Examples with SpectrumCountingParameters com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters used on opensource projects

Example 1 with SpectrumCountingParameters

use of com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters in project peptide-shaker by compomics.

the class PeptideShakerGUI method preferencesMenuItemActionPerformed.

// GEN-LAST:event_openJMenuItemActionPerformed
/**
 * Open the GUI Settings dialog.
 *
 * @param evt
 */
private void preferencesMenuItemActionPerformed(java.awt.event.ActionEvent evt) {
    // GEN-FIRST:event_preferencesMenuItemActionPerformed
    ProjectParametersDialog projectParametersDialog = new ProjectParametersDialog(this, getSpectrumCountingParameters(), getDisplayParameters());
    if (!projectParametersDialog.isCanceled()) {
        // See if the spectrum counting preferences need to be updated
        SpectrumCountingParameters newSpectrumCountingParameters = projectParametersDialog.getSpectrumCountingParameters();
        if (!newSpectrumCountingParameters.isSameAs(getSpectrumCountingParameters())) {
            setSpectrumCountingParameters(newSpectrumCountingParameters);
            getIdentificationFeaturesGenerator().clearSpectrumCounting();
            setUpdated(PeptideShakerGUI.OVER_VIEW_TAB_INDEX, false);
            setUpdated(PeptideShakerGUI.STRUCTURES_TAB_INDEX, false);
            setUpdated(PeptideShakerGUI.QC_PLOTS_TAB_INDEX, false);
            updateTabbedPanes();
            setDataSaved(false);
        // @TODO: update the metrics if necessary
        }
        // See if the display preferences need to be updated
        DisplayParameters newDisplayParameters = projectParametersDialog.getDisplayParameters();
        // }
        if (newDisplayParameters.getnAASurroundingPeptides() != getDisplayParameters().getnAASurroundingPeptides()) {
            getDisplayParameters().setnAASurroundingPeptides(newDisplayParameters.getnAASurroundingPeptides());
            updateSurroundingAminoAcids();
        }
    }
}

Example 2 with SpectrumCountingParameters

use of com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters 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 SpectrumCountingParameters

use of com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters in project peptide-shaker by compomics.

the class SpectrumCountingSettingsDialog method getSpectrumCountingPreferences.

/**
 * Returns the spectrum counting preferences as set by the user.
 *
 * @return the spectrum counting preferences as set by the user
 */
public SpectrumCountingParameters getSpectrumCountingPreferences() {
    SpectrumCountingParameters spectrumCountingPreferences = new SpectrumCountingParameters();
    spectrumCountingPreferences.setSelectedMethod((SpectrumCountingMethod) methodCmb.getSelectedItem());
    spectrumCountingPreferences.setMatchValidationLevel(validationLevelCmb.getSelectedIndex());
    if (normalizationCmb.getSelectedIndex() == 0) {
        spectrumCountingPreferences.setNormalize(false);
    } else {
        spectrumCountingPreferences.setNormalize(true);
        spectrumCountingPreferences.setUnit((UnitOfMeasurement) unitCmb.getSelectedItem());
        if (normalizationCmb.getSelectedIndex() == 1) {
            Double value = Double.valueOf(referenceTxt.getText());
            spectrumCountingPreferences.setReferenceMass(value);
        }
    }
    return spectrumCountingPreferences;
}

Example 4 with SpectrumCountingParameters

use of com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters in project peptide-shaker by compomics.

the class PsdbParent method setDefaultParameters.

/**
 * Sets the default preferences.
 */
public void setDefaultParameters() {
    SearchParameters searchParameters = new SearchParameters();
    identificationParameters = new IdentificationParameters(searchParameters);
    spectrumCountingParameters = new SpectrumCountingParameters();
    spectrumCountingParameters.setSelectedMethod(SpectrumCountingMethod.NSAF);
    spectrumCountingParameters.setMatchValidationLevel(MatchValidationLevel.doubtful.getIndex());
}