Examples of OutputGenerator

IOGenerating.OutputGenerator
@author Анна
eu.isas.peptideshaker.export.OutputGenerator
This class will generate the output as requested by the user. @author Marc Vaudel @author Harald Barsnes

Examples of IOGenerating.OutputGenerator

        }
    }


    private boolean testProgram(Program p) {
        InputGenerator inputGenerator = new InputFromFileGenerator(p);
        OutputGenerator outputGenerator = new OutputFromFileGenerator(p);
        InputDataProcessor inputDataProcessor = new SimpleInputDataProcessor();
        OutputDataProcessor outputDataProcessor = new SimpleOutputDataProcessor();
        ProgramTester tester = new ProgramTester(
                inputGenerator, outputGenerator,
                inputDataProcessor, outputDataProcessor);

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Examples of IOGenerating.OutputGenerator

            p.prepare();
            Compiler c = CompilerFactory.getInstance().getCompiler(p.lang);
            c.compile(p);
            System.err.println("success compilation");
            InputGenerator inputGenerator = new InputFromFileGenerator(p);
            OutputGenerator outputGenerator = new OutputFromFileGenerator(p);
            InputDataProcessor inputDataProcessor = new SimpleInputDataProcessor();
            OutputDataProcessor outputDataProcessor = new SimpleOutputDataProcessor();
            ProgramTester tester = new ProgramTester(
                    inputGenerator, outputGenerator,
                    inputDataProcessor, outputDataProcessor);

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Examples of eu.isas.peptideshaker.export.OutputGenerator


            if (evt.getDescription().equalsIgnoreCase("validated_proteins")) {


                if (peptideShakerGUI.getIdentification() != null) {


                    OutputGenerator outputGenerator = new OutputGenerator(peptideShakerGUI);


                    try {
                        outputGenerator.getProteinsOutput(
                                null, null, false, true, true, false, false, false,
                                false, false, false, false, false, false,
                                false, false, false, false, false, false, 
                                false, false, false, false, false);
                    } catch (Exception e) {

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Examples of eu.isas.peptideshaker.export.OutputGenerator

            new Thread(new Runnable() {
                @Override
                public void run() {
                    try {


                        OutputGenerator outputGenerator = new OutputGenerator(peptideShakerGUI);
                        String clipboardString = null;


                        if (tableIndex == TableIndex.MODIFIED_PEPTIDES_TABLE) {
                            outputGenerator.getPeptidesOutput(
                                    null, displayedPeptides, null, true, false, true, true, true, true, true,
                                    true, true, true, true, true, true, true, true, false, false, false, null, true);
                        } else if (tableIndex == TableIndex.RELATED_PEPTIDES_TABLE) {
                            outputGenerator.getPeptidesOutput(
                                    null, relatedPeptides, null, true, false, true, true, true, true, true,
                                    true, true, true, true, true, true, true, true, false, false, false, null, true);
                        } else if (tableIndex == TableIndex.MODIFIED_PSMS_TABLE) {
                            outputGenerator.getPSMsOutput(
                                    null, identification.getPeptideMatch(getSelectedPeptide(false)).getSpectrumMatches(),
                                    true, false, true, true, true, true,
                                    true, true, true, true, true, true, true, false, false);
                        } else if (tableIndex == TableIndex.RELATED_PSMS_TABLE) {
                            outputGenerator.getPSMsOutput(
                                    null, identification.getPeptideMatch(getSelectedPeptide(true)).getSpectrumMatches(),
                                    true, false, true, true, true, true,
                                    true, true, true, true, true, true, true, false, false);
                        } else if (tableIndex == TableIndex.PTM_TABLE) {
                            // @TODO: implement me!!

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Examples of eu.isas.peptideshaker.export.OutputGenerator


        final TableIndex tableIndex = index;


        if (tableIndex == TableIndex.PROTEIN_TABLE) {


            OutputGenerator outputGenerator = new OutputGenerator(peptideShakerGUI);


            if (tableIndex == TableIndex.PROTEIN_TABLE) {
                ArrayList<String> selectedProteins = getDisplayedProteins();
                outputGenerator.getProteinsOutput(
                        null, selectedProteins, true, false, true, true, true,
                        true, true, true, true, false, true,
                        true, true, true, true, true, false, true, false, false, false, true, true);
            }
        }

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Examples of eu.isas.peptideshaker.export.OutputGenerator

                || tableIndex == TableIndex.PEPTIDE_TABLE
                || tableIndex == TableIndex.PDB_MATCHES
                || tableIndex == TableIndex.PDB_CHAINS) {


            try {
                OutputGenerator outputGenerator = new OutputGenerator(peptideShakerGUI);


                if (tableIndex == TableIndex.PROTEIN_TABLE) {
                    ArrayList<String> selectedProteins = getDisplayedProteins();
                    outputGenerator.getProteinsOutput(
                            null, selectedProteins, true, false, true, true, true,
                            true, true, true, true, false, true,
                            true, true, true, true, true, false, true, false, false, false, true, true);
                } else if (tableIndex == TableIndex.PEPTIDE_TABLE) {
                    ArrayList<String> selectedPeptides = getDisplayedPeptides();
                    SelfUpdatingTableModel tableModel = (SelfUpdatingTableModel) proteinTable.getModel();
                    int proteinIndex = tableModel.getViewIndex(proteinTable.getSelectedRow());
                    String proteinKey = proteinKeys.get(proteinIndex);
                    outputGenerator.getPeptidesOutput(
                            null, selectedPeptides, peptidePdbArray, true, false, true, true, true, true, true,
                            true, true, true, true, true, true, true, true, false, false, false, proteinKey, true);
                } else if (tableIndex == TableIndex.PDB_MATCHES || tableIndex == TableIndex.PDB_CHAINS) {


                    // get the file to send the output to

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Examples of eu.isas.peptideshaker.export.OutputGenerator


        if (tableIndex == TableIndex.PROTEIN_TABLE
                || tableIndex == TableIndex.PEPTIDE_TABLE
                || tableIndex == TableIndex.PSM_TABLE) {


            OutputGenerator outputGenerator = new OutputGenerator(peptideShakerGUI);


            if (tableIndex == TableIndex.PROTEIN_TABLE) {
                ArrayList<String> selectedProteins = getDisplayedProteins();
                outputGenerator.getProteinsOutput(
                        null, selectedProteins, true, false, true, true, true,
                        true, true, true, true, false, true,
                        true, true, true, true, true, false, true, false, false, false, true, true);
            } else if (tableIndex == TableIndex.PEPTIDE_TABLE) {
                ArrayList<String> selectedPeptides = getDisplayedPeptides();
                SelfUpdatingTableModel tableModel = (SelfUpdatingTableModel) proteinTable.getModel();
                String proteinKey = proteinKeys.get(tableModel.getViewIndex(proteinTable.getSelectedRow()));
                outputGenerator.getPeptidesOutput(
                        null, selectedPeptides, null, true, false, true, true, true, true, true,
                        true, true, true, true, true, true, true, true, false, false, false, proteinKey, true);
            } else if (tableIndex == TableIndex.PSM_TABLE) {
                ArrayList<String> selectedPsms = getDisplayedPsms();
                outputGenerator.getPSMsOutput(
                        null, selectedPsms, true, false, true, true, true, true,
                        true, true, true, true, true, true, true, false, false);
            }
        }
    }

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Examples of eu.isas.peptideshaker.export.OutputGenerator

    public FeaturesPreferencesDialog(PeptideShakerGUI peptideShakerGUI) {
        super(peptideShakerGUI, true);
        this.peptideShakerGUI = peptideShakerGUI;
        initComponents();
        setUpGUI();
        this.outputGenerator = new OutputGenerator(peptideShakerGUI);
        this.pack();
        tabbedPane.setEnabledAt(4, peptideShakerGUI.getIdentification().getSpectrumFiles().size() > 1);
        this.setLocationRelativeTo(peptideShakerGUI);
        updateReportsList();
        setVisible(true);

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