public void Match(IIdentifiedPeptideResult sr)
{
foreach (IMatcher matcher in matchers)
{
matcher.Match(sr);
}
}
public void Match(IIdentifiedPeptideResult sr)
{
List <MatchedPeak> expPeaks = sr.ExperimentalPeakList;
double minIntensity = sr.ExperimentalPeakList.FindMaxIntensityPeak().Intensity *minIntensityScale;
MatchedPeakUtils.Match(expPeaks, sr.GetIonSeries()[ionType], mzTolerance, minIntensity);
}
public void Draw(Graphics g2, Rectangle rec, IIdentifiedPeptideResult sr)
{
g2.CompositingQuality = CompositingQuality.HighQuality;
g2.SmoothingMode = SmoothingMode.AntiAlias;
g2.TextRenderingHint = System.Drawing.Text.TextRenderingHint.AntiAliasGridFit;
Rectangle newRec = new Rectangle(rec.Left + 60, rec.Top, rec.Width - 80, rec.Height - 50 - bigFont.Height);
Pen blackPen = new Pen(Color.Black, 1);
Rectangle spectrumRec = GetSpectrumRectangle(g2, sr.ExperimentalPeakList, newRec);
var maxMz =
(from peak in sr.ExperimentalPeakList
orderby peak.Mz descending
select peak.Mz).FirstOrDefault();
double maxMzWidth = ((int)maxMz / 100 + 1) * 100.0;
int yFontShift = (int)(g2.MeasureString("M", bigFont).Height / 2);
RectangleTransform rt = new RectangleTransform(spectrumRec, maxMzWidth, sr.ExperimentalPeakList.FindMaxIntensityPeak().Intensity);
DrawXScale(g2, blackPen, spectrumRec, rt);
DrawYScale(g2, blackPen, spectrumRec);
foreach (MatchedPeak peak in sr.ExperimentalPeakList)
{
Brush brush;
Pen pen;
if (peak.Matched)
{
Color color = IonColorMap[peak.PeakType];
brush = new SolidBrush(color);
pen = new Pen(brush);
}
else
{
brush = Brushes.Black;
pen = blackPen;
}
int x = rt.GetTransformX(peak.Mz);
int y = rt.GetTransformY(peak.Intensity);
g2.DrawLine(pen, new Point(x, spectrumRec.Bottom), new Point(x, y));
if (peak.Matched)
{
DrawVerticalIonName(g2, brush, x - yFontShift, y, peak.Information);
}
}
}
public override void Match(IIdentifiedPeptideResult sr)
{
PeakList <MatchedPeak> peaks = sr.ExperimentalPeakList;
double minBYNeutralLossIntensity = peaks.FindMaxIntensityPeak().Intensity *minBYNeutralLossIntensityScale;
NeutralLossCandidates candidates = new NeutralLossCandidates(sr.Peptide);
List <MatchedPeak> byNeutralLossPeaks = GetNeutralLossPeaks(sr.GetIonSeries(), sr.ExperimentalPeakList.PrecursorCharge, candidates);
MatchedPeakUtils.Match(peaks, byNeutralLossPeaks, PeakMzTolerance, minBYNeutralLossIntensity);
}
public override void Match(IIdentifiedPeptideResult sr)
{
PeakList <MatchedPeak> peaks = sr.ExperimentalPeakList;
double minBYNeutralLossIntensity = peaks.FindMaxIntensityPeak().Intensity *minBYNeutralLossIntensityScale;
NeutralLossCandidates candidates = new NeutralLossCandidates(sr.Peptide);
List <MatchedPeak> byPhosphoNeutralLossPeaks = GetPhosphoNeutralLossPeaks(sr, candidates);
//byPhosphoNeutralLossPeaks.ForEach(m => Console.WriteLine(m.DisplayName + "," + m.Mz));
MatchedPeakUtils.Match(peaks, byPhosphoNeutralLossPeaks, PeakMzTolerance, minBYNeutralLossIntensity);
}
public override void Match(IIdentifiedPeptideResult sr)
{
NeutralLossCandidates candidates = new NeutralLossCandidates(sr.Peptide);
List <INeutralLossType> nlTypes = GetNeutralLossTypes(candidates.CanLossWater, candidates.CanLossAmmonia);
PeakList <MatchedPeak> expPeaks = sr.ExperimentalPeakList;
List <MatchedPeak> nlPeaks = GetNeutralLossPeaks(IonType.PRECURSOR_NEUTRAL_LOSS, new MatchedPeak(expPeaks.PrecursorMZ, 0.0, expPeaks.PrecursorCharge), nlTypes, (m => true));
//nlPeaks.ForEach(m => Console.WriteLine(m.DisplayName + "," + m.Mz));
double minNeutralLossIntensity = expPeaks.FindMaxIntensityPeak().Intensity *minPrecursorNeutralLossIntensityScale;
MatchedPeakUtils.Match(expPeaks, nlPeaks, PeakMzTolerance, minNeutralLossIntensity);
}
public List <MatchedPeak> GetPhosphoNeutralLossPeaks(IIdentifiedPeptideResult sr, NeutralLossCandidates candidates)
{
List <MatchedPeak> result = new List <MatchedPeak>();
Dictionary <int, string> bModifiedPosition = GetPhosphoModificationPositionMapB(sr.Peptide);
Dictionary <int, string> yModifiedPosition = GetPhosphoModificationPositionMapY(sr.Peptide);
result.AddRange(GetPhosphoNeutralLossPeaks(sr.GetIonSeries()[IonType.B], IonType.B_NEUTRAL_LOSS_PHOSPHO, 1, bModifiedPosition, candidates.BLossWater, candidates.BLossAmmonia));
result.AddRange(GetPhosphoNeutralLossPeaks(sr.GetIonSeries()[IonType.Y], IonType.B_NEUTRAL_LOSS_PHOSPHO, 1, yModifiedPosition, candidates.YLossWater, candidates.YLossAmmonia));
if (sr.ExperimentalPeakList.PrecursorCharge > 1)
{
result.AddRange(GetPhosphoNeutralLossPeaks(sr.GetIonSeries()[IonType.B2], IonType.B_NEUTRAL_LOSS_PHOSPHO, 2, bModifiedPosition, candidates.BLossWater, candidates.BLossAmmonia));
result.AddRange(GetPhosphoNeutralLossPeaks(sr.GetIonSeries()[IonType.Y2], IonType.B_NEUTRAL_LOSS_PHOSPHO, 2, yModifiedPosition, candidates.YLossWater, candidates.YLossAmmonia));
}
return(result);
}
public abstract void Match(IIdentifiedPeptideResult sr);
