protected override void PrepareIntensityFile(List <IIdentifiedSpectrum> spectra, string filename)
{
var pepfilename = Path.ChangeExtension(filename, ".pep.csv");
using (StreamWriter sw = new StreamWriter(pepfilename))
{
sw.WriteLine("RefIntensity,SamIntensity,Peptide,FileScan");
foreach (var pep in spectra)
{
if (pep.IsEnabled(true) && Option.IsPeptideRatioValid(pep))
{
string ratioFile = Option.GetRatioFile(pep);
if (ratioFile == null)
{
continue;
}
O18QuantificationSummaryItem item = new O18QuantificationSummaryItemXmlFormat().ReadFromFile(ratioFile);
item.CalculateIndividualAbundance();
foreach (var envelope in item.ObservedEnvelopes)
{
if (!envelope.Enabled)
{
continue;
}
double refIntensity = envelope.SampleAbundance.O16;
double sampleIntensity = envelope.SampleAbundance.O18;
if (refIntensity == 0.0 || sampleIntensity == 0.0)
{
continue;
}
sw.WriteLine("{0},{1},{2},{3}", refIntensity, sampleIntensity, pep.Sequence, pep.Query.FileScan);
}
}
}
}
}
public override void Update(object sender, UpdateQuantificationItemEventArgs e)
{
IQuantificationSummaryOption option = e.Option as IQuantificationSummaryOption;
panel.InitGraphPane(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 O18QuantificationSummaryItemXmlFormat();
foreach (var pep in spectra)
{
if (pep.IsEnabled(true) && option.IsPeptideRatioValid(pep))
{
string ratioFile = GetRatioFile(option, pep);
if (ratioFile == null)
{
continue;
}
O18QuantificationSummaryItem item = new O18QuantificationSummaryItemXmlFormat().ReadFromFile(ratioFile);
item.CalculateIndividualAbundance();
PointPairList ppl;
if (pep.Selected)
{
ppl = pplSelected;
}
else
{
ppl = pplNormal;
}
foreach (var envelope in item.ObservedEnvelopes)
{
if (!envelope.Enabled)
{
continue;
}
double refIntensity = envelope.SampleAbundance.O16;
double sampleIntensity = envelope.SampleAbundance.O18;
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 maxValue = (from p in pplTotal
select Math.Max(p.X, p.Y)).Max() * 1.1;
this.panel.XAxis.Scale.Max = maxValue;
this.panel.YAxis.Scale.Max = maxValue;
var ratio = option.GetProteinRatio(group[0]);
PointPairList line = pplTotal.GetRegressionLine(ratio);
var lineItem = this.panel.AddCurve(option.GetProteinRatioDescription(group[0]), line, RegressionLineColor, SymbolType.None);
lineItem.Label.FontSpec = new FontSpec()
{
Size = 15, Border = new Border()
{
IsVisible = false
}
};
}
}
finally
{
ZedGraphicExtension.UpdateGraph(this.zgcGraph);
}
}
