Examples with ValidationQcParameters com.compomics.util.parameters.identification.advanced.ValidationQcParameters used on opensource projects

Example 1 with ValidationQcParameters

use of com.compomics.util.parameters.identification.advanced.ValidationQcParameters in project peptide-shaker by compomics.

the class NewDialog method setIdentificationParameters.

/**
 * Sets the search parameters in the identification parameters and updates
 * the GUI.
 *
 * @param newIdentificationParameters the new identification parameters
 */
private void setIdentificationParameters(IdentificationParameters newIdentificationParameters) {
    try {
        ValidationQcParameters validationQcParameters = newIdentificationParameters.getIdValidationParameters().getValidationQCParameters();
        if (validationQcParameters == null || validationQcParameters.getPsmFilters() == null || validationQcParameters.getPeptideFilters() == null || validationQcParameters.getProteinFilters() == null || validationQcParameters.getPsmFilters().isEmpty() && validationQcParameters.getPeptideFilters().isEmpty() && validationQcParameters.getProteinFilters().isEmpty()) {
            MatchesValidator.setDefaultMatchesQCFilters(validationQcParameters);
            identificationParametersFactory.addIdentificationParameters(newIdentificationParameters);
        }
        this.identificationParameters = newIdentificationParameters;
        Vector parameterList = new Vector();
        parameterList.add("-- Select --");
        for (String tempParameters : identificationParametersFactory.getParametersList()) {
            parameterList.add(tempParameters);
        }
        settingsComboBox.setModel(new javax.swing.DefaultComboBoxModel(parameterList));
        settingsComboBox.setSelectedItem(identificationParameters.getName());
    } catch (Exception e) {
        JOptionPane.showMessageDialog(null, "Failed to import identification parameters from: " + newIdentificationParameters.getName() + ".", "Identification Parameters", JOptionPane.WARNING_MESSAGE);
        e.printStackTrace();
        // set the search settings to default
        this.identificationParameters = null;
    }
    validateInput();
}

Example 2 with ValidationQcParameters

use of com.compomics.util.parameters.identification.advanced.ValidationQcParameters in project peptide-shaker by compomics.

the class PeptideShakerCLI method createProject.

/**
 * Creates the PeptideShaker project based on the identification files
 * provided in the command line input
 *
 * @throws java.io.IOException exception thrown if an error occurs while
 * reading or writing a file
 * @throws java.lang.InterruptedException exception thrown if a thread is
 * interrupted
 * @throws java.util.concurrent.TimeoutException exception thrown if a
 * process times out
 */
public void createProject() throws IOException, InterruptedException, TimeoutException {
    // define new project reference
    projectParameters = new ProjectParameters(cliInputBean.getExperimentID());
    // set the project details
    projectDetails = new ProjectDetails();
    projectDetails.setCreationDate(new Date());
    projectDetails.setPeptideShakerVersion(new Properties().getVersion());
    // set up spectrum provider
    msFileHandler = new MsFileHandler();
    // get the input files
    ArrayList<File> identificationFilesInput = cliInputBean.getIdFiles();
    ArrayList<File> dataFolders = new ArrayList<>();
    ArrayList<File> spectrumFiles = cliInputBean.getSpectrumFiles();
    File fastaFile = null;
    // Extract data from zip files, try to find the search parameter and spectrum files
    ArrayList<File> identificationFiles = new ArrayList<>();
    IdentificationParameters tempIdentificationParameters = null;
    for (File inputFile : identificationFilesInput) {
        File parentFile = inputFile.getParentFile();
        if (!dataFolders.contains(parentFile)) {
            dataFolders.add(parentFile);
        }
        File dataFolder = new File(parentFile, "mgf");
        if (dataFolder.exists() && !dataFolders.contains(dataFolder)) {
            dataFolders.add(dataFolder);
        }
        dataFolder = new File(parentFile, "mzml");
        if (dataFolder.exists() && !dataFolders.contains(dataFolder)) {
            dataFolders.add(dataFolder);
        }
        dataFolder = new File(parentFile, "cms");
        if (dataFolder.exists() && !dataFolders.contains(dataFolder)) {
            dataFolders.add(dataFolder);
        }
        dataFolder = new File(parentFile, "fasta");
        if (dataFolder.exists() && !dataFolders.contains(dataFolder)) {
            dataFolders.add(dataFolder);
        }
        dataFolder = new File(parentFile, PeptideShaker.DATA_DIRECTORY);
        if (dataFolder.exists() && !dataFolders.contains(dataFolder)) {
            dataFolders.add(dataFolder);
        }
        String fileName = inputFile.getName();
        if (fileName.toLowerCase().endsWith(".zip")) {
            waitingHandler.appendReport("Unzipping " + fileName + ".", true, true);
            String newName = PsZipUtils.getTempFolderName(fileName);
            String parentFolder = PsZipUtils.getUnzipParentFolder();
            if (parentFolder == null) {
                parentFolder = parentFile.getAbsolutePath();
            }
            File parentFolderFile = new File(parentFolder, PsZipUtils.getUnzipSubFolder());
            File destinationFolder = new File(parentFolderFile, newName);
            destinationFolder.mkdir();
            TempFilesManager.registerTempFolder(parentFolderFile);
            ZipUtils.unzip(inputFile, destinationFolder, waitingHandler);
            if (waitingHandler instanceof WaitingHandlerCLIImpl) {
                waitingHandler.appendReportEndLine();
            }
            dataFolder = new File(destinationFolder, PeptideShaker.DATA_DIRECTORY);
            if (dataFolder.exists() && !dataFolders.contains(dataFolder)) {
                dataFolders.add(dataFolder);
            }
            dataFolder = new File(destinationFolder, ".mgf");
            if (dataFolder.exists() && !dataFolders.contains(dataFolder)) {
                dataFolders.add(dataFolder);
            }
            dataFolder = new File(parentFile, "mzml");
            if (dataFolder.exists() && !dataFolders.contains(dataFolder)) {
                dataFolders.add(dataFolder);
            }
            dataFolder = new File(destinationFolder, ".cms");
            if (dataFolder.exists() && !dataFolders.contains(dataFolder)) {
                dataFolders.add(dataFolder);
            }
            dataFolder = new File(destinationFolder, ".fasta");
            if (dataFolder.exists() && !dataFolders.contains(dataFolder)) {
                dataFolders.add(dataFolder);
            }
            for (File unzippedFile : destinationFolder.listFiles()) {
                String nameLowerCase = unzippedFile.getName().toLowerCase();
                if (nameLowerCase.endsWith(".omx") || nameLowerCase.endsWith(".t.xml") || nameLowerCase.endsWith(".pep.xml") || nameLowerCase.endsWith(".dat") || nameLowerCase.endsWith(".mzid") || nameLowerCase.endsWith(".ms-amanda.csv") || nameLowerCase.endsWith(".res") || nameLowerCase.endsWith(".tide-search.target.txt") || nameLowerCase.endsWith(".tags") || nameLowerCase.endsWith(".pnovo.txt") || nameLowerCase.endsWith(".novor.csv") || nameLowerCase.endsWith(".psm") || nameLowerCase.endsWith(".omx.gz") || nameLowerCase.endsWith(".t.xml.gz") || nameLowerCase.endsWith(".pep.xml.gz") || nameLowerCase.endsWith(".mzid.gz") || nameLowerCase.endsWith(".ms-amanda.csv.gz") || nameLowerCase.endsWith(".res.gz") || nameLowerCase.endsWith(".tide-search.target.txt.gz") || nameLowerCase.endsWith(".tags.gz") || nameLowerCase.endsWith(".pnovo.txt.gz") || nameLowerCase.endsWith(".novor.csv.gz") || nameLowerCase.endsWith(".psm.gz")) {
                    identificationFiles.add(unzippedFile);
                } else if (nameLowerCase.endsWith(".par")) {
                    try {
                        tempIdentificationParameters = IdentificationParameters.getIdentificationParameters(unzippedFile);
                        ValidationQcParameters validationQCParameters = tempIdentificationParameters.getIdValidationParameters().getValidationQCParameters();
                        if (validationQCParameters == null || validationQCParameters.getPsmFilters() == null || validationQCParameters.getPeptideFilters() == null || validationQCParameters.getProteinFilters() == null || validationQCParameters.getPsmFilters().isEmpty() && validationQCParameters.getPeptideFilters().isEmpty() && validationQCParameters.getProteinFilters().isEmpty()) {
                            MatchesValidator.setDefaultMatchesQCFilters(validationQCParameters);
                        }
                    } catch (Exception e) {
                        e.printStackTrace();
                        waitingHandler.appendReport("An error occurred while parsing the parameters file " + unzippedFile.getName() + ". " + getLogFileMessage(), true, true);
                        waitingHandler.setRunCanceled();
                    }
                }
            }
        } else {
            identificationFiles.add(inputFile);
        }
    }
    // list the spectrum files found
    HashSet<String> dataFileNamesRequired = new HashSet<>();
    for (File spectrumFile : spectrumFiles) {
        dataFileNamesRequired.add(IoUtil.getFileName(spectrumFile));
    }
    for (File dataFolder : dataFolders) {
        for (File file : dataFolder.listFiles()) {
            String name = file.getName();
            if (name.endsWith(".mgf") || name.endsWith(".mgf.gz") || name.endsWith(".mzml") || name.endsWith(".mzml.gz") || name.endsWith(".cms")) {
                if (!dataFileNamesRequired.contains(name)) {
                    spectrumFiles.add(file);
                    dataFileNamesRequired.add(name);
                }
            } else if (name.endsWith(".fasta")) {
                if (!dataFileNamesRequired.contains(name)) {
                    fastaFile = file;
                    dataFileNamesRequired.add(name);
                }
            }
        }
    }
    // Load the spectrum files
    for (File spectrumFile : spectrumFiles) {
        File folder = CmsFolder.getParentFolder() == null ? spectrumFile.getParentFile() : new File(CmsFolder.getParentFolder());
        msFileHandler.register(spectrumFile, folder, waitingHandler);
    }
    // If there is a specific fasta file chosen, it is used insted of the one included in the searchgui zip
    if (cliInputBean.getFastaFile() != null) {
        fastaFile = cliInputBean.getFastaFile();
    }
    // get the identification parameters
    IdentificationParametersInputBean identificationParametersInputBean = cliInputBean.getIdentificationParametersInputBean();
    if (tempIdentificationParameters != null && identificationParametersInputBean.getInputFile() == null) {
        identificationParametersInputBean.setIdentificationParameters(tempIdentificationParameters);
        identificationParametersInputBean.updateIdentificationParameters();
    }
    identificationParameters = identificationParametersInputBean.getIdentificationParameters();
    ValidationQcParameters validationQCParameters = identificationParameters.getIdValidationParameters().getValidationQCParameters();
    if (validationQCParameters == null || validationQCParameters.getPsmFilters() == null || validationQCParameters.getPeptideFilters() == null || validationQCParameters.getProteinFilters() == null || validationQCParameters.getPsmFilters().isEmpty() && validationQCParameters.getPeptideFilters().isEmpty() && validationQCParameters.getProteinFilters().isEmpty()) {
        MatchesValidator.setDefaultMatchesQCFilters(validationQCParameters);
    }
    if (identificationParameters == null) {
        waitingHandler.appendReport("Identification parameters not found!", true, true);
        waitingHandler.setRunCanceled();
    }
    SearchParameters searchParameters = identificationParameters.getSearchParameters();
    String error = PeptideShaker.loadModifications(searchParameters);
    if (error != null) {
        System.out.println(error);
    }
    // try to locate the fasta file
    if (fastaFile == null) {
        waitingHandler.appendReport("FASTA file not set (or not in zip file)!", true, true);
        waitingHandler.setRunCanceled();
    } else if (!fastaFile.exists()) {
        boolean found = false;
        // look in the database folder
        try {
            File tempDbFolder = utilitiesUserParameters.getDbFolder();
            File newFile = new File(tempDbFolder, fastaFile.getName());
            if (newFile.exists()) {
                fastaFile = newFile;
                projectDetails.setFastaFile(fastaFile);
                found = true;
            }
        } catch (Exception e) {
            e.printStackTrace();
        }
        if (!found) {
            // look in the data folders
            for (File dataFolder : dataFolders) {
                File newFile = new File(dataFolder, fastaFile.getName());
                if (newFile.exists()) {
                    fastaFile = newFile;
                    projectDetails.setFastaFile(fastaFile);
                    found = true;
                    break;
                }
            }
            if (!found) {
                waitingHandler.appendReport("FASTA file \'" + fastaFile.getName() + "\' not found.", true, true);
                waitingHandler.setRunCanceled();
            }
        }
    } else {
        projectDetails.setFastaFile(fastaFile);
    }
    // get the summary information for the FASTA file
    try {
        // get the FASTA summary
        FastaSummary fastaSummary = loadFastaFile(waitingHandler);
        // set the background species
        identificationParameters.getGeneParameters().setBackgroundSpeciesFromFastaSummary(fastaSummary);
    } catch (IOException e) {
        e.printStackTrace();
        waitingHandler.appendReport("An error occurred while parsing the FASTA file.", true, true);
        waitingHandler.setRunCanceled();
    }
    // set the processing settings
    ProcessingParameters processingParameters = new ProcessingParameters();
    Integer nThreads = cliInputBean.getnThreads();
    if (nThreads != null) {
        processingParameters.setnThreads(nThreads);
    }
    // set the spectrum counting prefrences
    spectrumCountingParameters = new SpectrumCountingParameters();
    // set the project type
    projectType = cliInputBean.getProjectType();
    // check the project reference
    for (String forbiddenChar : Util.FORBIDDEN_CHARACTERS) {
        if (cliInputBean.getExperimentID().contains(forbiddenChar)) {
            waitingHandler.appendReport("The project name cannot not contain " + forbiddenChar + ".", true, true);
            waitingHandler.setRunCanceled();
        }
    }
    // incrementing the counter for a new PeptideShaker start run via CLI
    if (utilitiesUserParameters.isAutoUpdate()) {
        Util.sendGAUpdate("UA-36198780-1", "startrun-cl", "peptide-shaker-" + PeptideShaker.getVersion());
    }
    // create a shaker which will perform the analysis
    PeptideShaker peptideShaker = new PeptideShaker(projectParameters);
    // import the files
    int outcome = peptideShaker.importFiles(waitingHandler, identificationFiles, msFileHandler, identificationParameters, projectDetails, processingParameters, exceptionHandler);
    if (outcome == 0) {
        peptideShaker.createProject(identificationParameters, processingParameters, spectrumCountingParameters, msFileHandler, projectDetails, projectType, waitingHandler, false, exceptionHandler);
    }
    if (!waitingHandler.isRunCanceled()) {
        // identification as created by PeptideShaker
        identification = peptideShaker.getIdentification();
        // metrics saved while processing the data
        metrics = peptideShaker.getMetrics();
        // fene maps
        geneMaps = peptideShaker.getGeneMaps();
        // the identification feature generator
        identificationFeaturesGenerator = peptideShaker.getIdentificationFeaturesGenerator();
        // the sequence provider
        sequenceProvider = peptideShaker.getSequenceProvider();
        // the protein details provider
        proteinDetailsProvider = peptideShaker.getProteinDetailsProvider();
        if (waitingHandler instanceof WaitingDialog) {
            projectDetails.setReport(((WaitingDialog) waitingHandler).getReport(null));
            ((WaitingDialog) waitingHandler).setRunNotFinished();
            ((WaitingDialog) waitingHandler).setCloseDialogWhenImportCompletes(true, false);
        }
    } else {
        if (waitingHandler instanceof WaitingDialog) {
            saveReport();
        }
        TempFilesManager.deleteTempFolders();
        waitingHandler.setWaitingText("PeptideShaker Processing Canceled.");
        System.out.println("<CompomicsError>PeptideShaker processing canceled. " + getLogFileMessage() + "</CompomicsError>");
    }
}

Example 3 with ValidationQcParameters

use of com.compomics.util.parameters.identification.advanced.ValidationQcParameters in project peptide-shaker by compomics.

the class MatchValidationDialog method populateGUI.

/**
 * Populates the GUI with information on a protein match.
 *
 * @param identificationFeaturesGenerator
 * @param proteinMap
 */
private void populateGUI(TargetDecoyMap targetDecoyMap) {
    ValidationQcParameters validationQCPreferences = identificationParameters.getIdValidationParameters().getValidationQCParameters();
    // Validation level
    validationLevelJComboBox.setSelectedItem(psParameter.getMatchValidationLevel().getName());
    // Database info
    FastaParameters fastaParameters = identificationParameters.getFastaParameters();
    boolean targetDecoy = fastaParameters.isTargetDecoy();
    if (!targetDecoy) {
        targetDecoyLbl.setText("Target only");
        targetDecoyLbl.setForeground(Color.red);
    } else {
        targetDecoyLbl.setForeground(GREEN);
    }
    try {
        FastaSummary fastaSummary = FastaSummary.getSummary(fastaFile, fastaParameters, null);
        int nTarget = fastaSummary.nTarget;
        nTargetLbl.setText(nTarget + " target sequences");
        if (nTarget < 10000) {
            nTargetLbl.setForeground(Color.red);
        } else if (nTarget > 1000000) {
            nTargetLbl.setForeground(ORANGE);
        } else {
            nTargetLbl.setForeground(GREEN);
        }
    } catch (IOException iOException) {
        nTargetLbl.setText("Database size not available");
        nTargetLbl.setForeground(Color.red);
    }
    // Target/Decoy group
    ((TitledBorder) targetDecoyGroupPanel.getBorder()).setTitle("Target/Decoy Distributions");
    targetDecoyGroupPanel.repaint();
    if (targetDecoy) {
        int nTargetOnly = targetDecoyMap.getnTargetOnly();
        matchesBeforeFirstDecoyLbl.setText(nTargetOnly + " matches before the first decoy hit");
        TargetDecoyResults targetDecoyResults = targetDecoyMap.getTargetDecoyResults();
        double desiredThreshold = targetDecoyResults.getUserInput();
        double nTargetLimit = 100.0 / desiredThreshold;
        if (nTargetOnly < nTargetLimit) {
            matchesBeforeFirstDecoyLbl.setForeground(Color.red);
        } else {
            matchesBeforeFirstDecoyLbl.setForeground(GREEN);
        }
        recommendedNumberOfTargetHitsLbl.setText("Recommended: " + Util.roundDouble(nTargetLimit, 0) + " matches before the first decoy hit");
        double resolution = targetDecoyMap.getResolution();
        confidenceResolutionLbl.setText("PEP/Confidence resolution of " + Util.roundDouble(resolution, 2) + "%");
        double minResolution = desiredThreshold;
        if (resolution > 10 * minResolution) {
            confidenceResolutionLbl.setForeground(Color.red);
        } else if (resolution > minResolution) {
            confidenceResolutionLbl.setForeground(ORANGE);
        } else {
            confidenceResolutionLbl.setForeground(GREEN);
        }
        recommendedResolutionLbl.setText("Recommended: resolution < " + Util.roundDouble(minResolution, 2) + "%");
    } else {
        matchesBeforeFirstDecoyLbl.setText("No decoy");
        matchesBeforeFirstDecoyLbl.setForeground(Color.gray);
        confidenceResolutionLbl.setText("Impossible to estimate confidence resolution");
        confidenceResolutionLbl.setForeground(Color.gray);
    }
    // Target/decoy results
    if (targetDecoy) {
        double confidence = psParameter.getConfidence();
        MatchValidationLevel matchValidationLevel = psParameter.getMatchValidationLevel();
        validationStatusLbl.setText("Validation Status: " + matchValidationLevel.getName());
        switch(matchValidationLevel) {
            case confident:
                validationStatusLbl.setForeground(GREEN);
                break;
            case doubtful:
                validationStatusLbl.setForeground(ORANGE);
                break;
            case not_validated:
                validationStatusLbl.setForeground(Color.red);
                break;
            case none:
                validationStatusLbl.setForeground(Color.gray);
        }
        TargetDecoyResults targetDecoyResults = targetDecoyMap.getTargetDecoyResults();
        String validationThresholdTxt = "";
        double threshold = targetDecoyResults.getUserInput();
        int thresholdType = targetDecoyResults.getInputType();
        if (thresholdType == 0) {
            validationThresholdTxt += "Validation Threshold: " + Util.roundDouble(threshold, 2) + "%";
        } else if (targetDecoyResults.getInputType() == 1) {
            validationThresholdTxt += "FDR Threshold: " + Util.roundDouble(threshold, 2) + "%";
        } else if (targetDecoyResults.getInputType() == 2) {
            validationThresholdTxt += "FNR Threshold: " + Util.roundDouble(threshold, 2) + "%";
        }
        validationThresholdLbl.setText(validationThresholdTxt);
        confidenceLbl.setText("Confidence: " + Util.roundDouble(confidence, 2) + "%");
        double validationThreshold = targetDecoyResults.getConfidenceLimit();
        confidenceThresholdLbl.setText("Expected Confidence: " + Util.roundDouble(validationThreshold, 2) + "%");
        double margin = validationQCPreferences.getConfidenceMargin() * targetDecoyMap.getResolution();
        double confidenceThreshold = validationThreshold + margin;
        if (confidenceThreshold > 100) {
            confidenceThreshold = 100;
        }
        confidenceThresholdLbl.setText("Confident confidence: " + Util.roundDouble(confidenceThreshold, 2) + "%");
        if (confidence < validationThreshold) {
            confidenceLbl.setForeground(Color.red);
        } else if (confidence < confidenceThreshold) {
            confidenceLbl.setForeground(ORANGE);
        } else {
            confidenceLbl.setForeground(GREEN);
        }
    } else {
        validationStatusLbl.setText("Validation Status: " + psParameter.getMatchValidationLevel().getName());
        validationThresholdLbl.setText("Impossible to estimate validation threshold");
        confidenceLbl.setText("Impossible to estimate confidence");
        confidenceThresholdLbl.setText("Impossible to estimate confidence threshold");
        validationStatusLbl.setForeground(Color.gray);
        confidenceLbl.setForeground(Color.gray);
    }
    // Quality filters
    final DefaultTableModel tableModel = new FiltersTableModel();
    qualityFiltersTable.setModel(tableModel);
    qualityFiltersTable.getColumn("").setMaxWidth(50);
    qualityFiltersTable.getColumn(" ").setMaxWidth(50);
    qualityFiltersTable.getColumn(" ").setCellRenderer(new TrueFalseIconRenderer(new ImageIcon(this.getClass().getResource("/icons/accept-new.png")), new ImageIcon(this.getClass().getResource("/icons/error-new.png")), "Yes", "No"));
    int valid = 0;
    for (String qcCheck : psParameter.getQcCriteria()) {
        if (psParameter.isQcPassed(qcCheck)) {
            valid++;
        }
    }
    ((TitledBorder) qualityFiltersPanel.getBorder()).setTitle("Quality Filters (" + valid + "/" + psParameter.getQcCriteria().size() + ")");
}

Example 4 with ValidationQcParameters

use of com.compomics.util.parameters.identification.advanced.ValidationQcParameters in project peptide-shaker by compomics.

the class NewDialog method importSearchParameters.

/**
 * Imports the search parameters from a file.
 *
 * @param file the selected searchGUI file
 * @param dataFolders folders where to look for the FASTA file
 * @param progressDialog the progress dialog
 *
 * @throws java.io.IOException exception thrown whenever an error occurred
 * while importing the search parameters
 * @throws java.io.FileNotFoundException exception thrown whenever an error
 * occurred while importing the search parameters
 * @throws java.lang.ClassNotFoundException exception thrown whenever an
 * error occurred while importing the search parameters
 */
public void importSearchParameters(File file, ArrayList<File> dataFolders, ProgressDialogX progressDialog) throws IOException, FileNotFoundException, ClassNotFoundException {
    progressDialog.setTitle("Importing Search Parameters. Please Wait...");
    IdentificationParameters tempIdentificationParameters = IdentificationParameters.getIdentificationParameters(file);
    SearchParameters searchParameters = tempIdentificationParameters.getSearchParameters();
    String toCheck = PeptideShaker.loadModifications(searchParameters);
    if (toCheck != null) {
        JOptionPane.showMessageDialog(this, toCheck, "Modification Definition Changed", JOptionPane.WARNING_MESSAGE);
    }
    ModificationParameters modificationProfile = searchParameters.getModificationParameters();
    ArrayList<String> missing = new ArrayList<>();
    for (String name : modificationProfile.getAllModifications()) {
        if (!modificationFactory.containsModification(name)) {
            missing.add(name);
            Modification mod = modificationFactory.getModification(name);
            mod.getMass();
        } else if (!modificationProfile.contains(name)) {
            modificationProfile.setColor(name, Color.lightGray.getRGB());
        }
    }
    if (!missing.isEmpty()) {
        if (missing.size() == 1) {
            JOptionPane.showMessageDialog(this, "The following modification is currently not recognized by PeptideShaker: " + missing.get(0) + ".\nPlease import it by editing the search parameters.", "Modification Not Found", JOptionPane.WARNING_MESSAGE);
        } else {
            String output = "The following modifications are currently not recognized by PeptideShaker:\n" + String.join(", ", missing) + ".\nPlease import it by editing the search parameters.";
            JOptionPane.showMessageDialog(this, output, "Modification Not Found", JOptionPane.WARNING_MESSAGE);
        }
    }
    boolean matchesValidationAdded;
    ValidationQcParameters validationQcParameters = tempIdentificationParameters.getIdValidationParameters().getValidationQCParameters();
    if (validationQcParameters == null || validationQcParameters.getPsmFilters() == null || validationQcParameters.getPeptideFilters() == null || validationQcParameters.getProteinFilters() == null || validationQcParameters.getPsmFilters().isEmpty() && validationQcParameters.getPeptideFilters().isEmpty() && validationQcParameters.getProteinFilters().isEmpty()) {
        MatchesValidator.setDefaultMatchesQCFilters(validationQcParameters);
        matchesValidationAdded = true;
    } else {
        matchesValidationAdded = false;
    }
    if (!identificationParametersFactory.getParametersList().contains(tempIdentificationParameters.getName())) {
        identificationParametersFactory.addIdentificationParameters(tempIdentificationParameters);
    } else {
        boolean parametersChanged = !identificationParametersFactory.getIdentificationParameters(tempIdentificationParameters.getName()).equals(tempIdentificationParameters);
        if (parametersChanged && !matchesValidationAdded) {
            int value = JOptionPane.showOptionDialog(null, "A settings file with the name \'" + tempIdentificationParameters.getName() + "\' already exists.\n" + "What do you want to do?", "Identification Settings", JOptionPane.YES_NO_CANCEL_OPTION, JOptionPane.QUESTION_MESSAGE, null, new String[] { "Replace File", "Use Existing File", "Keep Both Files" }, "default");
            switch(value) {
                case JOptionPane.YES_OPTION:
                    identificationParametersFactory.addIdentificationParameters(tempIdentificationParameters);
                    break;
                case JOptionPane.NO_OPTION:
                    tempIdentificationParameters = identificationParametersFactory.getIdentificationParameters(tempIdentificationParameters.getName());
                    break;
                case JOptionPane.CANCEL_OPTION:
                    tempIdentificationParameters.setName(getIdentificationSettingsFileName(tempIdentificationParameters));
                    identificationParametersFactory.addIdentificationParameters(tempIdentificationParameters);
                    break;
                default:
                    break;
            }
        } else if (matchesValidationAdded) {
            identificationParametersFactory.addIdentificationParameters(tempIdentificationParameters);
        }
    }
    setIdentificationParameters(tempIdentificationParameters);
}

Example 5 with ValidationQcParameters

use of com.compomics.util.parameters.identification.advanced.ValidationQcParameters in project peptide-shaker by compomics.

the class PeptideShakerGUI method validationQcMenuItemActionPerformed.

// GEN-LAST:event_configurationFilesSettingsActionPerformed
/**
 * Open the ValidationQCPreferencesDialog.
 *
 * @param evt
 */
private void validationQcMenuItemActionPerformed(java.awt.event.ActionEvent evt) {
    // GEN-FIRST:event_validationQcMenuItemActionPerformed
    final IdMatchValidationParameters idValidationParameters = getIdentificationParameters().getIdValidationParameters();
    final ValidationQcParameters validationQCParameters = idValidationParameters.getValidationQCParameters();
    ValidationQCParametersDialog validationQCParametersDialog = new ValidationQCParametersDialog(this, validationQCParameters, getIdentificationParameters().getSearchParameters().getModificationParameters().getAllModifications(), true);
    if (!validationQCParametersDialog.isCanceled()) {
        ValidationQcParameters newParameters = validationQCParametersDialog.getValidationQCParameters();
        if (!newParameters.isSameAs(validationQCParameters)) {
            idValidationParameters.setValidationQCParameters(newParameters);
            // Update the assumptions QC filters
            for (Filter filter : newParameters.getPsmFilters()) {
                PsmFilter psmFilter = (PsmFilter) filter;
                AssumptionFilter assumptionFilter = psmFilter.getAssumptionFilter();
                assumptionFilter.clear();
                for (String itemName : psmFilter.getItemsNames()) {
                    assumptionFilter.setFilterItem(itemName, psmFilter.getComparatorForItem(itemName), psmFilter.getValue(itemName));
                }
            }
            progressDialog = new ProgressDialogX(PeptideShakerGUI.this, Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/peptide-shaker.gif")), Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/peptide-shaker-orange.gif")), true);
            progressDialog.setTitle("Validating. Please Wait...");
            progressDialog.setPrimaryProgressCounterIndeterminate(false);
            new Thread(new Runnable() {

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

                @Override
                public void run() {
                    PeptideShakerGUI peptideShakerGUI = PeptideShakerGUI.this;
                    try {
                        PSMaps pSMaps = new PSMaps();
                        pSMaps = (PSMaps) peptideShakerGUI.getIdentification().getUrParam(pSMaps);
                        MatchesValidator matchesValidator = new MatchesValidator(pSMaps.getPsmMap(), pSMaps.getPeptideMap(), pSMaps.getProteinMap());
                        matchesValidator.validateIdentifications(peptideShakerGUI.getIdentification(), peptideShakerGUI.getMetrics(), pSMaps.getInputMap(), progressDialog, exceptionHandler, peptideShakerGUI.getIdentificationFeaturesGenerator(), peptideShakerGUI.getSequenceProvider(), peptideShakerGUI.getProteinDetailsProvider(), peptideShakerGUI.getSpectrumProvider(), peptideShakerGUI.getGeneMaps(), peptideShakerGUI.getIdentificationParameters(), peptideShakerGUI.getProjectType(), peptideShakerGUI.getProcessingParameters());
                        progressDialog.setPrimaryProgressCounterIndeterminate(true);
                        ProteinProcessor proteinProcessor = new ProteinProcessor(peptideShakerGUI.getIdentification(), peptideShakerGUI.getIdentificationParameters(), peptideShakerGUI.getIdentificationFeaturesGenerator(), peptideShakerGUI.getSequenceProvider());
                        proteinProcessor.processProteins(new ModificationLocalizationScorer(), peptideShakerGUI.getMetrics(), modificationFactory, progressDialog, peptideShakerGUI.getExceptionHandler(), peptideShakerGUI.getProcessingParameters());
                        if (!progressDialog.isRunCanceled()) {
                            // update the other tabs
                            peptideShakerGUI.getMetrics().setnValidatedProteins(-1);
                            peptideShakerGUI.getMetrics().setnConfidentProteins(-1);
                            peptideShakerGUI.setUpdated(PeptideShakerGUI.OVER_VIEW_TAB_INDEX, false);
                            peptideShakerGUI.setUpdated(PeptideShakerGUI.PROTEIN_FRACTIONS_TAB_INDEX, false);
                            peptideShakerGUI.setUpdated(PeptideShakerGUI.STRUCTURES_TAB_INDEX, false);
                            peptideShakerGUI.setUpdated(PeptideShakerGUI.MODIFICATIONS_TAB_INDEX, false);
                            peptideShakerGUI.setUpdated(PeptideShakerGUI.QC_PLOTS_TAB_INDEX, false);
                            peptideShakerGUI.setUpdated(PeptideShakerGUI.SPECTRUM_ID_TAB_INDEX, false);
                            peptideShakerGUI.setDataSaved(false);
                        } else {
                            idValidationParameters.setValidationQCParameters(validationQCParameters);
                        }
                    } catch (Exception e) {
                        peptideShakerGUI.catchException(e);
                    }
                    progressDialog.setRunFinished();
                    PeptideShakerGUI.this.repaintPanels();
                }
            }.start();
        }
    }
}