Examples with ProjectDetails eu.isas.peptideshaker.preferences.ProjectDetails used on opensource projects

Example 1 with ProjectDetails

use of eu.isas.peptideshaker.preferences.ProjectDetails in project peptide-shaker by compomics.

the class PeptideShakerGUI method importPeptideShakerFile.

/**
 * Imports information from a PeptideShaker file.
 *
 * @param psFile The PeptideShaker file to import.
 * @param importFromZip flag that determines if psdb was imported from a zip
 * file
 */
public void importPeptideShakerFile(File psFile, boolean importFromZip) {
    psdbParent.setPsdbFile(psFile);
    psdbParent.setPsdbImportFromZip(importFromZip);
    // needed due to threading issues
    final PeptideShakerGUI peptideShakerGUI = this;
    progressDialog = new ProgressDialogX(this, Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/peptide-shaker.gif")), Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/peptide-shaker-orange.gif")), true);
    progressDialog.setPrimaryProgressCounterIndeterminate(true);
    progressDialog.setTitle("Importing Project. Please Wait...");
    // reset the title
    resetFrameTitle();
    new Thread(new Runnable() {

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

        @Override
        public void run() {
            try {
                // reset enzymes, modifications and parameters
                resetModificationFactory();
                setDefaultParameters();
                setCurentNotes(new ArrayList<String>(0));
                updateNotesNotificationCounter();
                openingExistingProject = true;
                psdbParent.loadPsdbFile(PeptideShaker.getMatchesFolder(), progressDialog, psdbParent.getPsdbImportFromZip());
                // load project specific PTMs
                String error = PeptideShaker.loadModifications(getIdentificationParameters().getSearchParameters());
                if (error != null) {
                    JOptionPane.showMessageDialog(peptideShakerGUI, error, "Modification Definition Changed", JOptionPane.WARNING_MESSAGE);
                }
                // resets the display features generator according to the new project
                resetDisplayFeaturesGenerator();
                if (progressDialog.isRunCanceled()) {
                    clearData(true, true);
                    clearParameters();
                    progressDialog.setRunFinished();
                    openingExistingProject = false;
                    return;
                }
                progressDialog.setTitle("Loading FASTA File. Please Wait...");
                boolean fileFound = true;
                try {
                    FastaSummary fastaSummary = psdbParent.loadFastaFile(progressDialog);
                    if (fastaSummary == null) {
                        fileFound = false;
                    }
                } catch (IOException e) {
                    fileFound = false;
                }
                if (!fileFound && !locateFastaFileManually()) {
                    String fastaFilePath = getProjectDetails().getFastaFile();
                    JOptionPane.showMessageDialog(peptideShakerGUI, "An error occurred while reading:\n" + fastaFilePath + "." + "\n\nFile not found.", "File Input Error", JOptionPane.ERROR_MESSAGE);
                    clearData(true, true);
                    clearParameters();
                    progressDialog.setRunFinished();
                    openingExistingProject = false;
                    return;
                }
                if (progressDialog.isRunCanceled()) {
                    clearData(true, true);
                    clearParameters();
                    progressDialog.setRunFinished();
                    openingExistingProject = false;
                    return;
                }
                progressDialog.setTitle("Loading Spectrum Files. Please Wait...");
                progressDialog.resetPrimaryProgressCounter();
                progressDialog.setMaxPrimaryProgressCounter(getIdentification().getSpectrumIdentification().size() + 1);
                progressDialog.increasePrimaryProgressCounter();
                ProjectDetails projectParameters = psdbParent.getProjectDetails();
                Set<String> fileNames = getProjectDetails().getSpectrumFileNames();
                ArrayList<File> spectrumFiles = fileNames.stream().map(projectParameters::getSpectrumFilePath).map(path -> new File(path)).collect(Collectors.toCollection(ArrayList::new));
                int cpt = 0, total = fileNames.size();
                for (String spectrumFileName : getIdentification().getFractions()) {
                    progressDialog.setTitle("Loading Spectrum Files (" + ++cpt + " of " + total + "). Please Wait...");
                    progressDialog.increasePrimaryProgressCounter();
                    boolean found;
                    try {
                        found = psdbParent.loadSpectrumFile(spectrumFileName, spectrumFiles, progressDialog);
                    } catch (Exception e) {
                        found = false;
                    }
                    if (!found) {
                        JOptionPane.showMessageDialog(peptideShakerGUI, "Spectrum file not found: \'" + spectrumFileName + "\'." + "\nPlease select the spectrum file or the folder containing it manually.", "File Not Found", JOptionPane.WARNING_MESSAGE);
                        JFileChooser fileChooser = new JFileChooser(getLastSelectedFolder().getLastSelectedFolder());
                        fileChooser.setDialogTitle("Open Spectrum File");
                        FileFilter filter = new FileFilter() {

                            @Override
                            public boolean accept(File myFile) {
                                return myFile.getName().toLowerCase().endsWith(".mgf") || myFile.getName().toLowerCase().endsWith(".mgf.gz") || myFile.getName().toLowerCase().endsWith(".mzml") || myFile.getName().toLowerCase().endsWith(".mzml.gz") || myFile.isDirectory();
                            }

                            @Override
                            public String getDescription() {
                                return "Supported formats: mgf or mzML (.mgf, .mg.gz, .mzml, .mzml.gz)";
                            }
                        };
                        fileChooser.setFileFilter(filter);
                        int returnVal = fileChooser.showDialog(peptideShakerGUI, "Open");
                        if (returnVal == JFileChooser.APPROVE_OPTION) {
                            File spectrumFolder = fileChooser.getSelectedFile();
                            if (!spectrumFolder.isDirectory()) {
                                spectrumFolder = spectrumFolder.getParentFile();
                            }
                            lastSelectedFolder.setLastSelectedFolder(spectrumFolder.getAbsolutePath());
                            found = false;
                            for (File file : spectrumFolder.listFiles()) {
                                for (String spectrumFileName2 : getIdentification().getFractions()) {
                                    try {
                                        String fileName = IoUtil.removeExtension(file.getName());
                                        if (spectrumFileName2.equals(fileName)) {
                                            psdbParent.loadSpectrumFile(file, progressDialog);
                                            spectrumFiles.add(file);
                                        }
                                        if (fileName.equals(spectrumFileName2)) {
                                            found = true;
                                        }
                                    } catch (Exception e) {
                                    // ignore
                                    }
                                }
                            }
                            if (found) {
                                try {
                                    found = psdbParent.loadSpectrumFile(spectrumFileName, spectrumFiles, progressDialog);
                                } catch (Exception e) {
                                    found = false;
                                }
                            }
                            if (!found) {
                                JOptionPane.showMessageDialog(peptideShakerGUI, spectrumFileName + " was not found in the given folder.", "File Input Error", JOptionPane.ERROR_MESSAGE);
                                clearData(true, true);
                                clearParameters();
                                progressDialog.setRunFinished();
                                openingExistingProject = false;
                                return;
                            }
                        }
                    }
                    if (progressDialog.isRunCanceled()) {
                        clearData(true, true);
                        clearParameters();
                        progressDialog.setRunFinished();
                        openingExistingProject = false;
                        return;
                    }
                }
                progressDialog.setPrimaryProgressCounterIndeterminate(true);
                progressDialog.setRunFinished();
                peptideShakerGUI.displayResults();
                // display the overview tab data
                allTabsJTabbedPaneStateChanged(null);
                peptideShakerGUI.updateFrameTitle();
                dataSaved = true;
                SwingUtilities.invokeLater(new Runnable() {

                    public void run() {
                        openingExistingProject = false;
                    }
                });
            } catch (OutOfMemoryError error) {
                System.err.println("Ran out of memory!");
                System.err.println("Memory given to the Java virtual machine: " + Runtime.getRuntime().maxMemory() + ".");
                System.err.println("Memory used by the Java virtual machine: " + Runtime.getRuntime().totalMemory() + ".");
                System.err.println("Free memory in the Java virtual machine: " + Runtime.getRuntime().freeMemory() + ".");
                Runtime.getRuntime().gc();
                String message = "PeptideShaker used up all the available memory and had to be stopped.<br>" + "Memory boundaries are changed in the the Welcome Dialog (Settings<br>" + "& Help > Settings > Java Memory Settings) or in the Edit menu (Edit<br>" + "Java Options). See also <a href=\"https://compomics.github.io/projects/compomics-utilities/wiki/JavaTroubleShooting.html\">JavaTroubleShooting</a>.";
                JOptionPane.showMessageDialog(PeptideShakerGUI.this, JOptionEditorPane.getJOptionEditorPane(message), "Out Of Memory", JOptionPane.ERROR_MESSAGE);
                progressDialog.setRunFinished();
                error.printStackTrace();
            } catch (OptionalDataException e) {
                progressDialog.setRunFinished();
                if (e.eof) {
                    JOptionPane.showMessageDialog(peptideShakerGUI, "An error occurred while reading:\n" + psdbParent.getPsdbFile() + ".\n\n" + "The end of the file was reached unexpectedly. The file seems to be corrupt and cannot\n" + "be opened. If the file is a copy, make sure that it is identical to the original file.", "File Input Error", JOptionPane.ERROR_MESSAGE);
                } else {
                    JOptionPane.showMessageDialog(peptideShakerGUI, "An error occurred while reading:\n" + psdbParent.getPsdbFile() + ".\n\n" + "Please verify that the version used to create the file\n" + "is compatible with your version of PeptideShaker.", "File Input Error", JOptionPane.ERROR_MESSAGE);
                }
                e.printStackTrace();
            } catch (EOFException e) {
                progressDialog.setRunFinished();
                JOptionPane.showMessageDialog(peptideShakerGUI, "An error occurred while reading:\n" + psdbParent.getPsdbFile() + ".\n\n" + "The end of the file was reached unexpectedly. The file seems to be corrupt and cannot\n" + "be opened. If the file is a copy, make sure that it is identical to the original file.", "File Input Error", JOptionPane.ERROR_MESSAGE);
                e.printStackTrace();
            } catch (Exception e) {
                progressDialog.setRunFinished();
                JOptionPane.showMessageDialog(peptideShakerGUI, "An error occurred while reading:\n" + psdbParent.getPsdbFile() + ".\n\n" + "Please verify that the version used to create the file\n" + "is compatible with your version of PeptideShaker.", "File Input Error", JOptionPane.ERROR_MESSAGE);
                e.printStackTrace();
            }
        }
    }.start();
}

Example 2 with ProjectDetails

use of eu.isas.peptideshaker.preferences.ProjectDetails in project peptide-shaker by compomics.

the class MzIdentMLExportDialog method convertJButtonActionPerformed.

// GEN-LAST:event_contactEmailJTextFieldKeyReleased
/**
 * Convert the project to an mzIdentML file.
 *
 * @param evt
 */
private void convertJButtonActionPerformed(java.awt.event.ActionEvent evt) {
    // GEN-FIRST:event_convertJButtonActionPerformed
    final File finalOutputFile = new File(outputFolderJTextField.getText());
    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.setPrimaryProgressCounterIndeterminate(true);
    progressDialog.setTitle("Exporting mzIdentML. Please Wait...");
    new Thread(new Runnable() {

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

        @Override
        public void run() {
            IdentificationParameters identificationParameters = peptideShakerGUI.getIdentificationParameters();
            AnnotationParameters annotationParameters = identificationParameters.getAnnotationParameters();
            ProjectDetails projectDetails = peptideShakerGUI.getProjectDetails();
            // save the inserted mzid details with the project
            projectDetails.setContactFirstName(contactFirstNameJTextField.getText().trim());
            projectDetails.setContactLastName(contactLastNameJTextField.getText().trim());
            projectDetails.setContactEmail(contactEmailJTextField.getText().trim());
            projectDetails.setContactAddress(contactAddressJTextField.getText().trim());
            if (!contactUrlJTextField.getText().trim().isEmpty()) {
                projectDetails.setContactUrl(contactUrlJTextField.getText().trim());
            } else {
                projectDetails.setContactUrl(null);
            }
            projectDetails.setOrganizationName(organizationNameJTextField.getText().trim());
            projectDetails.setOrganizationEmail(organizationEmailJTextField.getText().trim());
            projectDetails.setOrganizationAddress(organizationAddressJTextField.getText().trim());
            if (!organizationUrlJTextField.getText().trim().isEmpty()) {
                projectDetails.setOrganizationUrl(organizationUrlJTextField.getText().trim());
            } else {
                projectDetails.setOrganizationUrl(null);
            }
            projectDetails.setIncludeProteinSequences(includeSequencesCheckBox.isSelected());
            projectDetails.setMzIdentOutputFile(outputFolderJTextField.getText());
            peptideShakerGUI.setDataSaved(false);
            boolean conversionCompleted = false;
            // make sure that all annotations are included
            double currentIntensityLimit = annotationParameters.getAnnotationIntensityLimit();
            annotationParameters.setIntensityLimit(0.0);
            try {
                FastaSummary fastaSummary = FastaSummary.getSummary(projectDetails.getFastaFile(), identificationParameters.getFastaParameters(), progressDialog);
                MzIdentMLExport mzIdentMLExport = new MzIdentMLExport(PeptideShaker.getVersion(), peptideShakerGUI.getIdentification(), projectDetails, identificationParameters, peptideShakerGUI.getSequenceProvider(), peptideShakerGUI.getProteinDetailsProvider(), peptideShakerGUI.getSpectrumProvider(), ModificationFactory.getInstance(), fastaSummary, peptideShakerGUI.getIdentificationFeaturesGenerator(), finalOutputFile, includeSequencesCheckBox.isSelected(), progressDialog, true);
                mzIdentMLExport.createMzIdentMLFile(mzIdentMLVersion);
                // validate the mzidentml file
                if (validateMzIdentML && !progressDialog.isRunCanceled()) {
                    progressDialog.setPrimaryProgressCounterIndeterminate(true);
                    progressDialog.setTitle("Validating mzIdentML. Please Wait...");
                    String errors = validateMzIdentML(finalOutputFile);
                    // see if any errors were found, and display them to the user
                    if (!errors.isEmpty()) {
                        JOptionPane.showMessageDialog(null, errors, "mzIdentML Errors", JOptionPane.ERROR_MESSAGE);
                    } else {
                        conversionCompleted = true;
                    }
                } else {
                    conversionCompleted = true;
                }
            } catch (Exception e) {
                peptideShakerGUI.catchException(e);
                progressDialog.setRunCanceled();
                progressDialog.dispose();
                return;
            } finally {
                // reset the annotation level
                annotationParameters.setIntensityLimit(currentIntensityLimit);
            }
            // close the progress dialog
            boolean processCancelled = progressDialog.isRunCanceled();
            progressDialog.setRunFinished();
            // display a conversion complete message to the user
            if (conversionCompleted && !processCancelled) {
                JOptionPane.showMessageDialog(MzIdentMLExportDialog.this, JOptionEditorPane.getJOptionEditorPane("mzIdentML file \'" + new File(outputFolderJTextField.getText()).getAbsolutePath() + "\' created." + "<br><br>" + "Review your mzIdentML files with <a href=\"https://github.com/PRIDE-Toolsuite/pride-inspector\">PRIDE Inspector</a>.<br>" + "Publish your mzIdentML files via <a href=\"http://www.proteomexchange.org/submission\">ProteomeXchange</a>."), "File Created", JOptionPane.INFORMATION_MESSAGE);
                dispose();
            }
            if (processCancelled) {
                JOptionPane.showMessageDialog(peptideShakerGUI, "mzIdentML conversion cancelled by the user.", "mzIdentML Conversion Cancelled", JOptionPane.WARNING_MESSAGE);
            }
        }
    }.start();
}

Example 3 with ProjectDetails

use of eu.isas.peptideshaker.preferences.ProjectDetails in project peptide-shaker by compomics.

the class MzIdentMLExportDialog method insertProjectData.

/**
 * Insert the available project data.
 */
private void insertProjectData() {
    ProjectDetails projectDetails = peptideShakerGUI.getProjectDetails();
    // use the saved mzIdentML annotation, if any
    contactFirstNameJTextField.setText(projectDetails.getContactFirstName());
    contactLastNameJTextField.setText(projectDetails.getContactLastName());
    contactEmailJTextField.setText(projectDetails.getContactEmail());
    contactAddressJTextField.setText(projectDetails.getContactAddress());
    contactUrlJTextField.setText(projectDetails.getContactUrl());
    organizationNameJTextField.setText(projectDetails.getOrganizationName());
    organizationEmailJTextField.setText(projectDetails.getOrganizationEmail());
    organizationAddressJTextField.setText(projectDetails.getOrganizationAddress());
    organizationUrlJTextField.setText(projectDetails.getOrganizationUrl());
    includeSequencesCheckBox.setSelected(projectDetails.getIncludeProteinSequences());
    if (projectDetails.getMzIdentMLOutputFile() != null && new File(projectDetails.getMzIdentMLOutputFile()).exists()) {
        outputFolderJTextField.setText(projectDetails.getMzIdentMLOutputFile());
    }
}

Example 4 with ProjectDetails

use of eu.isas.peptideshaker.preferences.ProjectDetails in project peptide-shaker by compomics.

the class CLIExportMethods method exportMzId.

/**
 * Exports the project in the mzIdentML format.
 *
 * @param mzidCLIInputBean the user input
 * @param psbdParent a psbd file parent allowing accessing the information it
 * contains
 * @param waitingHandler a waiting handler allowing display of progress and
 * interruption of the export
 *
 * @throws IOException exception thrown whenever an IO exception occurred
 * while reading or writing to a file
 */
public static void exportMzId(MzidCLIInputBean mzidCLIInputBean, PsdbParent psbdParent, WaitingHandler waitingHandler) throws IOException {
    ProjectDetails projectDetails = psbdParent.getProjectDetails();
    projectDetails.setContactFirstName(mzidCLIInputBean.getContactFirstName());
    projectDetails.setContactLastName(mzidCLIInputBean.getContactLastName());
    projectDetails.setContactEmail(mzidCLIInputBean.getContactEmail());
    projectDetails.setContactAddress(mzidCLIInputBean.getContactAddress());
    projectDetails.setContactUrl(mzidCLIInputBean.getContactUrl());
    projectDetails.setOrganizationName(mzidCLIInputBean.getOrganizationName());
    projectDetails.setOrganizationEmail(mzidCLIInputBean.getOrganizationMail());
    projectDetails.setOrganizationAddress(mzidCLIInputBean.getOrganizationAddress());
    projectDetails.setOrganizationUrl(mzidCLIInputBean.getOrganizationUrl());
    projectDetails.setIncludeProteinSequences(mzidCLIInputBean.getIncludeProteinSequences());
    projectDetails.setPrideOutputFolder(mzidCLIInputBean.getOutputFile().getAbsolutePath());
    IdentificationParameters identificationParameters = psbdParent.getIdentificationParameters();
    FastaSummary fastaSummary = FastaSummary.getSummary(projectDetails.getFastaFile(), identificationParameters.getFastaParameters(), waitingHandler);
    MzIdentMLExport mzIdentMLExport = new MzIdentMLExport(PeptideShaker.getVersion(), psbdParent.getIdentification(), psbdParent.getProjectDetails(), identificationParameters, psbdParent.getSequenceProvider(), psbdParent.getProteinDetailsProvider(), psbdParent.getSpectrumProvider(), ModificationFactory.getInstance(), fastaSummary, psbdParent.getIdentificationFeaturesGenerator(), mzidCLIInputBean.getOutputFile(), mzidCLIInputBean.getIncludeProteinSequences(), waitingHandler, mzidCLIInputBean.isGzip());
    mzIdentMLExport.createMzIdentMLFile(mzidCLIInputBean.getMzIdentMLVersion());
}

Example 5 with ProjectDetails

use of eu.isas.peptideshaker.preferences.ProjectDetails in project peptide-shaker by compomics.

the class PsSearchParametersSection method writeSection.

/**
 * Writes the desired section.
 *
 * @param searchParameters the search parameters of this project
 * @param projectDetails the project details
 * @param waitingHandler the waiting handler
 * @throws IOException exception thrown whenever an error occurred while
 * writing the file
 */
public void writeSection(SearchParameters searchParameters, ProjectDetails projectDetails, 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 (PsSearchFeature exportFeature : searchFeatures) {
        if (indexes) {
            writer.write(Integer.toString(line));
            writer.addSeparator();
        }
        writer.write(exportFeature.getTitle());
        writer.addSeparator();
        switch(exportFeature) {
            case database:
                String fastaFileName = IoUtil.getFileName(projectDetails.getFastaFile());
                writer.write(fastaFileName);
                break;
            case cleavage:
                DigestionParameters digestionPreferences = searchParameters.getDigestionParameters();
                writer.write(digestionPreferences.getCleavageParameter().toString());
                break;
            case enzyme:
                digestionPreferences = searchParameters.getDigestionParameters();
                if (digestionPreferences.getCleavageParameter() == DigestionParameters.CleavageParameter.enzyme) {
                    String enzymeString = digestionPreferences.getEnzymes().stream().map(enzyme -> enzyme.getName()).collect(Collectors.joining(", "));
                    writer.write(enzymeString);
                }
                break;
            case mc:
                digestionPreferences = searchParameters.getDigestionParameters();
                if (digestionPreferences.getCleavageParameter() == DigestionParameters.CleavageParameter.enzyme) {
                    String nMissedCleavagesString = digestionPreferences.getEnzymes().stream().map(enzyme -> digestionPreferences.getnMissedCleavages(enzyme.getName()).toString()).collect(Collectors.joining(", "));
                    writer.write(nMissedCleavagesString);
                }
                break;
            case specificity:
                digestionPreferences = searchParameters.getDigestionParameters();
                if (digestionPreferences.getCleavageParameter() == DigestionParameters.CleavageParameter.enzyme) {
                    String specificityString = digestionPreferences.getEnzymes().stream().map(enzyme -> digestionPreferences.getSpecificity(enzyme.getName()).name).collect(Collectors.joining(", "));
                    writer.write(specificityString);
                }
                break;
            case fixed_modifications:
                writer.write(searchParameters.getModificationParameters().getFixedModifications().stream().collect(Collectors.joining(", ")));
                break;
            case variable_modifications:
                writer.write(searchParameters.getModificationParameters().getVariableModifications().stream().collect(Collectors.joining(", ")));
                break;
            case refinement_variable_modifications:
                writer.write(searchParameters.getModificationParameters().getRefinementVariableModifications().stream().collect(Collectors.joining(", ")));
                break;
            case refinement_fixed_modifications:
                writer.write(searchParameters.getModificationParameters().getRefinementFixedModifications().stream().collect(Collectors.joining(", ")));
                break;
            case forward_ion:
                writer.write(searchParameters.getForwardIons().stream().map(ion -> ion.toString()).collect(Collectors.joining(", ")));
                break;
            case rewind_ion:
                writer.write(searchParameters.getRewindIons().stream().map(ion -> ion.toString()).collect(Collectors.joining(", ")));
                break;
            case fragment_tolerance:
                writer.write(Double.toString(searchParameters.getFragmentIonAccuracy()));
                break;
            case precursor_tolerance_unit:
                writer.write(searchParameters.getPrecursorAccuracyType().toString());
                break;
            case fragment_tolerance_unit:
                writer.write(searchParameters.getFragmentAccuracyType().toString());
                break;
            case precursor_tolerance:
                writer.write(Double.toString(searchParameters.getPrecursorAccuracy()));
                break;
            default:
                writer.write("Not implemented");
        }
        writer.newLine();
        line++;
    }
}