List of retainBestScoringGroups() Examples

Examples of retainBestScoringGroups()

eu.isas.peptideshaker.protein_inference.ProteinInference.retainBestScoringGroups()
Retains the best scoring of intricate groups. @param identification the identification class containing allidentification matches @param metrics if provided protein metrics will be loaded while iteratingthe groups @param proteinMap the protein matches scoring map @param searchParameters the identification parameters @param sequenceMatchingPreferences the sequence matching preferences @param waitingHandler the handler displaying feedback to the user @throws IOException @throws IllegalArgumentException @throws SQLException @throws ClassNotFoundException @throws InterruptedException

Examples of eu.isas.peptideshaker.protein_inference.ProteinInference.retainBestScoringGroups()

        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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Examples of eu.isas.peptideshaker.protein_inference.ProteinInference.retainBestScoringGroups()

        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);
    }


    /**
     * Processes the identifications if a change occurred in the peptide map.
     *

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Examples of eu.isas.peptideshaker.protein_inference.ProteinInference.retainBestScoringGroups()

        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);
    }


    /**
     * Processes the identifications if a change occurred in the protein map.
     *

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