public override object ReadRatioFile(string file)
{
return(format.ReadFromFile(file));
}
public void WriteToStream(System.IO.StreamWriter sw, IIdentifiedSpectrum peptide)
{
string detailFile = this.detailDirectory + "\\" + peptide.GetQuantificationItem().Filename;
if (File.Exists(detailFile))
{
SilacQuantificationSummaryItem item = format.ReadFromFile(detailFile);
Func <SilacPeakListPair, double> SampleIntensityFunc;
Func <SilacPeakListPair, double> ReferenceIntensityFunc;
if (item.SampleIsLight)
{
SampleIntensityFunc = m => m.LightIntensity;
ReferenceIntensityFunc = m => m.HeavyIntensity;
}
else
{
SampleIntensityFunc = m => m.HeavyIntensity;
ReferenceIntensityFunc = m => m.LightIntensity;
}
var valueFuncs = new List <Func <SilacPeakListPair, string> >();
foreach (var header in headers)
{
switch (header)
{
case "Scan": valueFuncs.Add(m => string.Format("{0}", m.Scan));
break;
case "Retentiontime": valueFuncs.Add(m => string.Format("{0:0.00}", m.Light.ScanTimes[0].RetentionTime));
break;
case "Identified": valueFuncs.Add(m => m.IsIdentified.ToString());
break;
case QuantificationItem.KEY_REFERENCE_INTENSITY: valueFuncs.Add(m => string.Format("{0:0.0}", ReferenceIntensityFunc(m)));
break;
case QuantificationItem.KEY_SAMPLE_INTENSITY: valueFuncs.Add(m => string.Format("{0:0.0}", SampleIntensityFunc(m)));
break;
case QuantificationItem.KEY_RATIO: valueFuncs.Add(m => string.Format("{0:0.0000}", SampleIntensityFunc(m) / ReferenceIntensityFunc(m)));
break;
case "Protein": valueFuncs.Add(m => peptide.GetProteins("/"));
break;
}
;
}
foreach (var scan in item.ObservedEnvelopes)
{
if (scan.Enabled)
{
var ri = ReferenceIntensityFunc(scan);
var si = SampleIntensityFunc(scan);
if (ri == 0.0 || si == 0.0)
{
continue;
}
sw.Write("\t");
foreach (var func in valueFuncs)
{
sw.Write("\t{0}", func(scan));
}
sw.WriteLine();
}
}
}
}
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);
}
}