/* * Writes the result database to a file, to make it faster to re-initialize the * software */ //public static void writeResultDatabaseToFile(String file_path, ResultDatabase rd) //{ // log.Debug("Writing Result Database to a file..."); // try // { // StreamWriter writer = new StreamWriter(file_path); // log.Debug("File name: " + file_path); // // Get all IDs // List<IDs> ids = new List<IDs>(rd.getIDs()); // // Sort by scan number // ids.Sort((IDs x, IDs y) => (x.getScanNum()).CompareTo(y.getScanNum())); // // Write header // String[] header = new String[] { "scan", "scan_t", "peptide_mass", "peptide_sequence", "parent_proteins", // "peptide_evidence", "peptide_reference", "database_sequence_id", "xCorr", "deltaCN", "deltaCNStar", // "spscore", "sprank", "evalue" }; // writer.Write(String.Join("\t", header)); // foreach (IDs id in ids) // { // writer.Write("\n" + outputIDToTSVFormat(id)); // writer.Flush(); // } // writer.Flush(); // writer.Close(); // } // catch (Exception e) // { // Console.WriteLine(e.ToString()); // log.Error("Writing file unsuccessful!!!"); // Environment.Exit(0); // } // log.Debug("Writing file successful."); //} /* * Write the identification features used for training the logistic regression * classifier */ //public static void writeIdentificationFeaturesFile(String file_path, // List<IdentificationFeatures> positiveTrainingSet, // List<IdentificationFeatures> negativeTrainingSet) //{ // log.Debug("Writing Identification Features to a file..."); // try // { // StreamWriter writer = new StreamWriter(file_path); // log.Debug("File name: " + file_path); // // Write header TODO remove // String header = "label," + IdentificationFeatures.getHeader(); // writer.Write(header); // // in the first column, 1 indicates positive training set // foreach (IdentificationFeatures i in positiveTrainingSet) // { // writer.Write("\n" + "1," + i.WriteToFile()); // writer.Flush(); // } // // in the first column, 0 indicates negative training set // foreach (IdentificationFeatures i in negativeTrainingSet) // { // writer.Write("\n" + "0," + i.WriteToFile()); // writer.Flush(); // } // writer.Flush(); // writer.Close(); // } // catch (Exception e) // { // e.printStackTrace(); // log.Error("Writing file unsuccessful!!!"); // System.exit(0); // } // log.Debug("Writing file successful."); //} /* * Useful for outputting the IDs object in the correct order for * writeResultDatabaseToFile */ private static String outputIDToTSVFormat(IDs id) { return(id.getScanNum() + "\t" + id.getScanTime() + "\t" + id.getPeptideMass() + "\t" + id.getPeptideSequence() + "\t" + id.getParentProteinAccessions() + "\t" + id.getPepEvid() + "\t" + id.getPepRef() + "\t" + id.getDBSeqID() + "\t" + id.getXCorr() + "\t" + id.getDeltaCN() + "\t" + id.getDeltaCNStar() + "\t" + id.getSPScore() + "\t" + id.getSPRank() + "\t" + id.getEValue()); }
public static void WritePSM(IDs id) { IDWriter.WriteLine(String.Join("\t", id.getScanNum().ToString(), id.getScanTime().ToString(), id.getPeptideSequence().ToString(), id.getPeptideMass().ToString(), id.getXCorr().ToString(), id.getDeltaCN().ToString(), String.Join(",", id.getParentProteinAccessions()))); }
protected void evaluateIdentification(IDs id) { log.Debug("NoExclusion. Scores added, but nothing added to the exclusion list"); // check if the peptide is identified or not if (id == null) { performanceEvaluator.countMS2UnidentifiedAnalyzed(); return; } Peptide pep = getPeptideFromIdentification(id); // if it was going to be null, it already returned // is fragmented // add decoy or non-existent protein connections // database.addProteinFromIdentification(pep, id.getParentProteinAccessions()); Double xCorr = id.getXCorr(); Double dCN = id.getDeltaCN(); pep.addScore(xCorr, 0.0, dCN); performanceEvaluator.evaluateAnalysis(exclusionList, pep); RetentionTime rt = pep.getRetentionTime(); if (!rtCalcPredictedRT.Keys.Contains(pep.getSequence())) { rtCalcPredictedRT.Add(pep.getSequence(), rt.getRetentionTimePeak()); } ObservedPeptideRtTrackerObject observedPep = new ObservedPeptideRtTrackerObject(pep.getSequence(), id.getScanTime(), id.getXCorr(), rt.getRetentionTimePeak(), rt.getRetentionTimeStart() + GlobalVar.retentionTimeWindowSize, RetentionTime.getRetentionTimeOffset(), rtCalcPredictedRT[pep.getSequence()], (rt.IsPredicted() ? 1 : 0)); if ((xCorr > 2.5)) { // calibrates our retention time alignment if the observed time is different // from the predicted only if it passes this threshold calibrateRetentionTime(pep); } observedPep.offset = RetentionTime.getRetentionTimeOffset(); peptideIDRT.Add(observedPep); }