private AnnotatedPeak matchXLIon(KeyValuePair <float, int> peak, int charge)
{
int tempSite1 = 0;
int tempSite2 = 0;
if (currentSite1 > 0)
{
tempSite1 = currentSite1 - 1;
}
if (currentSite2 > 0)
{
tempSite2 = currentSite2 - 1;
}
AnnotatedPeak annotatedPeak = null;
bool matched = false;
int bIonIdx = (charge - 1) * 2;
int yIonIdx = bIonIdx + 1;
for (int i = tempSite1; i < currentPeptideClIon1.GetLength(1); ++i)
{
if (Math.Abs(peak.Key - currentPeptideClIon1[bIonIdx, i]) <= ms2Tolerance)
{
annotatedPeak = new AnnotatedPeak(peak.Value, "\u03B1", i + 1, charge, "b");
matched = true;
break;
}
}
if (!matched)
{
for (int i = 0; i < tempSite1 + 1; ++i)
{
if (Math.Abs(peak.Key - currentPeptideClIon1[yIonIdx, i]) <= ms2Tolerance)
{
annotatedPeak = new AnnotatedPeak(peak.Value, "\u03B1", currentPeptideClIon1.GetLength(1) - i, charge, "y");
matched = true;
break;
}
}
}
if (!matched)
{
for (int i = tempSite2; i < currentPeptideClIon2.GetLength(1); ++i)
{
if (Math.Abs(peak.Key - currentPeptideClIon2[bIonIdx, i]) <= ms2Tolerance)
{
annotatedPeak = new AnnotatedPeak(peak.Value, "\u03B2", i + 1, charge, "b");
matched = true;
break;
}
}
}
if (!matched)
{
for (int i = 0; i < currentSite2 + 1; ++i)
{
if (Math.Abs(peak.Key - currentPeptideClIon2[yIonIdx, i]) <= ms2Tolerance)
{
annotatedPeak = new AnnotatedPeak(peak.Value, "\u03B2", currentPeptideClIon2.GetLength(1) - i, charge, "y");
matched = true;
break;
}
}
}
return(annotatedPeak);
}
private void plotSpectrum()
{
SortedDictionary <float, float> unmatchedPeaks = new SortedDictionary <float, float>();
SortedDictionary <float, AnnotatedPeak> matchedPeak = new SortedDictionary <float, AnnotatedPeak>();
float smallestMz = 99999;
float maxIntensity = 0;
foreach (KeyValuePair <float, int> peak in currentPeakList)
{
if (peak.Key < smallestMz)
{
smallestMz = peak.Key;
}
if (peak.Value > maxIntensity)
{
maxIntensity = peak.Value;
}
AnnotatedPeak annotatedPeak = null;
if (checkBox1.Checked)
{
annotatedPeak = matchLinearIon(peak, 1);
}
if ((annotatedPeak == null) && checkBox2.Checked)
{
annotatedPeak = matchLinearIon(peak, 2);
}
if ((annotatedPeak == null) && checkBox3.Checked)
{
annotatedPeak = matchLinearIon(peak, 3);
}
if ((annotatedPeak == null) && checkBox4.Checked)
{
annotatedPeak = matchXLIon(peak, 2);
}
if ((annotatedPeak == null) && checkBox5.Checked)
{
annotatedPeak = matchXLIon(peak, 3);
}
if ((annotatedPeak == null) && checkBox6.Checked)
{
annotatedPeak = matchXLIon(peak, 4);
}
if ((annotatedPeak == null) && checkBox7.Checked)
{
annotatedPeak = matchXLIon(peak, 5);
}
if (annotatedPeak == null)
{
unmatchedPeaks[peak.Key] = peak.Value;
}
else
{
matchedPeak[peak.Key] = annotatedPeak;
}
}
PlotModel plotModel = new PlotModel {
Title = String.Format("Spectrum: {0}.{1}", currentScanNum, currentCharge)
};
// make the y-axis limit bigger.
DataPointSeries transparntSeries = new StemSeries {
MarkerType = MarkerType.None, Color = OxyColors.Transparent
};
transparntSeries.Points.Add(new DataPoint(smallestMz - 1, maxIntensity * 1.1));
plotModel.Series.Add(transparntSeries);
// unmatched peaks
DataPointSeries unmatchedSeries = new StemSeries {
MarkerType = MarkerType.None, Color = OxyColors.Gray, StrokeThickness = 0.5
};
foreach (KeyValuePair <float, float> peak in unmatchedPeaks)
{
unmatchedSeries.Points.Add(new DataPoint(peak.Key, peak.Value));
}
plotModel.Series.Add(unmatchedSeries);
// matched peaks
DataPointSeries matchedSeries = new StemSeries {
MarkerType = MarkerType.None, Color = OxyColors.Blue, StrokeThickness = 0.5
};
foreach (KeyValuePair <float, AnnotatedPeak> peak in matchedPeak)
{
matchedSeries.Points.Add(new DataPoint(peak.Key, peak.Value.intensity));
AnnotatedPeak annotatedPeak = peak.Value;
string annotateText = annotatedPeak.chainType + annotatedPeak.byType + annotatedPeak.fragmentLocation;
for (int i = 0; i < annotatedPeak.charge; ++i)
{
annotateText += "+";
}
Annotation ann = new PointAnnotation {
Shape = MarkerType.None, Size = 0, TextVerticalAlignment = VerticalAlignment.Bottom, X = peak.Key, Y = annotatedPeak.intensity, Text = annotateText
};
plotModel.Annotations.Add(ann);
}
plotModel.Series.Add(matchedSeries);
plotViewSpectrum.Model = plotModel;
}
