Examples with ExportFeature com.compomics.util.io.export.ExportFeature used on opensource projects

Example 1 with ExportFeature

use of com.compomics.util.io.export.ExportFeature in project peptide-shaker by compomics.

the class ProteinFractionsPanel method copyTableContentToClipboardOrFile.

/**
 * Export the table contents to the file.
 *
 * @param index the table index
 */
private void copyTableContentToClipboardOrFile(TableIndex index) {
    final TableIndex tableIndex = index;
    if (tableIndex == TableIndex.PROTEIN_TABLE) {
        HashMap<String, ArrayList<ExportFeature>> exportFeatures = new HashMap<>();
        ArrayList<ExportFeature> sectionContent = new ArrayList<>();
        String textFileFilterDescription = "Tab separated text file (.txt)";
        String gzipFileFilterDescription = "Gzipped tab separated text file (.gz)";
        String excelFileFilterDescription = "Excel Workbook (.xls)";
        String lastSelectedFolderPath = peptideShakerGUI.getLastSelectedFolder().getLastSelectedFolder();
        FileAndFileFilter selectedFileAndFilter = FileChooserUtil.getUserSelectedFile(this, new String[] { ".xls", ".txt", ".gz" }, new String[] { excelFileFilterDescription, textFileFilterDescription, gzipFileFilterDescription }, "Export Report", lastSelectedFolderPath, "Protein table", false, true, false, 1);
        if (selectedFileAndFilter != null) {
            final File selectedFile = selectedFileAndFilter.getFile();
            final ExportFormat exportFormat;
            final boolean gzip;
            if (selectedFileAndFilter.getFileFilter().getDescription().equalsIgnoreCase(textFileFilterDescription)) {
                exportFormat = ExportFormat.text;
                gzip = false;
            } else if (selectedFileAndFilter.getFileFilter().getDescription().equalsIgnoreCase(gzipFileFilterDescription)) {
                exportFormat = ExportFormat.text;
                gzip = true;
            } else {
                exportFormat = ExportFormat.excel;
                gzip = false;
            }
            progressDialog = new ProgressDialogX(peptideShakerGUI, Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/peptide-shaker.gif")), Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/peptide-shaker-orange.gif")), true);
            progressDialog.setTitle("Exporting Data. Please Wait...");
            final String filePath = selectedFile.getPath();
            new Thread(new Runnable() {

                public void run() {
                    try {
                        progressDialog.setVisible(true);
                    } catch (IndexOutOfBoundsException e) {
                    // ignore
                    }
                }
            }, "ProgressDialog").start();
            new Thread("ExportThread") {

                @Override
                public void run() {
                    try {
                        sectionContent.add(PsProteinFeature.starred);
                        sectionContent.add(PsProteinFeature.pi);
                        sectionContent.add(PsProteinFeature.accession);
                        sectionContent.add(PsProteinFeature.protein_description);
                        sectionContent.add(PsProteinFeature.protein_group);
                        sectionContent.add(PsProteinFeature.descriptions);
                        sectionContent.add(PsProteinFeature.other_proteins);
                        sectionContent.add(PsProteinFeature.chromosome);
                        sectionContent.add(PsProteinFeature.coverage);
                        sectionContent.add(PsProteinFeature.confident_coverage);
                        sectionContent.add(PsProteinFeature.all_coverage);
                        sectionContent.add(PsProteinFeature.possible_coverage);
                        sectionContent.add(PsProteinFeature.validated_peptides);
                        sectionContent.add(PsProteinFeature.peptides);
                        sectionContent.add(PsProteinFeature.unique_peptides);
                        sectionContent.add(PsProteinFeature.unique_validated_peptides);
                        sectionContent.add(PsProteinFeature.validated_psms);
                        sectionContent.add(PsProteinFeature.psms);
                        sectionContent.add(PsProteinFeature.spectrum_counting_nsaf);
                        sectionContent.add(PsProteinFeature.spectrum_counting_empai);
                        sectionContent.add(PsProteinFeature.spectrum_counting_nsaf_percent);
                        sectionContent.add(PsProteinFeature.spectrum_counting_empai_percent);
                        sectionContent.add(PsProteinFeature.spectrum_counting_nsaf_ppm);
                        sectionContent.add(PsProteinFeature.spectrum_counting_empai_ppm);
                        sectionContent.add(PsProteinFeature.spectrum_counting_nsaf_fmol);
                        sectionContent.add(PsProteinFeature.spectrum_counting_empai_fmol);
                        sectionContent.add(PsProteinFeature.mw);
                        sectionContent.add(PsProteinFeature.confidence);
                        sectionContent.add(PsProteinFeature.validated);
                        exportFeatures.put(PsProteinFeature.type, sectionContent);
                        ExportScheme validatedProteinReport = new ExportScheme("Protein Table", false, exportFeatures, "\t", true, true, 0, false, false, false);
                        PSExportFactory.writeExport(validatedProteinReport, selectedFile, exportFormat, gzip, peptideShakerGUI.getProjectParameters().getProjectUniqueName(), peptideShakerGUI.getProjectDetails(), peptideShakerGUI.getIdentification(), peptideShakerGUI.getIdentificationFeaturesGenerator(), peptideShakerGUI.getGeneMaps(), getDisplayedProteins(), null, null, peptideShakerGUI.getDisplayParameters().getnAASurroundingPeptides(), peptideShakerGUI.getIdentificationParameters(), peptideShakerGUI.getSequenceProvider(), peptideShakerGUI.getProteinDetailsProvider(), peptideShakerGUI.getSpectrumProvider(), peptideShakerGUI.getSpectrumCountingParameters(), progressDialog);
                        boolean processCancelled = progressDialog.isRunCanceled();
                        progressDialog.setRunFinished();
                        if (!processCancelled) {
                            JOptionPane.showMessageDialog(peptideShakerGUI, "Data copied to file:\n" + filePath, "Data Exported", JOptionPane.INFORMATION_MESSAGE);
                        }
                    } catch (IllegalArgumentException e) {
                        if (e.getMessage().contains("Invalid row number (65536)")) {
                            progressDialog.setRunFinished();
                            JOptionPane.showMessageDialog(peptideShakerGUI, // @TODO: update the excel export library?
                            "An error occurred while generating the output. This format can contain only 65,535 lines.\n" + "Please use a text export instead.", "Output Error", JOptionPane.ERROR_MESSAGE);
                            e.printStackTrace();
                        } else {
                            progressDialog.setRunFinished();
                            JOptionPane.showMessageDialog(peptideShakerGUI, "An error occurred while generating the output.", "Output Error", JOptionPane.ERROR_MESSAGE);
                            e.printStackTrace();
                        }
                    } catch (Exception e) {
                        progressDialog.setRunFinished();
                        JOptionPane.showMessageDialog(peptideShakerGUI, "An error occurred while generating the output.", "Output Error", JOptionPane.ERROR_MESSAGE);
                        e.printStackTrace();
                    }
                }
            }.start();
        }
    }
}

Example 2 with ExportFeature

use of com.compomics.util.io.export.ExportFeature in project peptide-shaker by compomics.

the class ProteinStructurePanel method copyTableContentToClipboardOrFile.

/**
 * Export the table contents to the clipboard.
 *
 * @param index the table index type
 */
private void copyTableContentToClipboardOrFile(TableIndex index) throws IOException {
    final TableIndex tableIndex = index;
    if (tableIndex == TableIndex.PROTEIN_TABLE || tableIndex == TableIndex.PEPTIDE_TABLE) {
        HashMap<String, ArrayList<ExportFeature>> exportFeatures = new HashMap<>();
        ArrayList<ExportFeature> sectionContent = new ArrayList<>();
        String textFileFilterDescription = "Tab separated text file (.txt)";
        String gzipFileFilterDescription = "Gzipped tab separated text file (.gz)";
        String excelFileFilterDescription = "Excel Workbook (.xls)";
        String lastSelectedFolderPath = peptideShakerGUI.getLastSelectedFolder().getLastSelectedFolder();
        String exportName = "Export";
        switch(tableIndex) {
            case PROTEIN_TABLE:
                exportName = "Protein table";
                break;
            case PEPTIDE_TABLE:
                exportName = "Peptide table";
                break;
            default:
                break;
        }
        FileAndFileFilter selectedFileAndFilter = FileChooserUtil.getUserSelectedFile(this, new String[] { ".xls", ".txt", ".gz" }, new String[] { excelFileFilterDescription, textFileFilterDescription, gzipFileFilterDescription }, "Export Report", lastSelectedFolderPath, exportName, false, true, false, 1);
        if (selectedFileAndFilter != null) {
            final File selectedFile = selectedFileAndFilter.getFile();
            final ExportFormat exportFormat;
            final boolean gzip;
            if (selectedFileAndFilter.getFileFilter().getDescription().equalsIgnoreCase(textFileFilterDescription)) {
                exportFormat = ExportFormat.text;
                gzip = false;
            } else if (selectedFileAndFilter.getFileFilter().getDescription().equalsIgnoreCase(gzipFileFilterDescription)) {
                exportFormat = ExportFormat.text;
                gzip = true;
            } else {
                exportFormat = ExportFormat.excel;
                gzip = false;
            }
            progressDialog = new ProgressDialogX(peptideShakerGUI, Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/peptide-shaker.gif")), Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/peptide-shaker-orange.gif")), true);
            progressDialog.setTitle("Exporting Data. Please Wait...");
            final String filePath = selectedFile.getPath();
            new Thread(new Runnable() {

                public void run() {
                    try {
                        progressDialog.setVisible(true);
                    } catch (IndexOutOfBoundsException e) {
                    // ignore
                    }
                }
            }, "ProgressDialog").start();
            new Thread("ExportThread") {

                @Override
                public void run() {
                    try {
                        switch(tableIndex) {
                            case PROTEIN_TABLE:
                                sectionContent.add(PsProteinFeature.starred);
                                sectionContent.add(PsProteinFeature.pi);
                                sectionContent.add(PsProteinFeature.accession);
                                sectionContent.add(PsProteinFeature.protein_description);
                                sectionContent.add(PsProteinFeature.protein_group);
                                sectionContent.add(PsProteinFeature.descriptions);
                                sectionContent.add(PsProteinFeature.other_proteins);
                                sectionContent.add(PsProteinFeature.chromosome);
                                sectionContent.add(PsProteinFeature.coverage);
                                sectionContent.add(PsProteinFeature.confident_coverage);
                                sectionContent.add(PsProteinFeature.all_coverage);
                                sectionContent.add(PsProteinFeature.possible_coverage);
                                sectionContent.add(PsProteinFeature.validated_peptides);
                                sectionContent.add(PsProteinFeature.peptides);
                                sectionContent.add(PsProteinFeature.unique_peptides);
                                sectionContent.add(PsProteinFeature.unique_validated_peptides);
                                sectionContent.add(PsProteinFeature.validated_psms);
                                sectionContent.add(PsProteinFeature.psms);
                                sectionContent.add(PsProteinFeature.spectrum_counting_nsaf);
                                sectionContent.add(PsProteinFeature.spectrum_counting_empai);
                                sectionContent.add(PsProteinFeature.spectrum_counting_nsaf_percent);
                                sectionContent.add(PsProteinFeature.spectrum_counting_empai_percent);
                                sectionContent.add(PsProteinFeature.spectrum_counting_nsaf_ppm);
                                sectionContent.add(PsProteinFeature.spectrum_counting_empai_ppm);
                                sectionContent.add(PsProteinFeature.spectrum_counting_nsaf_fmol);
                                sectionContent.add(PsProteinFeature.spectrum_counting_empai_fmol);
                                sectionContent.add(PsProteinFeature.mw);
                                sectionContent.add(PsProteinFeature.confidence);
                                sectionContent.add(PsProteinFeature.validated);
                                exportFeatures.put(PsProteinFeature.type, sectionContent);
                                ExportScheme validatedProteinReport = new ExportScheme("Protein Table", false, exportFeatures, "\t", true, true, 0, false, false, false);
                                PSExportFactory.writeExport(validatedProteinReport, selectedFile, exportFormat, gzip, peptideShakerGUI.getProjectParameters().getProjectUniqueName(), peptideShakerGUI.getProjectDetails(), peptideShakerGUI.getIdentification(), peptideShakerGUI.getIdentificationFeaturesGenerator(), peptideShakerGUI.getGeneMaps(), getDisplayedProteins(), null, null, peptideShakerGUI.getDisplayParameters().getnAASurroundingPeptides(), peptideShakerGUI.getIdentificationParameters(), peptideShakerGUI.getSequenceProvider(), peptideShakerGUI.getProteinDetailsProvider(), peptideShakerGUI.getSpectrumProvider(), peptideShakerGUI.getSpectrumCountingParameters(), progressDialog);
                                break;
                            case PEPTIDE_TABLE:
                                sectionContent.add(PsPeptideFeature.starred);
                                sectionContent.add(PsPeptideFeature.pi);
                                sectionContent.add(PsPeptideFeature.accessions);
                                sectionContent.add(PsPeptideFeature.protein_description);
                                sectionContent.add(PsPeptideFeature.protein_groups);
                                sectionContent.add(PsPeptideFeature.sequence);
                                sectionContent.add(PsPeptideFeature.modified_sequence);
                                sectionContent.add(PsPeptideFeature.position);
                                sectionContent.add(PsPeptideFeature.aaBefore);
                                sectionContent.add(PsPeptideFeature.aaAfter);
                                sectionContent.add(PsPeptideFeature.missed_cleavages);
                                sectionContent.add(PsPeptideFeature.variable_ptms);
                                sectionContent.add(PsPeptideFeature.fixed_ptms);
                                sectionContent.add(PsPeptideFeature.psms);
                                sectionContent.add(PsPeptideFeature.validated_psms);
                                sectionContent.add(PsPeptideFeature.confidence);
                                sectionContent.add(PsPeptideFeature.validated);
                                exportFeatures.put(PsPeptideFeature.type, sectionContent);
                                validatedProteinReport = new ExportScheme("Peptide Table", false, exportFeatures, "\t", true, true, 0, false, false, false);
                                PSExportFactory.writeExport(validatedProteinReport, selectedFile, exportFormat, gzip, peptideShakerGUI.getProjectParameters().getProjectUniqueName(), peptideShakerGUI.getProjectDetails(), peptideShakerGUI.getIdentification(), peptideShakerGUI.getIdentificationFeaturesGenerator(), peptideShakerGUI.getGeneMaps(), null, getDisplayedPeptides(), null, peptideShakerGUI.getDisplayParameters().getnAASurroundingPeptides(), peptideShakerGUI.getIdentificationParameters(), peptideShakerGUI.getSequenceProvider(), peptideShakerGUI.getProteinDetailsProvider(), peptideShakerGUI.getSpectrumProvider(), peptideShakerGUI.getSpectrumCountingParameters(), progressDialog);
                                break;
                            default:
                                break;
                        }
                        boolean processCancelled = progressDialog.isRunCanceled();
                        progressDialog.setRunFinished();
                        if (!processCancelled) {
                            JOptionPane.showMessageDialog(peptideShakerGUI, "Data copied to file:\n" + filePath, "Data Exported", JOptionPane.INFORMATION_MESSAGE);
                        }
                    } catch (FileNotFoundException e) {
                        progressDialog.setRunFinished();
                        JOptionPane.showMessageDialog(peptideShakerGUI, "An error occurred while generating the output. Please make sure " + "that the destination file is not opened by another application.", "Output Error", JOptionPane.ERROR_MESSAGE);
                        e.printStackTrace();
                    } catch (IllegalArgumentException e) {
                        if (e.getMessage().contains("Invalid row number (65536)")) {
                            progressDialog.setRunFinished();
                            JOptionPane.showMessageDialog(peptideShakerGUI, // @TODO: update the excel export library?
                            "An error occurred while generating the output. This format can contain only 65,535 lines.\n" + "Please use a text export instead.", "Output Error", JOptionPane.ERROR_MESSAGE);
                            e.printStackTrace();
                        } else {
                            progressDialog.setRunFinished();
                            JOptionPane.showMessageDialog(peptideShakerGUI, "An error occurred while generating the output.", "Output Error", JOptionPane.ERROR_MESSAGE);
                            e.printStackTrace();
                        }
                    } catch (Exception e) {
                        progressDialog.setRunFinished();
                        JOptionPane.showMessageDialog(peptideShakerGUI, "An error occurred while generating the output.", "Output Error", JOptionPane.ERROR_MESSAGE);
                        e.printStackTrace();
                    }
                }
            }.start();
        }
    } else if (tableIndex == TableIndex.PDB_MATCHES || tableIndex == TableIndex.PDB_CHAINS) {
        // get the file to send the output to
        File selectedFile = peptideShakerGUI.getUserSelectedFile("pdb_details.txt", ".txt", "Tab separated text file (.txt)", "Export...", false);
        if (selectedFile != null) {
            if (tableIndex == TableIndex.PDB_CHAINS) {
                try (SimpleFileWriter writer = new SimpleFileWriter(selectedFile, false)) {
                    writer.writeLine("", "Chain", "PDB-Start", "PDB-End", "Coverage");
                    for (int i = 0; i < pdbChainsJTable.getRowCount(); i++) {
                        XYDataPoint pdbCoverage = (XYDataPoint) pdbChainsJTable.getValueAt(i, 2);
                        writer.writeLine(pdbChainsJTable.getValueAt(i, 0).toString(), pdbChainsJTable.getValueAt(i, 1).toString(), Double.toString(pdbCoverage.getX()), Double.toString(pdbCoverage.getY()), pdbChainsJTable.getValueAt(i, 3).toString());
                    }
                    JOptionPane.showMessageDialog(peptideShakerGUI, "Data copied to file:\n" + selectedFile.getPath(), "Data Exported", JOptionPane.INFORMATION_MESSAGE);
                }
            } else if (tableIndex == TableIndex.PDB_MATCHES) {
                try (BufferedWriter writer = new BufferedWriter(new FileWriter(selectedFile))) {
                    Util.tableToFile(pdbMatchesJTable, "\t", null, true, writer);
                    JOptionPane.showMessageDialog(peptideShakerGUI, "Data copied to file:\n" + selectedFile.getPath(), "Data Exported", JOptionPane.INFORMATION_MESSAGE);
                }
            }
        }
    }
}

Example 3 with ExportFeature

use of com.compomics.util.io.export.ExportFeature in project peptide-shaker by compomics.

the class OverviewPanel method copyTableContentToClipboardOrFile.

/**
 * Export the table contents to the clipboard.
 *
 * @param index the index type
 */
private void copyTableContentToClipboardOrFile(TableIndex index) {
    final TableIndex tableIndex = index;
    HashMap<String, ArrayList<ExportFeature>> exportFeatures = new HashMap<>();
    ArrayList<ExportFeature> sectionContent = new ArrayList<>();
    if (tableIndex == TableIndex.PROTEIN_TABLE || tableIndex == TableIndex.PEPTIDE_TABLE || tableIndex == TableIndex.PSM_TABLE) {
        String textFileFilterDescription = "Tab separated text file (.txt)";
        String gzipFileFilterDescription = "Gzipped tab separated text file (.gz)";
        String excelFileFilterDescription = "Excel Workbook (.xls)";
        String lastSelectedFolderPath = peptideShakerGUI.getLastSelectedFolder().getLastSelectedFolder();
        String exportName = "Export";
        switch(tableIndex) {
            case PROTEIN_TABLE:
                exportName = "Protein table";
                break;
            case PEPTIDE_TABLE:
                exportName = "Peptide table";
                break;
            case PSM_TABLE:
                exportName = "PSM table";
                break;
            default:
                break;
        }
        FileAndFileFilter selectedFileAndFilter = FileChooserUtil.getUserSelectedFile(this, new String[] { ".xls", ".txt", ".gz" }, new String[] { excelFileFilterDescription, textFileFilterDescription, gzipFileFilterDescription }, "Export Report", lastSelectedFolderPath, exportName, false, true, false, 1);
        if (selectedFileAndFilter != null) {
            final File selectedFile = selectedFileAndFilter.getFile();
            final ExportFormat exportFormat;
            final boolean gzip;
            if (selectedFileAndFilter.getFileFilter().getDescription().equalsIgnoreCase(textFileFilterDescription)) {
                exportFormat = ExportFormat.text;
                gzip = false;
            } else if (selectedFileAndFilter.getFileFilter().getDescription().equalsIgnoreCase(gzipFileFilterDescription)) {
                exportFormat = ExportFormat.text;
                gzip = true;
            } else {
                exportFormat = ExportFormat.excel;
                gzip = false;
            }
            progressDialog = new ProgressDialogX(peptideShakerGUI, Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/peptide-shaker.gif")), Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/peptide-shaker-orange.gif")), true);
            progressDialog.setTitle("Exporting Data. Please Wait...");
            final String filePath = selectedFile.getPath();
            new Thread(new Runnable() {

                public void run() {
                    try {
                        progressDialog.setVisible(true);
                    } catch (IndexOutOfBoundsException e) {
                    // ignore
                    }
                }
            }, "ProgressDialog").start();
            new Thread("ExportThread") {

                @Override
                public void run() {
                    try {
                        switch(tableIndex) {
                            case PROTEIN_TABLE:
                                sectionContent.add(PsProteinFeature.starred);
                                sectionContent.add(PsProteinFeature.pi);
                                sectionContent.add(PsProteinFeature.accession);
                                sectionContent.add(PsProteinFeature.protein_description);
                                sectionContent.add(PsProteinFeature.protein_group);
                                sectionContent.add(PsProteinFeature.descriptions);
                                sectionContent.add(PsProteinFeature.other_proteins);
                                sectionContent.add(PsProteinFeature.chromosome);
                                sectionContent.add(PsProteinFeature.coverage);
                                sectionContent.add(PsProteinFeature.confident_coverage);
                                sectionContent.add(PsProteinFeature.all_coverage);
                                sectionContent.add(PsProteinFeature.possible_coverage);
                                sectionContent.add(PsProteinFeature.validated_peptides);
                                sectionContent.add(PsProteinFeature.peptides);
                                sectionContent.add(PsProteinFeature.unique_peptides);
                                sectionContent.add(PsProteinFeature.unique_validated_peptides);
                                sectionContent.add(PsProteinFeature.validated_psms);
                                sectionContent.add(PsProteinFeature.psms);
                                sectionContent.add(PsProteinFeature.spectrum_counting_nsaf);
                                sectionContent.add(PsProteinFeature.spectrum_counting_empai);
                                sectionContent.add(PsProteinFeature.spectrum_counting_nsaf_percent);
                                sectionContent.add(PsProteinFeature.spectrum_counting_empai_percent);
                                sectionContent.add(PsProteinFeature.spectrum_counting_nsaf_ppm);
                                sectionContent.add(PsProteinFeature.spectrum_counting_empai_ppm);
                                sectionContent.add(PsProteinFeature.spectrum_counting_nsaf_fmol);
                                sectionContent.add(PsProteinFeature.spectrum_counting_empai_fmol);
                                sectionContent.add(PsProteinFeature.mw);
                                sectionContent.add(PsProteinFeature.confidence);
                                sectionContent.add(PsProteinFeature.validated);
                                exportFeatures.put(PsProteinFeature.type, sectionContent);
                                ExportScheme validatedProteinReport = new ExportScheme("Protein Table", false, exportFeatures, "\t", true, true, 0, false, false, false);
                                PSExportFactory.writeExport(validatedProteinReport, selectedFile, exportFormat, gzip, peptideShakerGUI.getProjectParameters().getProjectUniqueName(), peptideShakerGUI.getProjectDetails(), peptideShakerGUI.getIdentification(), peptideShakerGUI.getIdentificationFeaturesGenerator(), peptideShakerGUI.getGeneMaps(), getDisplayedProteins(), null, null, peptideShakerGUI.getDisplayParameters().getnAASurroundingPeptides(), peptideShakerGUI.getIdentificationParameters(), peptideShakerGUI.getSequenceProvider(), peptideShakerGUI.getProteinDetailsProvider(), peptideShakerGUI.getSpectrumProvider(), peptideShakerGUI.getSpectrumCountingParameters(), progressDialog);
                                break;
                            case PEPTIDE_TABLE:
                                sectionContent.add(PsPeptideFeature.starred);
                                sectionContent.add(PsPeptideFeature.pi);
                                sectionContent.add(PsPeptideFeature.accessions);
                                sectionContent.add(PsPeptideFeature.protein_description);
                                sectionContent.add(PsPeptideFeature.protein_groups);
                                sectionContent.add(PsPeptideFeature.sequence);
                                sectionContent.add(PsPeptideFeature.modified_sequence);
                                sectionContent.add(PsPeptideFeature.position);
                                sectionContent.add(PsPeptideFeature.aaBefore);
                                sectionContent.add(PsPeptideFeature.aaAfter);
                                sectionContent.add(PsPeptideFeature.missed_cleavages);
                                sectionContent.add(PsPeptideFeature.variable_ptms);
                                sectionContent.add(PsPeptideFeature.fixed_ptms);
                                sectionContent.add(PsPeptideFeature.psms);
                                sectionContent.add(PsPeptideFeature.validated_psms);
                                sectionContent.add(PsPeptideFeature.confidence);
                                sectionContent.add(PsPeptideFeature.validated);
                                exportFeatures.put(PsPeptideFeature.type, sectionContent);
                                validatedProteinReport = new ExportScheme("Peptide Table", false, exportFeatures, "\t", true, true, 0, false, false, false);
                                PSExportFactory.writeExport(validatedProteinReport, selectedFile, exportFormat, gzip, peptideShakerGUI.getProjectParameters().getProjectUniqueName(), peptideShakerGUI.getProjectDetails(), peptideShakerGUI.getIdentification(), peptideShakerGUI.getIdentificationFeaturesGenerator(), peptideShakerGUI.getGeneMaps(), null, getDisplayedPeptides(), null, peptideShakerGUI.getDisplayParameters().getnAASurroundingPeptides(), peptideShakerGUI.getIdentificationParameters(), peptideShakerGUI.getSequenceProvider(), peptideShakerGUI.getProteinDetailsProvider(), peptideShakerGUI.getSpectrumProvider(), peptideShakerGUI.getSpectrumCountingParameters(), progressDialog);
                                break;
                            case PSM_TABLE:
                                // @TODO: replace by the PSExportFactory when all of the missing values are supported
                                BufferedWriter writer = new BufferedWriter(new FileWriter(selectedFile));
                                Util.tableToFile(psmTable, "\t", progressDialog, true, writer);
                                writer.close();
                                // peptideShakerGUI.getSequenceProvider(), peptideShakerGUI.getProteinDetailsProvider(), peptideShakerGUI.getSpectrumCountingParameters(), progressDialog);
                                break;
                            default:
                                break;
                        }
                        boolean processCancelled = progressDialog.isRunCanceled();
                        progressDialog.setRunFinished();
                        if (!processCancelled) {
                            JOptionPane.showMessageDialog(peptideShakerGUI, "Data copied to file:\n" + filePath, "Data Exported", JOptionPane.INFORMATION_MESSAGE);
                        }
                    } catch (FileNotFoundException e) {
                        progressDialog.setRunFinished();
                        JOptionPane.showMessageDialog(peptideShakerGUI, "An error occurred while generating the output. Please make sure " + "that the destination file is not opened by another application.", "Output Error", JOptionPane.ERROR_MESSAGE);
                        e.printStackTrace();
                    } catch (IllegalArgumentException e) {
                        if (e.getMessage().contains("Invalid row number (65536)")) {
                            progressDialog.setRunFinished();
                            JOptionPane.showMessageDialog(peptideShakerGUI, // @TODO: update the excel export library?
                            "An error occurred while generating the output. This format can contain only 65,535 lines.\n" + "Please use a text export instead.", "Output Error", JOptionPane.ERROR_MESSAGE);
                            e.printStackTrace();
                        } else {
                            progressDialog.setRunFinished();
                            JOptionPane.showMessageDialog(peptideShakerGUI, "An error occurred while generating the output.", "Output Error", JOptionPane.ERROR_MESSAGE);
                            e.printStackTrace();
                        }
                    } catch (Exception e) {
                        progressDialog.setRunFinished();
                        JOptionPane.showMessageDialog(peptideShakerGUI, "An error occurred while generating the output.", "Output Error", JOptionPane.ERROR_MESSAGE);
                        e.printStackTrace();
                    }
                }
            }.start();
        }
    }
}

Example 4 with ExportFeature

use of com.compomics.util.io.export.ExportFeature in project peptide-shaker by compomics.

the class AnnotationPanel method helpEditorPaneHyperlinkUpdate.

// GEN-LAST:event_webIntActLabelMouseExited
/**
 * Enable the hyperlinks in the help panel.
 *
 * @param evt
 */
private void helpEditorPaneHyperlinkUpdate(javax.swing.event.HyperlinkEvent evt) {
    // GEN-FIRST:event_helpEditorPaneHyperlinkUpdate
    if (evt.getEventType().toString().equalsIgnoreCase(javax.swing.event.HyperlinkEvent.EventType.ACTIVATED.toString())) {
        if (evt.getDescription().equalsIgnoreCase("validated_proteins")) {
            if (peptideShakerGUI.getIdentification() != null) {
                String textFileFilterDescription = "Tab separated text file (.txt)";
                String gzipFileFilterDescription = "Gzipped tab separated text file (.gz)";
                String excelFileFilterDescription = "Excel Workbook (.xls)";
                String lastSelectedFolderPath = peptideShakerGUI.getLastSelectedFolder().getLastSelectedFolder();
                FileAndFileFilter selectedFileAndFilter = FileChooserUtil.getUserSelectedFile(this, new String[] { ".xls", ".txt", ".gz" }, new String[] { excelFileFilterDescription, textFileFilterDescription, gzipFileFilterDescription }, "Export Report", lastSelectedFolderPath, "All Validated Proteins", false, true, false, 1);
                if (selectedFileAndFilter != null) {
                    final File selectedFile = selectedFileAndFilter.getFile();
                    final ExportFormat exportFormat;
                    final boolean gzip;
                    if (selectedFileAndFilter.getFileFilter().getDescription().equalsIgnoreCase(textFileFilterDescription)) {
                        exportFormat = ExportFormat.text;
                        gzip = false;
                    } else if (selectedFileAndFilter.getFileFilter().getDescription().equalsIgnoreCase(gzipFileFilterDescription)) {
                        exportFormat = ExportFormat.text;
                        gzip = true;
                    } else {
                        exportFormat = ExportFormat.excel;
                        gzip = false;
                    }
                    progressDialog = new ProgressDialogX(peptideShakerGUI, Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/peptide-shaker.gif")), Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/peptide-shaker-orange.gif")), true);
                    progressDialog.setTitle("Exporting Data. Please Wait...");
                    final String filePath = selectedFile.getPath();
                    new Thread(new Runnable() {

                        public void run() {
                            try {
                                progressDialog.setVisible(true);
                            } catch (IndexOutOfBoundsException e) {
                            // ignore
                            }
                        }
                    }, "ProgressDialog").start();
                    new Thread("ExportThread") {

                        @Override
                        public void run() {
                            try {
                                HashMap<String, ArrayList<ExportFeature>> exportFeatures = new HashMap<>();
                                ArrayList<ExportFeature> sectionContent = new ArrayList<>();
                                sectionContent.add(PsProteinFeature.accession);
                                exportFeatures.put(PsProteinFeature.type, sectionContent);
                                ExportScheme validatedProteinReport = new ExportScheme("Validated Proteins", false, exportFeatures, "\t", false, false, 0, false, true, false);
                                PSExportFactory.writeExport(validatedProteinReport, selectedFile, exportFormat, gzip, peptideShakerGUI.getProjectParameters().getProjectUniqueName(), peptideShakerGUI.getProjectDetails(), peptideShakerGUI.getIdentification(), peptideShakerGUI.getIdentificationFeaturesGenerator(), peptideShakerGUI.getGeneMaps(), null, null, null, peptideShakerGUI.getDisplayParameters().getnAASurroundingPeptides(), peptideShakerGUI.getIdentificationParameters(), peptideShakerGUI.getSequenceProvider(), peptideShakerGUI.getProteinDetailsProvider(), peptideShakerGUI.getSpectrumProvider(), peptideShakerGUI.getSpectrumCountingParameters(), progressDialog);
                                boolean processCancelled = progressDialog.isRunCanceled();
                                progressDialog.setRunFinished();
                                if (!processCancelled) {
                                    JOptionPane.showMessageDialog(peptideShakerGUI, "Data copied to file:\n" + filePath, "Data Exported.", JOptionPane.INFORMATION_MESSAGE);
                                }
                            } catch (IllegalArgumentException e) {
                                if (e.getMessage().contains("Invalid row number (65536)")) {
                                    progressDialog.setRunFinished();
                                    JOptionPane.showMessageDialog(peptideShakerGUI, // @TODO: update the excel export library?
                                    "An error occurred while generating the output. This format can contain only 65,535 lines.\n" + "Please use a text export instead.", "Output Error.", JOptionPane.ERROR_MESSAGE);
                                    e.printStackTrace();
                                } else {
                                    progressDialog.setRunFinished();
                                    JOptionPane.showMessageDialog(peptideShakerGUI, "An error occurred while generating the output.", "Output Error.", JOptionPane.ERROR_MESSAGE);
                                    e.printStackTrace();
                                }
                            } catch (Exception e) {
                                progressDialog.setRunFinished();
                                JOptionPane.showMessageDialog(peptideShakerGUI, "An error occurred while generating the output.", "Output Error.", JOptionPane.ERROR_MESSAGE);
                                e.printStackTrace();
                            }
                        }
                    }.start();
                }
            } else {
                JOptionPane.showMessageDialog(peptideShakerGUI, "You have to load a project first!", "No Project", JOptionPane.WARNING_MESSAGE);
            }
        }
    }
}

Example 5 with ExportFeature

use of com.compomics.util.io.export.ExportFeature in project peptide-shaker by compomics.

the class PsAnnotationSection method writeSection.

/**
 * Writes the desired section.
 *
 * @param annotationPreferences the annotation preferences of the project
 * @param waitingHandler the waiting handler
 *
 * @throws IOException exception thrown whenever an error occurred while
 * writing the file.
 */
public void writeSection(AnnotationParameters annotationPreferences, WaitingHandler waitingHandler) throws IOException {
    if (waitingHandler != null) {
        waitingHandler.setSecondaryProgressCounterIndeterminate(true);
    }
    if (header) {
        if (indexes) {
            writer.writeHeaderText("");
            writer.addSeparator();
        }
        writer.writeHeaderText("Parameter");
        writer.addSeparator();
        writer.writeHeaderText("Value");
        writer.newLine();
    }
    int line = 1;
    for (ExportFeature exportFeature : annotationFeatures) {
        if (indexes) {
            writer.write(Integer.toString(line));
            writer.addSeparator();
        }
        writer.write(exportFeature.getTitle());
        writer.addSeparator();
        PsAnnotationFeature annotationFeature = (PsAnnotationFeature) exportFeature;
        switch(annotationFeature) {
            case automatic_annotation:
                if (annotationPreferences.isAutomaticAnnotation()) {
                    writer.write("Yes");
                } else {
                    writer.write("No");
                }
                break;
            case fragment_ion_accuracy:
                writer.write(Double.toString(annotationPreferences.getFragmentIonAccuracy()));
                break;
            case intensity_limit:
                writer.write(Double.toString(annotationPreferences.getAnnotationIntensityLimit()));
                break;
            case neutral_losses:
                String neutralLosses = annotationPreferences.getNeutralLosses().stream().map(neutralLoss -> neutralLoss.name).collect(Collectors.joining(", "));
                writer.write(neutralLosses);
                break;
            case neutral_losses_sequence_dependence:
                String value = annotationPreferences.areNeutralLossesSequenceAuto() ? "Yes" : "No";
                writer.write(value);
                break;
            case selected_ions:
                String ions = annotationPreferences.getFragmentIonTypes().stream().map(fragmentType -> PeptideFragmentIon.getSubTypeAsString(fragmentType)).collect(Collectors.joining(", "));
                writer.write(ions);
                break;
            default:
                writer.write("Not implemented");
        }
        writer.newLine();
        line++;
    }
}