public static List <ModificationItem> GetVMods(string peptide)
{
List <string> broken = SpectraPredictor.SplitPeptide(peptide);
List <string> withPTMs = broken.FindAll(a => a.Contains("("));
List <ModificationItem> mods = new List <ModificationItem>();
foreach (string s in withPTMs)
{
string cleanAA = PatternTools.pTools.CleanPeptide(s, true);
Match delta = Regex.Match(s, @"-?[\d|\.]+");
double no = double.Parse(delta.Value.ToString());
mods.Add(new ModificationItem(cleanAA, "", no, false, false, true, true));
}
return(mods);
}
public void Plot(List <PredictedIon> peaks = null)
{
myMS.Sort((a, b) => a.MZ.CompareTo(b.MZ));
if (peaks == null)
{
SpectralPredictionParameters spp = new SpectralPredictionParameters
((bool)checkBoxA.IsChecked,
(bool)checkBoxB.IsChecked,
(bool)checkBoxC.IsChecked,
(bool)checkBoxX.IsChecked,
(bool)checkBoxY.IsChecked,
(bool)checkBoxZ.IsChecked,
(bool)checkBoxNLH2O.IsChecked,
(bool)checkBoxNLNH3.IsChecked,
3,
(bool)checkBoxIsMonoisotopic.IsChecked,
Modifications
);
if (Modifications == null)
{
spp.MyModifications = new List <ModificationItem>();
}
PatternTools.SpectraPrediction.SpectraPredictor sp = new PatternTools.SpectraPrediction.SpectraPredictor(spp);
if (textBoxSequence.Text.Length > 0)
{
peaks = sp.PredictPeaks(textBoxSequence.Text, ChargeState, TheoreticalMH);
if (!(bool)checkBoxZ1.IsChecked)
{
peaks.RemoveAll(a => a.Charge == 1 && a.Series != IonSeries.Precursor);
}
if (!(bool)checkBoxZ2.IsChecked)
{
peaks.RemoveAll(a => a.Charge == 2 && a.Series != IonSeries.Precursor);
}
if (!(bool)checkBoxZ3.IsChecked)
{
peaks.RemoveAll(a => a.Charge == 3 && a.Series != IonSeries.Precursor);
}
}
else
{
peaks = new List <PredictedIon>();
}
}
dataGridPeakViewer.ItemsSource = peaks;
try
{
if (textBoxSequence.Text.Length == 0)
{
FuncPrintMS(myMS, IonsInDisplay[0].MZ, IonsInDisplay[IonsInDisplay.Count - 1].MZ, false);
}
else
{
FuncPrintMS(myMS, IonsInDisplay[0].MZ, IonsInDisplay[IonsInDisplay.Count - 1].MZ, true);
}
}
catch (Exception eee)
{
Console.WriteLine(eee.Message);
}
double matches = peaks.FindAll(a => a.Matched == true).Count;
double total = peaks.Count;
labelPeaksProduced.Content = matches + " / " + total + " = " + Math.Round(matches / total, 1) * 100 + "%";
// Plot the denovo
canvasDenovo.Children.Clear();
if ((bool)checkBoxB.IsChecked)
{
labelABC.Content = "B:";
PlotSequence(peaks, IonSeries.B, 13, Brushes.Red);
}
else if ((bool)checkBoxC.IsChecked)
{
labelABC.Content = "C:";
PlotSequence(peaks, IonSeries.C, 13, Brushes.Red);
}
else if ((bool)checkBoxA.IsChecked)
{
labelABC.Content = "A:";
PlotSequence(peaks, IonSeries.A, 13, Brushes.Red);
}
else
{
labelABC.Content = "";
}
if ((bool)checkBoxY.IsChecked)
{
labelXYZ.Content = "Y:";
PlotSequence(peaks, IonSeries.Y, 40, Brushes.Blue);
}
else if ((bool)checkBoxZ.IsChecked)
{
labelXYZ.Content = "Z:";
PlotSequence(peaks, IonSeries.Z, 40, Brushes.Blue);
}
else if ((bool)checkBoxX.IsChecked)
{
labelXYZ.Content = "X:";
PlotSequence(peaks, IonSeries.X, 40, Brushes.Blue);
}
else
{
labelXYZ.Content = "";
}
//Display peptide of theoretical spectrum
Label peptideSequenceLabel = new Label();
peptideSequenceLabel.FontSize = 10;
peptideSequenceLabel.Content = textBoxSequence.Text + " (" + textBoxSequence.Text.Count() + ")";
peptideSequenceLabel.FontWeight = FontWeights.Light;
peptideSequenceLabel.Foreground = Brushes.Gray;
canvasMS.Children.Add(peptideSequenceLabel);
Canvas.SetLeft(peptideSequenceLabel, -2);
Canvas.SetTop(peptideSequenceLabel, 0);
}
