protected void evaluateIdentification(IDs id)
{
// 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, xCorrThreshold, dCN);
performanceEvaluator.evaluateAnalysis(exclusionList, pep);
// add the peptide to the exclusion list if it is over the xCorr threshold
if ((xCorr > xCorrThreshold))
{
performanceEvaluator.countPeptidesExcluded();
log.Debug("xCorrThreshold passed. Peptide added to the exclusion list.");
exclusionList.addPeptide(pep);
// calibrates our retention time alignment if the observed time is different
// from the predicted only if it passes this threshold
calibrateRetentionTime(pep);
}
// add all of the other peptides belonging to the parent protein(s) if numDB
// threshold is passed
foreach (Protein parentProtein in pep.getProteins())
{
if ((parentProtein.getNumDB() >= numDBThreshold) && (!parentProtein.IsExcluded()))
{
parentProtein.setExcluded(true);
log.Debug("Parent protein " + parentProtein.getAccession() + " is identified confidently "
+ parentProtein.getNumDB() + " times!");
performanceEvaluator.countProteinsExcluded();
exclusionList.addProtein(parentProtein);
}
log.Debug(parentProtein);
}
log.Debug(pep);
}
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);
}
protected void evaluateIdentification(IDs id)
{
log.Debug("RandomExclusion. 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
Double xCorr = id.getXCorr();
Double dCN = id.getDeltaCN();
pep.addScore(xCorr, 0.0, dCN);
performanceEvaluator.evaluateAnalysis(exclusionList, pep);
}
protected void evaluateIdentification(IDs id)
{
// check if the peptide is identified or not
if (id == null)
{
performanceEvaluator.countMS2UnidentifiedAnalyzed();
return;
}
Peptide pep = getPeptideFromIdentification(id); // id is null, it already returned
// add decoy or non-existent protein connections
// database.AddProteinFromIdentification(pep, id.getParentProteinAccessions());
Double xCorr = id.getXCorr();
Double dCN = id.getDeltaCN();
pep.addScore(xCorr, dCN);
#if (!DONTEVALUATE)
performanceEvaluator.evaluateAnalysis(exclusionList, pep);
#endif
// exclude this peptide for analysis if the xCorr score is above a threshold
const double XCORR_THRESHOLD = 2.5;
// add the peptide to the exclusion list if it is over the xCorr threshold
if ((xCorr > XCORR_THRESHOLD))
{
performanceEvaluator.countPeptidesExcluded();
log.Debug("xCorrThreshold passed. Peptide added to the exclusion list.");
exclusionList.addPeptide(pep);
// calibrates our retention time alignment if the observed time is different
// from the predicted only if it passes this threshold
calibrateRetentionTime(pep);
}
// Add all the peptides corresponding to the parent protein, if the parent
// protein is deemed confidently identified by the logisitc regression
// classifier
Dictionary <String, Boolean> identificationPredictions = IdentificationFeatureExtractionUtil
.assessProteinIdentificationConfidence(pep.getProteins(), lrAccord);
List <Protein> proteinsToExclude = new List <Protein>();
foreach (Protein parentProtein in pep.getProteins())
{
// prevents repeated exclusion of a protein already excluded
if ((!parentProtein.IsExcluded()))
{
// determine if parent protein is confidently identified
bool isConfidentlyIdentified = identificationPredictions[parentProtein.getAccession()];
if (isConfidentlyIdentified)
{
// exclude all peptides of that protein
parentProtein.setExcluded(true);
log.Debug("Parent protein " + parentProtein.getAccession() + " is identified confidently "
+ parentProtein.getNumDB() + " times!");
performanceEvaluator.countProteinsExcluded();
proteinsToExclude.Add(parentProtein);
}
}
}
exclusionList.addProteins(proteinsToExclude);
}
protected void evaluateIdentification(IDs id)
{
// check if the peptide is identified or not
if (id == null)
{
performanceEvaluator.countMS2UnidentifiedAnalyzed();
return;
}
Peptide pep = getPeptideFromIdentification(id); // id is null, it already returned
//log.Info("Peptide Observed Time: {0}\tPredicted Time: {1} -----------------", id.getScanTime(),pep.getRetentionTime().getRetentionTimeStart());
// add decoy or non-existent protein connections
// database.AddProteinFromIdentification(pep, id.getParentProteinAccessions());
Double xCorr = id.getXCorr();
double dCN = id.getDeltaCN();
pep.addScore(xCorr, dCN);
#if (!DONTEVALUATE)
performanceEvaluator.evaluateAnalysis(exclusionList, pep);
#endif
//RetentionTime rt = pep.getRetentionTime();
//if (!rtCalcPredictedRT.Keys.Contains(pep.getSequence()))
//{
// rtCalcPredictedRT.Add(pep.getSequence(), rt.getRetentionTimePeak());
//}
//double[] values = new double[] { id.getScanTime(), id.getXCorr(), rt.getRetentionTimePeak(), rt.getRetentionTimeStart() + GlobalVar.retentionTimeWindowSize, RetentionTime.getRetentionTimeOffset(), rtCalcPredictedRT[pep.getSequence()], rt.IsPredicted() ? 1 : 0 };
// exclude this peptide for analysis if the xCorr score is above a threshold
const double XCORR_THRESHOLD = 2.5;
// add the peptide to the exclusion list if it is over the xCorr threshold
if ((xCorr > XCORR_THRESHOLD))
{
performanceEvaluator.countPeptidesExcluded();
log.Debug("xCorrThreshold passed. Peptide added to the exclusion list.");
exclusionList.addPeptide(pep);
// calibrates our retention time alignment if the observed time is different
// from the predicted only if it passes this threshold
calibrateRetentionTime(pep);
}
// Add all the peptides corresponding to the parent protein, if the parent
// protein is deemed confidently identified by the logisitc regression
// classifier
Dictionary <String, Boolean> identificationPredictions = IdentificationFeatureExtractionUtil
.assessProteinIdentificationConfidence(pep.getProteins(), lrAccord);
List <Protein> proteinsToExclude = new List <Protein>();
foreach (Protein parentProtein in pep.getProteins())
{
// prevents repeated exclusion of a protein already excluded
if ((!parentProtein.IsExcluded()))
{
// determine if parent protein is confidently identified
bool isConfidentlyIdentified = identificationPredictions[parentProtein.getAccession()];
if (isConfidentlyIdentified)
{
// exclude all peptides of that protein
#if TRACKEXCLUDEDPROTEINFEATURE
excludedProteinFeatureList.Add(parentProtein.vectorize().ItemArray);
#endif
parentProtein.setExcluded(true);
log.Debug("Parent protein " + parentProtein.getAccession() + " is identified confidently "
+ parentProtein.getNumDB() + " times!");
performanceEvaluator.countProteinsExcluded();
proteinsToExclude.Add(parentProtein);
}
}
}
exclusionList.addProteins(proteinsToExclude);
}
