Examples of PeptideShakerGUI

                    new Thread("SaveThread") {
                        @Override
                        public void run() {


                            try {
                                PeptideShakerGUI peptideShakerGUI = followupPreferencesDialog.getPeptideShakerGUI();
                                InclusionListExport.exportInclusionList(outputFile, peptideShakerGUI.getIdentification(), 
                                        peptideShakerGUI.getIdentificationFeaturesGenerator(), getProteinFilters(), getPeptideFilters(), 
                                        exportFormat, peptideShakerGUI.getSearchParameters(), WIDTH, progressDialog, peptideShakerGUI.getFilterPreferences());


                                boolean processCancelled = progressDialog.isRunCanceled();
                                progressDialog.setRunFinished();


                                if (!processCancelled) {

Examples of eu.isas.peptideshaker.gui.PeptideShakerGUI

                } catch (Exception e) {
                    tips = new ArrayList<String>();
                    // Do something here?
                }


                PeptideShakerGUI peptideShakerGUI = new PeptideShakerGUI(); // dummy object to get at the version and tips
                peptideShakerGUI.setUpLogFile(false); // redirect the error stream to the PeptideShaker log file
                waitingHandler = new WaitingDialog(new DummyFrame("PeptideShaker " + PeptideShaker.getVersion(), "/icons/peptide-shaker.gif"),
                        Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/peptide-shaker.gif")),
                        Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/peptide-shaker-orange.gif")),
                        false, tips, "Importing Data", "PeptideShaker", PeptideShaker.getVersion(), true);
                ((WaitingDialog) waitingHandler).setCloseDialogWhenImportCompletes(false, false);

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