private bool isOnCurrentObservedExclusionList(ExclusionList exclusionList, Peptide p)
{
exclusionList.retentionTense(p).Equals(ExclusionList.CURRENT_OBSERVED);
List <Peptide> list = exclusionList.getCurrentObservedPeptides();
return(containsPeptideSequence(list, p));
}
private bool isOnPastExclusionList(ExclusionList exclusionList, Peptide p)
{
return(exclusionList.retentionTense(p).Equals(ExclusionList.PAST));
List <Peptide> list = exclusionList.getPastExcludedPeptides();
return(containsPeptideSequence(list, p));
}
public void finalizePerformanceEvaluator(String experimentName, String experimentType, double analysisTime,
double totalRunTime, ExclusionList exclusionList, ProteinProphetResult ppr, int ddaNum, ExclusionProfile exclusionProfile)
{
setExperimentName(experimentName, experimentType);
setExperimentDuration(analysisTime, totalRunTime);
setExperimentParams();
setExclusionList(exclusionList);
postProcessingCalculations(ddaNum, ppr, exclusionProfile);
}
/*
* 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);
}
private void ExclusionListToolStripMenuItem_Click(object sender, EventArgs e)
{
ExclusionList ExList = new ExclusionList();
ExList.PersonalShips = this.PersonalShips;
if (ExList.ShowDialog(this) == DialogResult.OK)
{
}
LoadExcludedShips();
ExList.Dispose();
lblExcludedShips.Text = ExcludedShips.Count.ToString() + " excluded from randomization.";
}
private void setExclusionList(ExclusionList exclusionList)
{
int pastSize = exclusionList.getPastExcludedPeptides().Count;
int currentSize = exclusionList.getCurrentExcludedPeptides().Count;
int futureSize = exclusionList.getFutureExcludedPeptides().Count;
int pastObservedSize = exclusionList.getPastObservedPeptides().Count;
int currentObservedSize = exclusionList.getCurrentObservedPeptides().Count;
int totalExclusionListSize = pastSize + currentSize + futureSize + pastObservedSize + currentObservedSize;
ChangeValue(Header.ExclusionListPastSize, pastSize);
ChangeValue(Header.ExclusionListCurrentSize, currentSize);
ChangeValue(Header.ExclusionListFutureSize, futureSize);
ChangeValue(Header.ExclusionListPastObserved, pastObservedSize);
ChangeValue(Header.ExclusionListCurrentObserved, currentObservedSize);
ChangeValue(Header.ExclusionListFinalTotalSize, totalExclusionListSize);
}
public void massValidator(double spectra_mass, double id_mass, double database_mass, ExclusionList exclusionList)
{
// make sure each double falls ewithin ppmTolerance of each other
bool spectraMassOnExclusionList = exclusionList.isExcluded(spectra_mass);
bool idMassOnExclusionList = exclusionList.isExcluded(id_mass);
bool databaseMassOnExclusionList = exclusionList.isExcluded(database_mass);
if (!(spectraMassOnExclusionList && idMassOnExclusionList && databaseMassOnExclusionList))
{
log.Debug("$" + spectra_mass + "\t" + id_mass + "\t" + database_mass + "\t" + (spectra_mass - id_mass)
+ "\t" + (database_mass - id_mass) + "\t" + (spectra_mass - database_mass));
// spectra_mass id_mass database_mass spec-id db-id spec-db
}
}
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++;
}
