private void setRetentionTimes()
{
// if retention time isn't included, do nothing
if (includeRetentionTime)
{
// compute the retention times if not already computed
if (peptideRetentionTimes == null)
{
peptideRetentionTimes = RetentionTimeUtil.calculateRetentionTime(peptides);
if (GlobalVar.useMeasuredRT)
{
MealTimeMS.Tester.RandomTesterFunctions.LoadAndReplaceRT(ref peptideRetentionTimes);
}
}
log.Debug("Setting retention times...");
log.Debug("Retention time window size: " + retentionTimeWindow);
foreach (String peptideSequence in peptideRetentionTimes.Keys)
{
Peptide pep = getPeptide(peptideSequence);
double rt = peptideRetentionTimes[peptideSequence];
pep.setRetentionTime(
RetentionTimeUtil.convertDoubleToRetentionTime(rt, retentionTimeWindow, retentionTimeWindow));
}
log.Debug("Done setting retention times.");
}
}
/*
* 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);
}
