/*
* Pre-requisite: the peptide p was selected to be excluded from analysis, and
* thus its mass is on the exclusion list Purpose: check if the sequence of
* peptide p is truly on the exclusion list or not. If the sequence is not on
* the exclusion list, then the peptide was incorrectly excluded. This is
* because the mass is on the current exclusion list
*/
public void evaluateExclusion(ExclusionList exclusionList, Peptide p)
{
log.Debug("Evaluating peptide mass exclusion...");
// // // sanity check for the pre-requisite
// if (!exclusionList.isExcluded(p.getMass())) {
// // log.Warn(
// // "ERROR: Theoretical peptide mass was found on the exclusion list, but was
// // excluded... the spectra mass does not match the mass of the theoretical
// // database.");
// numWarnings_EvaluateExclusion++;
// // return;
// }
#if WRITE_RT_TIME
WriteRetention(String.Format("EX\t{0}\t{1}", exclusionList.getCurrentTime(), p.getRetentionTime().getRetentionTimeStart()));
#endif
if (containsPeptideSequence(exclusionList.getExclusionList(), p))
{
if (isOnCurrentExclusionList(exclusionList, p))
{
log.Debug("Peptide sequence was found on the exclusion list! This is what we want.");
incrementValue(Header.EvaluateExclusion_FoundOnCurrentExclusionList);
}
else if (isOnFutureExclusionList(exclusionList, p))
{
log.Debug("Peptide sequence was found on the future exclusion list.");
incrementValue(Header.EvaluateExclusion_FoundOnFutureExclusionList);
}
else if (isOnPastExclusionList(exclusionList, p))
{
log.Debug("Peptide sequence was found on the past exclusion list.");
incrementValue(Header.EvaluateExclusion_FoundOnPastExclusionList);
}
else if (isOnPastObservedExclusionList(exclusionList, p))
{
log.Debug("Peptide sequence was found on the past observed exclusion list.");
// this means that this peptide sequence was excluded, but not anymore
incrementValue(Header.EvaluateExclusion_FoundOnPastObservedExclusionList);
}
else if (isOnCurrentObservedExclusionList(exclusionList, p))
{
log.Debug("Peptide sequence was found on the observed exclusion list! This is what we want.");
incrementValue(Header.EvaluateExclusion_FoundOnCurrentObservedExclusionList);
}
}
else
{
log.Debug("Peptide sequence was not found on any of the lists! It was wrongly excluded!");
// TODO figure out why this is happening.........
// Solved: if a peptide not on the ex list has a similar mass within ppm tolorence of a peptide that's supposed to be excluded, this will happen
incrementValue(Header.EvaluateExclusion_NotFoundOnExclusionList);
}
incrementValue(Header.TotalNumEvaluateExclusion);
}
public void evaluateAnalysis(ExclusionList exclusionList, Peptide p)
{
log.Debug("Evaluating peptide analysis...");
#if WRITE_RT_TIME
WriteRetention(String.Format("AN\t{0}\t{1}", exclusionList.getCurrentTime(), p.getRetentionTime().getRetentionTimeStart()));
#endif
// // sanity check for the pre-requisite
// if (exclusionList.isExcluded(p.getMass())) {
// // log.Warn(
// // "ERROR: Theoretical peptide mass was found on the exclusion list, but was
// // analyzed... the spectra mass does not match the mass of the theoretical
// // database.");
// numWarnings_EvaluateAnalysis++;
// }
if (containsPeptideSequence(exclusionList.getExclusionList(), p))
{
if (isOnCurrentExclusionList(exclusionList, p))
{
WriteEvaluation("Peptide sequence was found in the current exclusion list, but was analyzed anyways");
log.Debug("Peptide sequence was found in the current exclusion list, but was analyzed anyways");
log.Debug("Mass of peptide: " + p.getMass());
log.Debug("ppmTolerance: " + exclusionList.getPPMTolerance());
// this means the ppm mass tolerance is not high enough
// it's on the EL but not excluded this is a ppm tolerance problem
incrementValue(Header.EvaluateAnalysis_FoundOnCurrentExclusionList);
}
else if (isOnFutureExclusionList(exclusionList, p))
{
WriteEvaluation("Peptide sequence was found on the future exclusion list.");
log.Debug("Peptide sequence was found on the future exclusion list.");
log.Debug("Retention time of peptide: " + p.getRetentionTime());
log.Debug("current_time: " + exclusionList.getCurrentTime());
// this means that this peptide sequence is to be excluded, but not rn
// this is a retention time prediction problem
incrementValue(Header.EvaluateAnalysis_FoundOnFutureExclusionList);
}
else if (isOnPastExclusionList(exclusionList, p))
{
WriteEvaluation("Peptide sequence was found on the past exclusion list.");
log.Debug("Peptide sequence was found on the past exclusion list.");
log.Debug("Retention time of peptide: " + p.getRetentionTime());
log.Debug("current_time: " + exclusionList.getCurrentTime());
// this means that this peptide sequence was excluded, but not anymore
// this is a retention time prediction problem
incrementValue(Header.EvaluateAnalysis_FoundOnPastExclusionList);
}
else if (isOnPastObservedExclusionList(exclusionList, p))
{
WriteEvaluation("Peptide sequence was found on the past observed exclusion list.");
log.Debug("Peptide sequence was found on the past observed exclusion list.");
// this means that this peptide sequence was excluded, but not anymore
incrementValue(Header.EvaluateAnalysis_FoundOnPastObservedExclusionList);
}
else if (isOnCurrentObservedExclusionList(exclusionList, p))
{
WriteEvaluation("Peptide sequence was found on the observed exclusion list but was analyzed anyways.");
log.Debug("Peptide sequence was found on the observed exclusion list but was analyzed anyways.");
log.Debug("Retention time of peptide: " + p.getRetentionTime());
log.Debug("current_time: " + exclusionList.getCurrentTime());
log.Debug("Mass of peptide: " + p.getMass());
log.Debug("ppmTolerance: " + exclusionList.getPPMTolerance());
incrementValue(Header.EvaluateAnalysis_FoundOnCurrentObservedExclusionList);
}
}
else
{
WriteEvaluation("Peptide sequence was not found on any of the lists!");
log.Debug("Peptide sequence was not found on any of the lists!");
incrementValue(Header.EvaluateAnalysis_NotFoundOnExclusionList);
}
incrementValue(Header.TotalNumEvaluateAnalysis);
count++;
}
