Examples of eu.isas.peptideshaker.PeptideShaker.importFiles()

eu.isas.peptideshaker.PeptideShaker.importFiles()

Method used to import identification from identification result files. @param waitingHandler the handler displaying feedback to the user @param idFilter The identification filter to use @param idFiles The files to import @param spectrumFiles The corresponding spectra (can be empty: spectrawill not be loaded) @param searchParameters the identification parameters used for the search @param annotationPreferences The annotation preferences to use for PTMscoring @param projectDetails The project details @param processingPreferences the initial processing preferences @param ptmScoringPreferences the PTM scoring preferences @param spectrumCountingPreferences the spectrum counting preferences @param sequenceMatchingPreferences the sequence matching preferences @param backgroundThread boolean indicating whether the import should bedone in a background thread (GUI mode) or in the current thread (command line mode).


        // create a shaker which will perform the analysis
        PeptideShaker peptideShaker = new PeptideShaker(experiment, sample, replicateNumber);


        // import the files
        peptideShaker.importFiles(waitingHandler, idFilter, identificationFiles, spectrumFiles, searchParameters,
                annotationPreferences, projectDetails, processingPreferences, ptmScoringPreferences,
                spectrumCountingPreferences, sequenceMatchingPreferences, false);


        // show the warnings
        Iterator<String> iterator = peptideShaker.getWarnings().keySet().iterator();

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