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.");
}
}
/*-
* Reset the exclusion list and any scores in the database
*/
public void reset()
{
database.reset();
exclusionList.reset();
performanceEvaluator.clear();
includedSpectra.Clear();
excludedSpectra.Clear();
RetentionTimeUtil.resetRTOffset();
}
/*
* Computes the difference between the predicted retention time and when we
* actually observed this peptide. This difference is then used to calibrate the
* retention time using the RetentionTimeCalibrator class by calculating a
* retention time offset. This offset will shift all retention time windows by
* this value.
*/
protected void calibrateRetentionTime(Peptide pep) //called when we observe a peptide that passes the xcorr threshold
{
bool isPredictedRT = pep.getRetentionTime().IsPredicted(); // if isPredictedRT is true, then that means this is the first time you observed it
// if false, then you already have observed it and would have already
// readjusted the offset, so no need to to it again.
// isPredictedRT is false means that you have observed it before, excluded it, but then
//it shows up again
if (isPredictedRT)
{
// only calibrate RT prediction if it was a predicted peptide...
// peptides which were observed should not affect RT prediction calibration
double predictedRT = pep.getRetentionTime().getRetentionTimePeak();
double rtPredictionError = currentTime - predictedRT;
double newOffset = RetentionTimeUtil.computeRTOffset(rtPredictionError, currentTime);
RetentionTime.setRetentionTimeOffset(newOffset);
performanceEvaluator.countPeptideCalibration();
}
//changes the status of the peptide from isPredicted = true to false, because now you have observed it
exclusionList.observedPeptide(pep, currentTime, database.getRetentionTimeWindow());
}
