Package com.compomics.util.io.export

Examples of com.compomics.util.io.export.ExportScheme

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        return getDefaultExportSchemes().get(schemeName);
    }

    @Override
    public ExportScheme getExportScheme(String schemeName) {
        ExportScheme exportScheme = userSchemes.get(schemeName);
        if (exportScheme == null) {
            exportScheme = getDefaultExportSchemes().get(schemeName);
        }
        return exportScheme;
    }
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        sectionContent.add(PsIdentificationAlgorithmMatchesFeature.decoy);
        sectionContent.add(PsPsmFeature.validated);

        exportFeatures.put(PsProteinFeature.type, sectionContent);

        ExportScheme topDownReport = new ExportScheme("Default Hierarchical Report", false, exportFeatures, "\t", true, true, 0, false, true, false);

        ///////////////////////////
        // Default protein report
        ///////////////////////////
        exportFeatures = new HashMap<String, ArrayList<ExportFeature>>();
        sectionContent = new ArrayList<ExportFeature>();

        // protein accessions and protein inferences
        sectionContent.add(PsProteinFeature.accession);
        sectionContent.add(PsProteinFeature.protein_description);
        sectionContent.add(PsProteinFeature.gene_name);
        sectionContent.add(PsProteinFeature.chromosome);
        sectionContent.add(PsProteinFeature.pi);
        sectionContent.add(PsProteinFeature.other_proteins);
        sectionContent.add(PsProteinFeature.protein_group);

        // peptide and spectrum counts
        sectionContent.add(PsProteinFeature.peptides);
        sectionContent.add(PsProteinFeature.validated_peptides);
        sectionContent.add(PsProteinFeature.unique_peptides);
        sectionContent.add(PsProteinFeature.psms);
        sectionContent.add(PsProteinFeature.validated_psms);

        // protein coverage
        sectionContent.add(PsProteinFeature.coverage);
        sectionContent.add(PsProteinFeature.possible_coverage);

        // molecular weight and spectrum counting
        sectionContent.add(PsProteinFeature.mw);
        sectionContent.add(PsProteinFeature.spectrum_counting_nsaf);
        sectionContent.add(PsProteinFeature.spectrum_counting_empai);

        // variable_ptms
        sectionContent.add(PsProteinFeature.confident_modification_sites);
        sectionContent.add(PsProteinFeature.confident_modification_sites_number);
        sectionContent.add(PsProteinFeature.ambiguous_modification_sites);
        sectionContent.add(PsProteinFeature.ambiguous_modification_sites_number);

        // protein scores
        sectionContent.add(PsProteinFeature.confidence);
        sectionContent.add(PsProteinFeature.decoy);
        sectionContent.add(PsProteinFeature.validated);

        exportFeatures.put(PsProteinFeature.type, sectionContent);

        ExportScheme proteinReport = new ExportScheme("Default Protein Report", false, exportFeatures, "\t", true, true, 0, false, true, false);

        ///////////////////////////
        // Default peptide report
        ///////////////////////////
        exportFeatures = new HashMap<String, ArrayList<ExportFeature>>();
        sectionContent = new ArrayList<ExportFeature>();

        // accessions
        sectionContent.add(PsPeptideFeature.accessions);

        // peptide sequence
        sectionContent.add(PsPeptideFeature.aaBefore);
        sectionContent.add(PsPeptideFeature.sequence);
        sectionContent.add(PsPeptideFeature.aaAfter);

        // variable_ptms
        sectionContent.add(PsPeptideFeature.modified_sequence);
        sectionContent.add(PsPeptideFeature.variable_ptms);
        sectionContent.add(PsPeptideFeature.localization_confidence);
        sectionContent.add(PsPeptideFeature.fixed_ptms);

        // psms
        sectionContent.add(PsPeptideFeature.validated_psms);
        sectionContent.add(PsPeptideFeature.psms);

        // peptide scores
        sectionContent.add(PsPeptideFeature.confidence);
        sectionContent.add(PsPeptideFeature.decoy);
        sectionContent.add(PsPeptideFeature.validated);

        exportFeatures.put(PsPeptideFeature.type, sectionContent);

        ExportScheme peptideReport = new ExportScheme("Default Peptide Report", false, exportFeatures, "\t", true, true, 0, false, true, false);

        ///////////////////////////
        // Default PSM report
        ///////////////////////////
        exportFeatures = new HashMap<String, ArrayList<ExportFeature>>();
        sectionContent = new ArrayList<ExportFeature>();

        // protein accessions
        sectionContent.add(PsIdentificationAlgorithmMatchesFeature.accessions);
        sectionContent.add(PsIdentificationAlgorithmMatchesFeature.sequence);

        // ptms
        sectionContent.add(PsIdentificationAlgorithmMatchesFeature.variable_ptms);
        sectionContent.add(PsPsmFeature.d_score);
        sectionContent.add(PsPsmFeature.probabilistic_score);
        sectionContent.add(PsPsmFeature.localization_confidence);
        sectionContent.add(PsIdentificationAlgorithmMatchesFeature.fixed_ptms);

        // spectrum file
        sectionContent.add(PsIdentificationAlgorithmMatchesFeature.spectrum_file);
        sectionContent.add(PsIdentificationAlgorithmMatchesFeature.spectrum_title);
        sectionContent.add(PsIdentificationAlgorithmMatchesFeature.spectrum_scan_number);

        // spectrum details
        sectionContent.add(PsIdentificationAlgorithmMatchesFeature.rt);
        sectionContent.add(PsIdentificationAlgorithmMatchesFeature.mz);
        sectionContent.add(PsIdentificationAlgorithmMatchesFeature.spectrum_charge);
        sectionContent.add(PsIdentificationAlgorithmMatchesFeature.identification_charge);
        sectionContent.add(PsIdentificationAlgorithmMatchesFeature.theoretical_mass);
        sectionContent.add(PsIdentificationAlgorithmMatchesFeature.isotope);
        sectionContent.add(PsIdentificationAlgorithmMatchesFeature.mz_error);

        // psm scores
        sectionContent.add(PsPsmFeature.confidence);
        sectionContent.add(PsIdentificationAlgorithmMatchesFeature.decoy);
        sectionContent.add(PsPsmFeature.validated);

        exportFeatures.put(PsPsmFeature.type, sectionContent);

        ExportScheme psmReport = new ExportScheme("Default PSM Report", false, exportFeatures, "\t", true, true, 1, false, true, false);

        ///////////////////////////
        // Certificate of analysis
        ///////////////////////////
        exportFeatures = new HashMap<String, ArrayList<ExportFeature>>();
        ArrayList<String> sectionsList = new ArrayList<String>();

        // project details
        sectionContent = new ArrayList<ExportFeature>();
        sectionsList.add(PsProjectFeature.type);
        sectionContent.add(PsProjectFeature.peptide_shaker);
        sectionContent.add(PsProjectFeature.date);
        sectionContent.add(PsProjectFeature.experiment);
        sectionContent.add(PsProjectFeature.sample);
        sectionContent.add(PsProjectFeature.replicate);
        sectionContent.add(PsProjectFeature.identification_algorithms);
        exportFeatures.put(PsProjectFeature.type, sectionContent);

        // search parameters
        sectionsList.add(PsSearchFeature.type);
        exportFeatures.put(PsSearchFeature.type, PsSearchFeature.values()[0].getExportFeatures(false));

        // input filters
        sectionsList.add(PsInputFilterFeature.type);
        exportFeatures.put(PsInputFilterFeature.type, PsInputFilterFeature.values()[0].getExportFeatures(false));

        // validation details
        sectionsList.add(PsValidationFeature.type);
        exportFeatures.put(PsValidationFeature.type, PsValidationFeature.values()[0].getExportFeatures(false));

        // ptms
        sectionsList.add(PsPtmScoringFeature.type);
        exportFeatures.put(PsPtmScoringFeature.type, PsPtmScoringFeature.values()[0].getExportFeatures(false));

        // spectrum counting details
        sectionsList.add(PsSpectrumCountingFeature.type);
        exportFeatures.put(PsSpectrumCountingFeature.type, PsSpectrumCountingFeature.values()[0].getExportFeatures(false));

        // annotation settings
        sectionsList.add(PsAnnotationFeature.type);
        exportFeatures.put(PsAnnotationFeature.type, PsAnnotationFeature.values()[0].getExportFeatures(false));

        ExportScheme coa = new ExportScheme("Certificate of Analysis", false, sectionsList, exportFeatures, ": ", true, false, 2, true, false, true);

        HashMap<String, ExportScheme> defaultSchemes = new HashMap<String, ExportScheme>();
        defaultSchemes.put(topDownReport.getName(), topDownReport);
        defaultSchemes.put(proteinReport.getName(), proteinReport);
        defaultSchemes.put(peptideReport.getName(), peptideReport);
        defaultSchemes.put(psmReport.getName(), psmReport);
        defaultSchemes.put(coa.getName(), coa);
        return defaultSchemes;
    }
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            reportsTable.setRowSelectionInterval(reportsTable.rowAtPoint(evt.getPoint()), reportsTable.rowAtPoint(evt.getPoint()));
        }

        if (evt != null && evt.getButton() == MouseEvent.BUTTON3 && reportsTable.getSelectedRow() != -1) {
            String schemeName = (String) reportsTable.getValueAt(reportsTable.getSelectedRow(), 1);
            ExportScheme exportScheme = exportFactory.getExportScheme(schemeName);
            editReportMenuItem.setVisible(exportScheme.isEditable());
            removeReportMenuItem.setVisible(exportScheme.isEditable());
            reportDocumentationPopupMenu.show(reportsTable, evt.getX(), evt.getY());
        }

        if (evt != null && evt.getButton() == MouseEvent.BUTTON1 && evt.getClickCount() == 2) {
            writeSelectedReport();
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                    @Override
                    public void run() {

                        try {
                            String schemeName = (String) reportsTable.getValueAt(reportsTable.getSelectedRow(), 1);
                            ExportScheme exportScheme = exportFactory.getExportScheme(schemeName);
                            progressDialog.setTitle("Exporting. Please Wait...");
                            PSExportFactory.writeExport(exportScheme, selectedFile, exportFormat, peptideShakerGUI.getExperiment().getReference(),
                                    peptideShakerGUI.getSample().getReference(), peptideShakerGUI.getReplicateNumber(),
                                    peptideShakerGUI.getProjectDetails(), peptideShakerGUI.getIdentification(),
                                    peptideShakerGUI.getIdentificationFeaturesGenerator(), peptideShakerGUI.getSearchParameters(),
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                    @Override
                    public void run() {
                        boolean error = false;
                        try {
                            String schemeName = (String) reportsTable.getValueAt(reportsTable.getSelectedRow(), 1);
                            ExportScheme exportScheme = exportFactory.getExportScheme(schemeName);
                            PSExportFactory.writeDocumentation(exportScheme, exportFormat, selectedFile);
                        } catch (Exception e) {
                            error = true;
                            peptideShakerGUI.catchException(e);
                        }
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            PTMScoringPreferences ptmcoringPreferences, SpectrumCountingPreferences spectrumCountingPreferences, WaitingHandler waitingHandler)
            throws IOException, IllegalArgumentException, SQLException, ClassNotFoundException,
            InterruptedException, MzMLUnmarshallerException, MathException {

        PSExportFactory exportFactory = PSExportFactory.getInstance();
        ExportScheme exportScheme = exportFactory.getExportScheme(reportType);
        File reportFile = new File(reportCLIInputBean.getReportOutputFolder(), PSExportFactory.getDefaultReportName(experiment, sample, replicateNumber, reportType));

        //@TODO: allow format selection
        PSExportFactory.writeExport(exportScheme, reportFile, ExportFormat.text, experiment, sample, replicateNumber, projectDetails, identification, identificationFeaturesGenerator,
                searchParameters, null, null, null, null, nSurroundingAA, annotationPreferences, sequenceMatchingPreferences, idFilter, ptmcoringPreferences, spectrumCountingPreferences, waitingHandler);
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     *
     * @throws IOException thrown of IOException occurs
     */
    public static void exportDocumentation(ReportCLIInputBean reportCLIInputBean, String reportType, WaitingHandler waitingHandler) throws IOException {
        PSExportFactory exportFactory = PSExportFactory.getInstance();
        ExportScheme exportScheme = exportFactory.getExportScheme(reportType);
        File reportFile = new File(reportCLIInputBean.getReportOutputFolder(), PSExportFactory.getDefaultDocumentation(reportType));

        //@TODO: allow format selection
        PSExportFactory.writeDocumentation(exportScheme, ExportFormat.text, reportFile);
    }
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                    @Override
                    public void run() {

                        try {
                            String schemeName = "Certificate of Analysis"; //TODO: get this from the PSExportFactory
                            ExportScheme exportScheme = PSExportFactory.getInstance().getExportScheme(schemeName);
                            progressDialog.setTitle("Exporting. Please Wait...");
                            PSExportFactory.writeExport(exportScheme, selectedFile, exportFormat, peptideShakerGUI.getExperiment().getReference(),
                                    peptideShakerGUI.getSample().getReference(), peptideShakerGUI.getReplicateNumber(),
                                    peptideShakerGUI.getProjectDetails(), peptideShakerGUI.getIdentification(),
                                    peptideShakerGUI.getIdentificationFeaturesGenerator(), peptideShakerGUI.getSearchParameters(),
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Related Classes of com.compomics.util.io.export.ExportScheme

  • eu.isas.peptideshaker.cmd.CLIMethods
  • eu.isas.peptideshaker.export.PSExportFactory
  • eu.isas.peptideshaker.gui.exportdialogs.FeaturesPreferencesDialog
  • eu.isas.peptideshaker.gui.exportdialogs.MethodsSectionDialog
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