private List <IIdentifiedSpectrum> DuplicateSpectrum(List <IIdentifiedSpectrum> spectra, string detailDir)
{
List <IIdentifiedSpectrum> result = new List <IIdentifiedSpectrum>();
Dictionary <string, List <string> > rawmap = new Dictionary <string, List <string> >();
foreach (var raws in rawpairs.Values)
{
foreach (var raw in raws)
{
rawmap[raw] = raws;
}
}
var format = new MascotPeptideTextFormat();
foreach (var spectrum in spectra)
{
if (spectrum.HasRatio())
{
var silacFile = spectrum.GetRatioFile(detailDir);
var silacResult = new SilacQuantificationSummaryItemXmlFormat().ReadFromFile(silacFile);
var maxIntensity = silacResult.ObservedEnvelopes.Max(m => Math.Max(m.LightIntensity, m.HeavyIntensity));
var scan = silacResult.ObservedEnvelopes.Find(m => m.LightIntensity == maxIntensity || m.HeavyIntensity == maxIntensity).Scan;
var str = format.PeptideFormat.GetString(spectrum);
var oldraw = spectrum.Query.FileScan.Experimental;
var lst = rawmap[oldraw];
foreach (var otherraw in lst)
{
if (otherraw.Equals(oldraw))
{
continue;
}
var newspectrum = format.PeptideFormat.ParseString(str);
newspectrum.Query.FileScan.Experimental = otherraw;
newspectrum.Query.FileScan.FirstScan = scan;
newspectrum.Query.FileScan.LastScan = scan;
newspectrum.SetExtendedIdentification(true);
result.Add(newspectrum);
spectrum.AddDuplicatedSpectrum(newspectrum);
}
}
}
return(result);
}
public override void Update(object sender, UpdateQuantificationItemEventArgs e)
{
IQuantificationSummaryOption option = e.Option as IQuantificationSummaryOption;
panel.InitGraphPane(this.title, option.Func.ReferenceKey, option.Func.SampleKey, true, 0.0);
IIdentifiedProteinGroup group = e.Item as IIdentifiedProteinGroup;
try
{
var pplNormal = new PointPairList();
var pplSelected = new PointPairList();
var spectra = group.GetPeptides();
var format = new SilacQuantificationSummaryItemXmlFormat();
foreach (var pep in spectra)
{
if (option.IsPeptideRatioValid(pep))
{
string ratioFile = GetRatioFile(option, pep);
if (ratioFile == null)
{
continue;
}
var item = format.ReadFromFile(ratioFile);
Func <SilacPeakListPair, double> getSamIntensity;
Func <SilacPeakListPair, double> getRefIntensity;
if (item.SampleIsLight)
{
getSamIntensity = m => m.LightIntensity;
getRefIntensity = m => m.HeavyIntensity;
}
else
{
getSamIntensity = m => m.HeavyIntensity;
getRefIntensity = m => m.LightIntensity;
}
PointPairList ppl;
if (pep.Selected)
{
ppl = pplSelected;
}
else
{
ppl = pplNormal;
}
foreach (var envelope in item.ObservedEnvelopes)
{
if (!envelope.Enabled)
{
continue;
}
double refIntensity = getRefIntensity(envelope);
double sampleIntensity = getSamIntensity(envelope);
if (refIntensity == 0.0 || sampleIntensity == 0.0)
{
continue;
}
ppl.Add(refIntensity, sampleIntensity);
ppl[ppl.Count - 1].Tag = pep;
Debug.Assert(ppl[ppl.Count - 1].Tag == pep);
}
}
}
this.panel.ClearData();
this.panel.AddPoints(pplSelected, SelectedColor);
this.panel.AddPoints(pplNormal, NormalColor);
var pplTotal = new PointPairList();
pplTotal.AddRange(pplSelected);
pplTotal.AddRange(pplNormal);
if (pplTotal.Count > 0)
{
var lr = pplTotal.GetRegression();
var lr_text = MyConvert.Format("Ratio={0:0.00}, Correl={1:0.00}, FValue={2:0.00}, FProb={3:E4}", lr.Ratio, lr.RSquare, lr.TValue, lr.PValue);
PointPairList line = pplTotal.GetRegressionLine();
var lineItem = this.panel.AddCurve(lr_text, line, RegressionLineColor, SymbolType.None);
lineItem.Label.FontSpec = new FontSpec()
{
Size = 15, Border = new Border()
{
IsVisible = false
}
};
}
}
finally
{
ZedGraphicExtension.UpdateGraph(this.zgcGraph);
}
}
