public O18QuantificationSummaryItem ReadFromFile(string filename)
{
var result = new O18QuantificationSummaryItem();
var root = XElement.Load(filename);
result.RawFilename = root.Element("RawFilename").Value;
var ele = root.Element("SoftwareVersion");
if (ele != null)
{
result.SoftwareVersion = ele.Value;
}
result.PeptideSequence = root.Element("PeptideSequence").Value;
result.AdditionalFormula = root.Element("AdditionalFormula").Value;
result.PeptideAtomComposition = root.Element("PeptideAtomComposition").Value;
result.PurityOfO18Water = MyConvert.ToDouble(root.Element("PurityOfO18Water").Value);
result.IsPostDigestionLabelling = bool.Parse(root.Element("IsPostDigestionLabelling").Value);
if (root.Element("TheoreticalO16Mz") != null)
{
result.TheoreticalO16Mz = MyConvert.ToDouble(root.Element("TheoreticalO16Mz").Value);
result.Charge = Convert.ToInt32(root.Element("Charge").Value);
}
result.PeptideProfile = (from x in root.Element("PeptideProfile").Elements()
let mzEle = x.Attribute("Mz")
let mz = mzEle == null ? 0.0 : MyConvert.ToDouble(mzEle.Value)
let intensity = MyConvert.ToDouble(x.Value)
select new Peak(mz, intensity)).ToList();
if (result.PeptideProfile[0].Mz == 0.0)
{
var pkls = IsotopicBuilderFactory.GetBuilder().GetProfile(new AtomComposition(result.PeptideAtomComposition), result.Charge, 10);
for (int i = 0; i < Math.Min(result.PeptideProfile.Count, pkls.Count); i++)
{
result.PeptideProfile[i].Mz = pkls[i].Mz;
result.PeptideProfile[i].Intensity = pkls[i].Intensity;
}
}
var observed = root.Element("ObservedEnvelopes");
result.ObservedEnvelopes = new List <O18QuanEnvelope>();
foreach (var pkl in observed.Elements())
{
var peakList = new O18QuanEnvelope();
int scan = int.Parse(pkl.Attribute("Scan").Value);
double retentiontime = MyConvert.ToDouble(pkl.Attribute("Retentiontime").Value);
peakList.Enabled = bool.Parse(pkl.Attribute("Enabled").Value);
peakList.IsIdentified = bool.Parse(pkl.Attribute("Identified").Value);
peakList.ScanTimes.Add(new ScanTime(scan, retentiontime));
foreach (var peak in pkl.Elements())
{
double mz = MyConvert.ToDouble(peak.Attribute("Mz").Value);
double intensity = MyConvert.ToDouble(peak.Attribute("Intensity").Value);
var p = new Peak(mz, intensity);
peakList.Add(p);
}
result.ObservedEnvelopes.Add(peakList);
}
var species = root.Element("SpeciesAbundance");
result.SpeciesAbundance.O16 = MyConvert.ToDouble(species.Element("O16").Value);
result.SpeciesAbundance.O181 = MyConvert.ToDouble(species.Element("O181").Value);
result.SpeciesAbundance.O182 = MyConvert.ToDouble(species.Element("O182").Value);
var regression = species.Element("Regression");
result.SpeciesAbundance.RegressionCorrelation = MyConvert.ToDouble(regression.Attribute("Correlation").Value);
result.SpeciesAbundance.RegressionItems.Clear();
foreach (var item in regression.Elements())
{
var ritem = new SpeciesRegressionItem();
ritem.Mz = MyConvert.ToDouble(item.Attribute("Mz").Value);
ritem.ObservedIntensity = MyConvert.ToDouble(item.Attribute("Observed").Value);
ritem.RegressionIntensity = MyConvert.ToDouble(item.Attribute("Regression").Value);
result.SpeciesAbundance.RegressionItems.Add(ritem);
}
var samples = root.Element("SampleAbundance");
result.SampleAbundance.LabellingEfficiency = MyConvert.ToDouble(samples.Attribute("LabellingEfficiency").Value);
result.SampleAbundance.Ratio = MyConvert.ToDouble(samples.Attribute("Ratio").Value);
result.SampleAbundance.O16 = MyConvert.ToDouble(samples.Element("O16").Value);
result.SampleAbundance.O18 = MyConvert.ToDouble(samples.Element("O18").Value);
return(result);
}
public void TestWriteToFile()
{
var item = new O18QuantificationSummaryItem();
item.RawFilename = @"D:\sqh\Science\Project/4NLFOR.raw";
item.PeptideSequence = "AFATDITDAEEDK";
item.PeptideAtomComposition = "C60H92N14O26";
item.PurityOfO18Water = 0.95;
item.PeptideProfile = IsotopicBuilderFactory.GetBuilder().GetProfile(new AtomComposition(item.PeptideAtomComposition), 1, 10);
item.ObservedEnvelopes = new List <O18QuanEnvelope> ();
var pkl1 = new O18QuanEnvelope();
pkl1.ScanTimes.Add(new ScanTime(6741, 12.34));
pkl1.Enabled = true;
pkl1.IsIdentified = true;
pkl1.Add(new Peak(713.3209, 424345.9));
pkl1.Add(new Peak(713.8254, 198378.3));
pkl1.Add(new Peak(714.3221, 246866.8));
pkl1.Add(new Peak(714.8242, 221648.0));
pkl1.Add(new Peak(715.3243, 107701.3));
pkl1.Add(new Peak(715.8316, 0.0));
item.ObservedEnvelopes.Add(pkl1);
var pkl2 = new O18QuanEnvelope();
pkl2.ScanTimes.Add(new ScanTime(6746, 13.34));
pkl2.Enabled = false;
pkl2.Add(new Peak(713.3209, 796597.7));
pkl2.Add(new Peak(713.8254, 530778.4));
pkl2.Add(new Peak(714.3221, 456099.6));
pkl2.Add(new Peak(714.8242, 339509.8));
pkl2.Add(new Peak(715.3243, 182812.3));
pkl2.Add(new Peak(715.8316, 0.0));
item.ObservedEnvelopes.Add(pkl2);
item.SpeciesAbundance = new SpeciesAbundanceInfo();
item.SpeciesAbundance.O16 = 79184307.0;
item.SpeciesAbundance.O181 = 39464386.0;
item.SpeciesAbundance.O182 = 440969.4;
item.SampleAbundance = new SampleAbundanceInfo();
item.SampleAbundance.LabellingEfficiency = 0.0219;
item.SampleAbundance.Ratio = 50;
item.SampleAbundance.O16 = 0;
item.SampleAbundance.O18 = 922867772.7;
item.SpeciesAbundance.RegressionCorrelation = 0.9999;
item.SpeciesAbundance.RegressionItems.Clear();
item.SpeciesAbundance.RegressionItems.Add(new SpeciesRegressionItem(713.3209, 36513020.6, 36512100.5));
item.SpeciesAbundance.RegressionItems.Add(new SpeciesRegressionItem(713.8254, 26438219.2, 26447909.0));
item.SpeciesAbundance.RegressionItems.Add(new SpeciesRegressionItem(714.3221, 29639265.4, 29595148.6));
item.SpeciesAbundance.RegressionItems.Add(new SpeciesRegressionItem(714.8242, 16687280.4, 16812006.0));
item.SpeciesAbundance.RegressionItems.Add(new SpeciesRegressionItem(715.3243, 7087781.0, 6823450.3));
item.SpeciesAbundance.RegressionItems.Add(new SpeciesRegressionItem(715.8316, 1799203.9, 2164120.0));
new O18QuantificationSummaryItemXmlFormat().WriteToFile(@TestContext.CurrentContext.TestDirectory + "/../../../data//O18QuantificationInformation.xml.tmp", item);
AssertUtils.AssertFileEqual(@TestContext.CurrentContext.TestDirectory + "/../../../data//O18QuantificationInformation.xml.tmp",
@TestContext.CurrentContext.TestDirectory + "/../../../data//O18QuantificationInformation.xml");
new FileInfo(@TestContext.CurrentContext.TestDirectory + "/../../../data//O18QuantificationInformation.xml.tmp").Delete();
}
