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);
}
}
public void TestLoadFromFile()
{
O18QuantificationSummaryItem item =
new O18QuantificationSummaryItemXmlFormat().ReadFromFile(TestContext.CurrentContext.TestDirectory + "/../../../data/O18QuantificationInformation.xml");
Assert.AreEqual(@"D:\sqh\Science\Project/4NLFOR.raw", item.RawFilename);
Assert.AreEqual("AFATDITDAEEDK", item.PeptideSequence);
Assert.AreEqual("C60H92N14O26", item.PeptideAtomComposition);
Assert.AreEqual(0.95, item.PurityOfO18Water, 0.01);
var expectPeptideProfile = new List <double>(new[] { 0.4611, 0.3340, 0.1439, 0.0459, 0.0119, 0.0026, 0.0005, 0.0001 });
Assert.AreEqual(expectPeptideProfile, item.PeptideProfile);
Assert.AreEqual(713.3209, item.SpeciesAbundance.RegressionItems[0].Mz);
Assert.AreEqual(36513020.6, item.SpeciesAbundance.RegressionItems[0].ObservedIntensity);
Assert.AreEqual(36512100.5, item.SpeciesAbundance.RegressionItems[0].RegressionIntensity);
Assert.AreEqual(713.8254, item.SpeciesAbundance.RegressionItems[1].Mz);
Assert.AreEqual(26438219.2, item.SpeciesAbundance.RegressionItems[1].ObservedIntensity);
Assert.AreEqual(26447909.0, item.SpeciesAbundance.RegressionItems[1].RegressionIntensity);
Assert.AreEqual(714.3221, item.SpeciesAbundance.RegressionItems[2].Mz);
Assert.AreEqual(29639265.4, item.SpeciesAbundance.RegressionItems[2].ObservedIntensity);
Assert.AreEqual(29595148.6, item.SpeciesAbundance.RegressionItems[2].RegressionIntensity);
Assert.AreEqual(714.8242, item.SpeciesAbundance.RegressionItems[3].Mz);
Assert.AreEqual(16687280.4, item.SpeciesAbundance.RegressionItems[3].ObservedIntensity);
Assert.AreEqual(16812006.0, item.SpeciesAbundance.RegressionItems[3].RegressionIntensity);
Assert.AreEqual(715.3243, item.SpeciesAbundance.RegressionItems[4].Mz);
Assert.AreEqual(7087781.0, item.SpeciesAbundance.RegressionItems[4].ObservedIntensity);
Assert.AreEqual(6823450.3, item.SpeciesAbundance.RegressionItems[4].RegressionIntensity);
Assert.AreEqual(715.8316, item.SpeciesAbundance.RegressionItems[5].Mz);
Assert.AreEqual(1799203.9, item.SpeciesAbundance.RegressionItems[5].ObservedIntensity);
Assert.AreEqual(2164120.0, item.SpeciesAbundance.RegressionItems[5].RegressionIntensity);
Assert.AreEqual(2, item.ObservedEnvelopes.Count);
Assert.AreEqual(6741, item.ObservedEnvelopes[0].ScanTimes[0].Scan);
Assert.AreEqual(12.34, item.ObservedEnvelopes[0].ScanTimes[0].RetentionTime);
Assert.IsTrue(item.ObservedEnvelopes[0].Enabled);
Assert.IsTrue(item.ObservedEnvelopes[0].IsIdentified);
Assert.AreEqual(713.3209, item.ObservedEnvelopes[0][0].Mz);
Assert.AreEqual(424345.9, item.ObservedEnvelopes[0][0].Intensity);
Assert.AreEqual(713.8254, item.ObservedEnvelopes[0][1].Mz);
Assert.AreEqual(198378.3, item.ObservedEnvelopes[0][1].Intensity);
Assert.AreEqual(714.3221, item.ObservedEnvelopes[0][2].Mz);
Assert.AreEqual(246866.8, item.ObservedEnvelopes[0][2].Intensity);
Assert.AreEqual(714.8242, item.ObservedEnvelopes[0][3].Mz);
Assert.AreEqual(221648.0, item.ObservedEnvelopes[0][3].Intensity);
Assert.AreEqual(715.3243, item.ObservedEnvelopes[0][4].Mz);
Assert.AreEqual(107701.3, item.ObservedEnvelopes[0][4].Intensity);
Assert.AreEqual(715.8316, item.ObservedEnvelopes[0][5].Mz);
Assert.AreEqual(0.0, item.ObservedEnvelopes[0][5].Intensity);
Assert.AreEqual(6746, item.ObservedEnvelopes[1].ScanTimes[0].Scan);
Assert.AreEqual(13.34, item.ObservedEnvelopes[1].ScanTimes[0].RetentionTime);
Assert.IsFalse(item.ObservedEnvelopes[1].Enabled);
Assert.IsFalse(item.ObservedEnvelopes[1].IsIdentified);
Assert.AreEqual(713.3209, item.ObservedEnvelopes[1][0].Mz);
Assert.AreEqual(796597.7, item.ObservedEnvelopes[1][0].Intensity);
Assert.AreEqual(713.8254, item.ObservedEnvelopes[1][1].Mz);
Assert.AreEqual(530778.4, item.ObservedEnvelopes[1][1].Intensity);
Assert.AreEqual(714.3221, item.ObservedEnvelopes[1][2].Mz);
Assert.AreEqual(456099.6, item.ObservedEnvelopes[1][2].Intensity);
Assert.AreEqual(714.8242, item.ObservedEnvelopes[1][3].Mz);
Assert.AreEqual(339509.8, item.ObservedEnvelopes[1][3].Intensity);
Assert.AreEqual(715.3243, item.ObservedEnvelopes[1][4].Mz);
Assert.AreEqual(182812.3, item.ObservedEnvelopes[1][4].Intensity);
Assert.AreEqual(715.8316, item.ObservedEnvelopes[1][5].Mz);
Assert.AreEqual(0.0, item.ObservedEnvelopes[1][5].Intensity);
Assert.AreEqual(79184307.0, item.SpeciesAbundance.O16);
Assert.AreEqual(39464386.0, item.SpeciesAbundance.O181);
Assert.AreEqual(440969.4, item.SpeciesAbundance.O182);
Assert.AreEqual(0.0219, item.SampleAbundance.LabellingEfficiency);
Assert.AreEqual(50, item.SampleAbundance.Ratio);
Assert.AreEqual(0.0, item.SampleAbundance.O16);
Assert.AreEqual(922867772.7, item.SampleAbundance.O18);
}
