1) && (thisRange.Item1 < a.Item2))
||
((thisRange.Item2 > a.Item1)) && (thisRange.Item2 < a.Item2))
)
{
CanvasPeakDisplay.Children.Add(tb);
Canvas.SetLeft(tb, addedPos);
Canvas.SetBottom(tb, p.Item2);
addedPositions.Add(thisRange);
}
}
}
}
