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(); }