Package eu.isas.peptideshaker.protein_inference

Examples of eu.isas.peptideshaker.protein_inference.ProteinInference

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        if (waitingHandler.isRunCanceled()) {
            return;
        }

        waitingHandler.appendReport("Simplifying protein groups.", true, true);
        ProteinInference proteinInference = new ProteinInference();
        proteinInference.removeRedundantGroups(identification, searchParameters, sequenceMatchingPreferences, waitingHandler);
        waitingHandler.increasePrimaryProgressCounter();
        if (waitingHandler.isRunCanceled()) {
            return;
        }

        waitingHandler.appendReport("Generating peptide map.", true, true); // slow?
        matchesValidator.fillPeptideMaps(identification, metrics, waitingHandler, sequenceMatchingPreferences);
        matchesValidator.getPeptideMap().clean();
        if (waitingHandler.isRunCanceled()) {
            return;
        }

        waitingHandler.appendReport("Computing peptide probabilities.", true, true); // should be fast
        matchesValidator.getPeptideMap().estimateProbabilities(waitingHandler);
        if (waitingHandler.isRunCanceled()) {
            return;
        }

        waitingHandler.appendReport("Saving peptide probabilities.", true, true); // could be slow
        matchesValidator.attachPeptideProbabilities(identification, waitingHandler);
        waitingHandler.increasePrimaryProgressCounter();
        if (waitingHandler.isRunCanceled()) {
            return;
        }

        waitingHandler.appendReport("Generating protein map.", true, true); // could be slow
        matchesValidator.fillProteinMap(identification, waitingHandler);
        waitingHandler.increasePrimaryProgressCounter();
        if (waitingHandler.isRunCanceled()) {
            return;
        }

        waitingHandler.appendReport("Resolving protein inference issues, inferring peptide and protein PI status.", true, true); // could be slow
        proteinInference.retainBestScoringGroups(identification, metrics, matchesValidator.getProteinMap(), searchParameters, sequenceMatchingPreferences, waitingHandler);
        waitingHandler.increasePrimaryProgressCounter();
        if (waitingHandler.isRunCanceled()) {
            return;
        }
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        peptideMap.estimateProbabilities(waitingHandler);
        matchesValidator.attachPeptideProbabilities(identification, waitingHandler);
        matchesValidator.fillProteinMap(identification, waitingHandler);
        proteinMap.estimateProbabilities(waitingHandler);
        matchesValidator.attachProteinProbabilities(identification, metrics, waitingHandler, processingPreferences);
        ProteinInference proteinInference = new ProteinInference();
        proteinInference.retainBestScoringGroups(identification, metrics, proteinMap, searchParameters, sequenceMatchingPreferences, waitingHandler);
    }
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        matchesValidator.setProteinMap(proteinMap);
        matchesValidator.attachPeptideProbabilities(identification, waitingHandler);
        matchesValidator.fillProteinMap(identification, waitingHandler);
        proteinMap.estimateProbabilities(waitingHandler);
        matchesValidator.attachProteinProbabilities(identification, metrics, waitingHandler, processingPreferences);
        ProteinInference proteinInference = new ProteinInference();
        proteinInference.retainBestScoringGroups(identification, metrics, proteinMap, searchParameters, sequenceMatchingPreferences, waitingHandler);
    }
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Related Classes of eu.isas.peptideshaker.protein_inference.ProteinInference

  • com.compomics.util.experiment.biology.Enzyme
  • com.compomics.util.experiment.biology.Protein
  • com.compomics.util.experiment.identification.matches.PeptideMatch
  • com.compomics.util.experiment.identification.matches.ProteinMatch
  • eu.isas.peptideshaker.myparameters.PSParameter
  • eu.isas.peptideshaker.PeptideShaker
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