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++; }