/*
* Determines if a peptide's retention time is in the past, future, or present
* Returns PAST(-1) if the retention window has passed, PRESENT(0) if the
* retention window is in the future, FUTURE(1) if the retention window is
* active.
*/
public String retentionTense(Peptide pep)
{
RetentionTime rt = pep.getRetentionTime();
bool isObserved = !rt.IsPredicted();
double rtStart = rt.getRetentionTimeStart();
double rtEnd = rt.getRetentionTimeEnd();
if (isObserved)
{
if (pep.isExcluded(currentTime))
{
return(CURRENT_OBSERVED);
}
else
{
return(PAST_OBSERVED);
}
}
else if (pep.isExcluded(currentTime))
{
return(PRESENT);
}
else if (rtStart > currentTime)
{
return(FUTURE);
}
else if (rtEnd < currentTime)
{
return(PAST);
}
return(ERROR);
}
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);
}