/*
* 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);
}
