Examples of MzIdentMLExport

        projectDetails.setOrganizationEmail(mzidCLIInputBean.getOrganizationMail());
        projectDetails.setOrganizationAddress(mzidCLIInputBean.getOrganizationAddress());
        projectDetails.setOrganizationUrl(mzidCLIInputBean.getOrganizationUrl());
        projectDetails.setPrideOutputFolder(mzidCLIInputBean.getOutputFile().getAbsolutePath());


        MzIdentMLExport mzIdentMLExport = new MzIdentMLExport(PeptideShaker.getVersion(), cpsParent.getIdentification(), cpsParent.getProjectDetails(),
                cpsParent.getProcessingPreferences(), cpsParent.getSearchParameters(), cpsParent.getPtmScoringPreferences(),
                cpsParent.getSpectrumCountingPreferences(), cpsParent.getIdentificationFeaturesGenerator(),
                cpsParent.getAnnotationPreferences(), cpsParent.getSequenceMatchingPreferences(), mzidCLIInputBean.getOutputFile(), waitingHandler);
        mzIdentMLExport.createMzIdentMLFile(false);
    }

                peptideShakerGUI.setDataSaved(false); // @TODO: this might not always be true, e.g., if nothing has changed, but better than not saving at all


                boolean conversionCompleted = false;


                try {
                    MzIdentMLExport mzIdentMLExport = new MzIdentMLExport(PeptideShaker.getVersion(), peptideShakerGUI.getIdentification(), peptideShakerGUI.getProjectDetails(),
                            peptideShakerGUI.getProcessingPreferences(), peptideShakerGUI.getSearchParameters(), peptideShakerGUI.getPtmScoringPreferences(),
                            peptideShakerGUI.getSpectrumCountingPreferences(), peptideShakerGUI.getIdentificationFeaturesGenerator(),
                            peptideShakerGUI.getAnnotationPreferences(), peptideShakerGUI.getSequenceMatchingPreferences(), finalOutputFile, progressDialog);
                    mzIdentMLExport.createMzIdentMLFile(false);


                    // validate the mzidentml file
                    if (validateMzIdentML && !progressDialog.isRunCanceled()) {
                        progressDialog.setPrimaryProgressCounterIndeterminate(true);
                        progressDialog.setTitle("Validating mzIdentML. Please Wait...");

Examples of MzIdentMLExport

Examples of eu.isas.peptideshaker.export.MzIdentMLExport

Examples of eu.isas.peptideshaker.export.MzIdentMLExport