public void SetSummaryFilename(string summaryFilename, IAnnotation parentObj) { if (this.summaryFilename.Equals(summaryFilename)) { return; } this.parentObj = parentObj; this.summary = this.fileFormat.ReadFromFile(summaryFilename); this.summaryFilename = summaryFilename; Text = summaryFilename; ShowSummary(); this.btnSave.Enabled = false; }
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 void Quantify(string rawFileName, List <IIdentifiedSpectrum> spectra, string detailDir) { if (!Directory.Exists(detailDir)) { Directory.CreateDirectory(detailDir); } var experimental = RawFileFactory.GetExperimental(rawFileName); Dictionary <string, DifferentRetentionTimeEnvelopes> spectrumKeyMap = new Dictionary <string, DifferentRetentionTimeEnvelopes>(); Dictionary <SilacEnvelopes, List <IIdentifiedSpectrum> > envelopeSpectrumGroup = new Dictionary <SilacEnvelopes, List <IIdentifiedSpectrum> >(); double precursorPPM = GetPrecursorPPM(spectra); try { _rawReader.Open(rawFileName); int firstScanNumber = _rawReader.GetFirstSpectrumNumber(); int lastScanNumber = _rawReader.GetLastSpectrumNumber(); Progress.SetRange(1, spectra.Count); int pepCount = 0; for (int s = 0; s < spectra.Count; s++) { Console.WriteLine(s); IIdentifiedSpectrum spectrum = spectra[s]; SilacQuantificationSummaryItem.ClearAnnotation(spectrum); if (Progress.IsCancellationPending()) { throw new UserTerminatedException(); } int startScan = spectrum.Query.FileScan.FirstScan; if (startScan > lastScanNumber) { spectrum.GetOrCreateQuantificationItem().RatioStr = "OUT_OF_RANGE"; continue; } Progress.SetPosition(pepCount++); IIdentifiedPeptide sp = spectrum.Peptide; string seq = GetMatchSequence(spectrum); IPeptideInfo peptideInfo = new IdentifiedPeptideInfo(seq, spectrum.TheoreticalMH, spectrum.Query.Charge); SilacCompoundInfo sci = GetSilacCompoundInfo(peptideInfo); //如果轻重离子理论质荷比一样,忽略 if (!sci.IsSilacData()) { spectrum.GetOrCreateQuantificationItem().RatioStr = "NOT_SILAC"; continue; } //如果轻重离子理论质荷比与观测值不一致,忽略 if (!sci.IsMzEquals(spectrum.ObservedMz, MAX_DELTA_MZ)) { ValidateModifications(seq); spectrum.GetOrCreateQuantificationItem().RatioStr = "WRONG_IDENTIFICATION"; continue; } //如果没有找到相应的FullScan,忽略 int identifiedFullScan = _rawReader.FindPreviousFullScan(startScan, firstScanNumber); if (-1 == identifiedFullScan) { spectrum.GetOrCreateQuantificationItem().RatioStr = "NO_PROFILE"; continue; } DifferentRetentionTimeEnvelopes pkls = FindEnvelopes(spectrumKeyMap, spectrum, sci); SilacEnvelopes envelope = pkls.FindSilacEnvelope(identifiedFullScan); //如果该scan被包含在已经被定量的结果中,忽略 if (envelope != null) { envelope.SetScanIdentified(identifiedFullScan, spectrum.IsExtendedIdentification()); envelopeSpectrumGroup[envelope].Add(spectrum); continue; } //从原始文件中找出该spectrum的定量信息 int maxIndex = Math.Min(option.ProfileLength - 1, pkls.LightProfile.FindMaxIndex()); double mzTolerance = PrecursorUtils.ppm2mz(sci.Light.Mz, option.PPMTolerance); //如果FullScan没有相应的离子,忽略。(鉴定错误或者扩展定量时候,会出现找不到pair的现象) SilacPeakListPair splp = GetLightHeavyPeakList(_rawReader, sci, maxIndex, mzTolerance, identifiedFullScan); if (null == splp) { spectrum.GetOrCreateQuantificationItem().RatioStr = "NO_PROFILE"; continue; } splp.IsIdentified = true; splp.IsExtendedIdentification = spectrum.IsExtendedIdentification(); SilacEnvelopes envelopes = new SilacEnvelopes(); envelopes.Add(splp); //向前查找定量信息 int fullScan = identifiedFullScan; int scanNumber = 0; while ((fullScan = _rawReader.FindPreviousFullScan(fullScan - 1, firstScanNumber)) != -1) { if (_rawReader.IsBadDataScan(fullScan)) { continue; } scanNumber++; var item = GetLightHeavyPeakList(_rawReader, sci, maxIndex, mzTolerance, fullScan, scanNumber <= MinScanNumber); if (null == item) { break; } envelopes.Add(item); } envelopes.Reverse(); //向后查找定量信息 fullScan = identifiedFullScan; scanNumber = 0; while ((fullScan = _rawReader.FindNextFullScan(fullScan + 1, lastScanNumber)) != -1) { if (_rawReader.IsBadDataScan(fullScan)) { continue; } scanNumber++; var item = GetLightHeavyPeakList(_rawReader, sci, maxIndex, mzTolerance, fullScan, scanNumber <= MinScanNumber); if (null == item) { break; } envelopes.Add(item); } //对每个scan计算轻重的离子丰度 envelopes.ForEach(m => m.CalculateIntensity(pkls.LightProfile, pkls.HeavyProfile)); pkls.Add(envelopes); envelopeSpectrumGroup.Add(envelopes, new List <IIdentifiedSpectrum>()); envelopeSpectrumGroup[envelopes].Add(spectrum); } } finally { _rawReader.Close(); } foreach (string key in spectrumKeyMap.Keys) { DifferentRetentionTimeEnvelopes pkls = spectrumKeyMap[key]; foreach (SilacEnvelopes envelopes in pkls) { if (0 == envelopes.Count) { continue; } List <IIdentifiedSpectrum> mps = envelopeSpectrumGroup[envelopes]; double mzTolerance = PrecursorUtils.ppm2mz(mps[0].Query.ObservedMz, option.PPMTolerance); string scanStr = GetScanRange(envelopes); string resultFilename = detailDir + "\\" + mps[0].Query.FileScan.Experimental + "." + PeptideUtils.GetPureSequence(mps[0].Sequence) + "." + mps[0].Query.Charge + scanStr + ".silac"; IPeptideInfo peptideInfo = new IdentifiedPeptideInfo(mps[0].GetMatchSequence(), mps[0].TheoreticalMH, mps[0].Query.Charge); SilacCompoundInfo sci = GetSilacCompoundInfo(peptideInfo); SilacQuantificationSummaryItem item = new SilacQuantificationSummaryItem(sci.Light.IsSample); item.RawFilename = rawFileName; item.SoftwareVersion = this.SoftwareVersion; item.PeptideSequence = mps[0].Sequence; item.Charge = mps[0].Charge; item.LightAtomComposition = sci.Light.Composition.ToString(); item.HeavyAtomComposition = sci.Heavy.Composition.ToString(); item.LightProfile = pkls.LightProfile; item.HeavyProfile = pkls.HeavyProfile; item.ObservedEnvelopes = envelopes; item.ValidateScans(sci, precursorPPM); item.Smoothing(); item.CalculateRatio(); new SilacQuantificationSummaryItemXmlFormat().WriteToFile(resultFilename, item); int maxScoreItemIndex = FindMaxScoreItemIndex(mps); for (int i = 0; i < mps.Count; i++) { if (maxScoreItemIndex == i) { item.AssignToAnnotation(mps[i], resultFilename); } else { item.AssignDuplicationToAnnotation(mps[i], resultFilename); } } } } foreach (IIdentifiedSpectrum mph in spectra) { mph.InitializeRatioEnabled(); } }