public List <MatchedPeak> GetNeutralLossPeaks(IonType targetPeakType, MatchedPeak sourcePeak, List <INeutralLossType> nlCandidates, Func <INeutralLossType, bool> filter)
{
List <INeutralLossType> nlTypes = new NeutralLossGenerator().GetTotalCombinationValues(nlCandidates, NeutralLossLevel);
nlTypes.RemoveAll(m => !filter(m));
List <MatchedPeak> result = new List <MatchedPeak>();
foreach (INeutralLossType nlType in nlTypes)
{
double nlMass = sourcePeak.Mz - nlType.Mass / sourcePeak.Charge;
MatchedPeak nlPeak = new MatchedPeak(nlMass, 1.0, sourcePeak.Charge)
{
PeakType = targetPeakType,
PeakIndex = sourcePeak.PeakIndex
};
nlPeak.DisplayName = GetDisplayName(nlType, sourcePeak, nlPeak);
result.Add(nlPeak);
}
result.Sort();
return(result);
}
public void TestGetPrecursorNeutralLossPeaks()
{
List <INeutralLossType> nls = new INeutralLossType[] { NeutralLossConstants.NL_H3PO4 }.ToList();
MatchedPeak precursor = new MatchedPeak(1000, 0, 2);
List <MatchedPeak> pkls = matcher.GetNeutralLossPeaks(IonType.PRECURSOR_NEUTRAL_LOSS_PHOSPHO, precursor, nls, (m => m.IsPhosphoNeutralLossType()));
Assert.AreEqual("[MH2-H3PO4]", pkls[0].DisplayName);
Assert.AreEqual(1000 - NeutralLossConstants.NL_H3PO4.Mass / 2, pkls[0].Mz, 0.01);
precursor.Charge = 1;
pkls = matcher.GetNeutralLossPeaks(IonType.PRECURSOR_NEUTRAL_LOSS_PHOSPHO, precursor, nls, (m => m.IsPhosphoNeutralLossType()));
Assert.AreEqual("[MH-H3PO4]", pkls[0].DisplayName);
Assert.AreEqual(1000 - NeutralLossConstants.NL_H3PO4.Mass, pkls[0].Mz, 0.01);
}
private static Rectangle GetSpectrumRectangle(Graphics g2, PeakList <MatchedPeak> peaks, Rectangle rec)
{
MatchedPeak maxIntensityPeak = peaks.FindMaxIntensityPeak();
MatchedPeak highestPeak = maxIntensityPeak;
RectangleTransform rt = new RectangleTransform(rec, 1.0, highestPeak.Intensity);
int top = rt.GetTransformY(highestPeak.Intensity);
int highestTextLength = 0;
if (highestPeak.Matched)
{
highestTextLength = 10 + (int)GetStringWidth(g2, bigFont, highestPeak.Information);
top -= highestTextLength;
}
foreach (MatchedPeak peak in peaks)
{
if (!peak.Matched)
{
continue;
}
int textLength = 10 + (int)GetStringWidth(g2, bigFont, peak.Information);
int totalLength = rt.GetTransformY(peak.Intensity) - textLength;
if (totalLength < top)
{
highestTextLength = textLength;
top = totalLength;
highestPeak = peak;
}
}
int peakIntensityLength = rec.Height - highestTextLength;
int recHeight = (int)(peakIntensityLength * maxIntensityPeak.Intensity / highestPeak.Intensity);
return(new Rectangle(rec.Left, rec.Bottom - recHeight, rec.Width, recHeight));
}
public void TestInformation()
{
MatchedPeak p = new MatchedPeak(1000, 0.0, 2);
p.DisplayName = "TEST";
Assert.AreEqual("TEST++ 1000.0000", p.Information);
p.Charge = 1;
Assert.AreEqual("TEST 1000.0000", p.Information);
p.DisplayName = null;
p.PeakType = IonType.PRECURSOR;
Assert.AreEqual("[MH] 1000.0000", p.Information);
p.Charge = 2;
Assert.AreEqual("[MH2]++ 1000.0000", p.Information);
p.PeakType = IonType.B2;
p.PeakIndex = 5;
Assert.AreEqual("b5++ 1000.0000", p.Information);
p.Charge = 1;
Assert.AreEqual("b5 1000.0000", p.Information);
}
public static string GetBYIonDisplayName(INeutralLossType nlType, MatchedPeak sourcePeak, MatchedPeak targetPeak)
{
return(MyConvert.Format("[{0}{1}-{2}]", sourcePeak.PeakType.GetDisplayName(), sourcePeak.PeakIndex, nlType.Name));
}
public static string GetPrecursorDisplayName(INeutralLossType nlType, MatchedPeak sourcePeak, MatchedPeak targetPeak)
{
return(MyConvert.Format("[MH{0}-{1}]", targetPeak.Charge == 1 ? "" : targetPeak.Charge.ToString(), nlType.Name));
}
protected void AssertPeak(MatchedPeak p, string displayName, double mz)
{
Assert.AreEqual(displayName, p.DisplayName);
Assert.AreEqual(mz, p.Mz, 0.01);
}
