protected string GetRatioFile(IQuantificationSummaryOption option, IIdentifiedSpectrum mph) { string ratioFile = mph.GetQuantificationItem().Filename; if (ratioFile.Equals("-")) { return(null); } FileInfo fi = new FileInfo(SummaryFilename); string result; if (IsRelativeDir(ratioFile)) { result = fi.DirectoryName + "/" + ratioFile; } else { result = fi.DirectoryName + "/" + DefaultDetailDirectory + "/" + ratioFile; } result = new FileInfo(result).FullName; if (!File.Exists(result)) { return(null); } return(result); }
protected virtual string GetRatioFile(IIdentifiedSpectrum mph) { string ratioFile; if (mph.GetQuantificationItem() != null) { ratioFile = mph.GetQuantificationItem().Filename; } else { ratioFile = (string)mph.Annotations[option.RatioFileKey]; } if (string.IsNullOrEmpty(ratioFile) || ratioFile.Equals("-")) { return(null); } FileInfo fi = new FileInfo(summaryFilename); string result; if (IsRelativeDir(ratioFile)) { result = fi.DirectoryName + "/" + ratioFile; } else { result = fi.DirectoryName + "/" + GetDetailDirectoryName() + "/" + ratioFile; } result = new FileInfo(result).FullName; if (!File.Exists(result)) { MessageBox.Show(this, "Cannot find file " + result, "Error", MessageBoxButtons.OK, MessageBoxIcon.Error); return(null); } return(result); }
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 double CalculatePeptideRatio(IIdentifiedSpectrum spectrum) { return(spectrum.GetQuantificationItem().Ratio); }
public bool HasPeptideRatio(IIdentifiedSpectrum spectrum) { return(spectrum.GetQuantificationItem() != null); }