List of scorePsms() Examples

Examples of scorePsms()

eu.isas.peptideshaker.scoring.psm_scoring.PsmScorer.scorePsms()

Attaches a score to the PSMs. @param identification the object containing the identification matches @param inputMap the input map scores @param processingPreferences the processing preferences @param waitingHandler the handler displaying feedback to the user @param searchParameters the identification parameters @param sequenceMatchingPreferences the sequence matching preferences @throws SQLException @throws IOException @throws InterruptedException @throws ClassNotFoundException @throws uk.ac.ebi.jmzml.xml.io.MzMLUnmarshallerException

                    waitingHandler.appendReport("No decoy sequences found. Impossible to estimate intermediate scores probabilities.", true, true);
                }
            }


            waitingHandler.appendReport("Scoring PSMs.", true, true);
            psmScorer.scorePsms(identification, inputMap, processingPreferences, searchParameters, sequenceMatchingPreferences, waitingHandler);
        }


        waitingHandler.appendReport("Computing assumptions probabilities.", true, true);
        if (sequenceFactory.concatenatedTargetDecoy()) {
            inputMap.estimateProbabilities(waitingHandler);

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Examples of scorePsms()

Examples of eu.isas.peptideshaker.scoring.psm_scoring.PsmScorer.scorePsms()