/*
* 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());
}
/*
* These are from the experiment and will be removed if you call reset on the
* graph
*/
public Peptide addPeptideFromIdentification(IDs id, double currentTime)
{
String peptideSequence = id.getPeptideSequence();
double peptideMass = id.getPeptideMass();
HashSet <String> parentProteinAccessions = id.getParentProteinAccessions();
Peptide pep;
if (containsPeptide(peptideSequence))
{
return(getPeptide(peptideSequence));
}
else
{
// Adds the peptide from the identification into the database
pep = new Peptide(peptideSequence, peptideMass, false);
// these peptides will be removed if reset() is called
SequenceToPeptide.Add(peptideSequence, pep);
peptides.Add(pep);
if (includeRetentionTime)
{
// TODO right now this takes the current time as the peak retention time...
// should we run it through RTCalc so we can better estimate our RT alignment?
// 2019-04-29 No, do not. Observed times are better than predicted
// pep.setRetentionTime(RetentionTimeUtil.convertDoubleToRetentionTime(rt,
// retentionTimeWindow,
// retentionTimeWindow));
RetentionTime rt = new RetentionTime(currentTime + retentionTimeWindow, retentionTimeWindow,
retentionTimeWindow, false);
pep.setRetentionTime(rt);
}
}
// update its parent proteins
foreach (String acc in parentProteinAccessions)
{
Protein parentProtein = AccesstionToProtein[acc];
if (parentProtein != null)
{
pep.addProtein(parentProtein);
}
else if (acc.Contains(GlobalVar.DecoyPrefix))
{
log.Info("WARNINGin Decoy parent protein for this peptide was not found!!");
log.Info(acc);
}
else
{
log.Warn("WARNINGin Non-decoy parent protein for this peptide was not found!!");
log.Warn(acc);
}
}
return(pep);
}
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())));
}