Examples with ParameterSet net.sf.mzmine.parameters.ParameterSet used on opensource projects

Example 26 with ParameterSet

use of net.sf.mzmine.parameters.ParameterSet in project mzmine2 by mzmine.

the class ClusteringTask method run.

@Override
public void run() {
    status = TaskStatus.PROCESSING;
    logger.info("Clustering");
    double[][] rawData;
    if (typeOfData == ClusteringDataType.VARIABLES) {
        rawData = createMatrix(false);
        dataset = createVariableWekaDataset(rawData);
    } else {
        rawData = createMatrix(true);
        dataset = createSampleWekaDataset(rawData);
    }
    // Run the clustering algorithm
    ClusteringAlgorithm clusteringAlgorithm = clusteringStep.getModule();
    ParameterSet clusteringParameters = clusteringStep.getParameterSet();
    ClusteringResult result = clusteringAlgorithm.performClustering(dataset, clusteringParameters);
    String cluster = "";
    if (clusteringAlgorithm.getName().toString().equals("Hierarchical clusterer")) {
        progress = 0;
        // Getting the result of the clustering in Newick format
        cluster = result.getHiearchicalCluster();
        // Getting the number of clusters counting the number of times the
        // word "cluster" is in the result
        Pattern p = Pattern.compile("Cluster", Pattern.LITERAL | Pattern.CASE_INSENSITIVE);
        int numberOfClusters = p.split(cluster, -1).length - 1;
        if (numberOfClusters == 0) {
            numberOfClusters = 1;
        }
        // Visualization window for each cluster
        for (int i = 0; i < numberOfClusters; i++) {
            String c = null;
            String clusterNumber = "Cluster " + i;
            if (cluster.indexOf(clusterNumber) > 0) {
                int nextNumber = i + 1;
                String clusterNumber2 = "Cluster " + nextNumber;
                if (cluster.indexOf(clusterNumber2) < 0) {
                    c = cluster.substring(cluster.indexOf(clusterNumber) + clusterNumber.length(), cluster.length());
                } else {
                    c = cluster.substring(cluster.indexOf(clusterNumber) + clusterNumber.length(), cluster.indexOf(clusterNumber2));
                }
            } else {
                c = cluster;
            }
            JFrame visualizationWindow = new JFrame(clusterNumber);
            visualizationWindow.setSize(600, 500);
            visualizationWindow.setLayout(new BorderLayout());
            HierarchyVisualizer visualizer = new HierarchyVisualizer(c);
            visualizationWindow.add(visualizer, BorderLayout.CENTER);
            visualizer.fitToScreen();
            // Text field with the clustering result in Newick format
            JTextField data = new JTextField(c);
            visualizationWindow.add(data, BorderLayout.SOUTH);
            visualizationWindow.setVisible(true);
            visualizationWindow.pack();
            visualizationWindow.setVisible(true);
        }
        progress = 100;
    } else {
        List<Integer> clusteringResult = result.getClusters();
        // Report window
        Desktop desktop = MZmineCore.getDesktop();
        if (typeOfData == ClusteringDataType.SAMPLES) {
            String[] sampleNames = new String[selectedRawDataFiles.length];
            for (int i = 0; i < selectedRawDataFiles.length; i++) {
                sampleNames[i] = selectedRawDataFiles[i].getName();
            }
            ClusteringReportWindow reportWindow = new ClusteringReportWindow(sampleNames, clusteringResult.toArray(new Integer[0]), "Clustering Report");
            reportWindow.setVisible(true);
        } else {
            String[] variableNames = new String[selectedRows.length];
            for (int i = 0; i < selectedRows.length; i++) {
                variableNames[i] = selectedRows[i].getID() + " - " + selectedRows[i].getAverageMZ() + " - " + selectedRows[i].getAverageRT();
                if (selectedRows[i].getPeakIdentities() != null && selectedRows[i].getPeakIdentities().length > 0) {
                    variableNames[i] += " - " + selectedRows[i].getPeakIdentities()[0].getName();
                }
            }
            ClusteringReportWindow reportWindow = new ClusteringReportWindow(variableNames, clusteringResult.toArray(new Integer[0]), "Clustering Report");
            reportWindow.setVisible(true);
        }
        // Visualization
        if (typeOfData == ClusteringDataType.VARIABLES) {
            for (int ind = 0; ind < selectedRows.length; ind++) {
                groupsForSelectedVariables[ind] = clusteringResult.get(ind);
            }
        } else {
            for (int ind = 0; ind < selectedRawDataFiles.length; ind++) {
                groupsForSelectedRawDataFiles[ind] = clusteringResult.get(ind);
            }
        }
        this.finalNumberOfGroups = result.getNumberOfGroups();
        parameterValuesForGroups = new Object[finalNumberOfGroups];
        for (int i = 0; i < finalNumberOfGroups; i++) {
            parameterValuesForGroups[i] = "Group " + i;
        }
        int numComponents = xAxisDimension;
        if (yAxisDimension > numComponents) {
            numComponents = yAxisDimension;
        }
        if (result.getVisualizationType() == VisualizationType.PCA) {
            // Scale data and do PCA
            Preprocess.scaleToUnityVariance(rawData);
            PCA pcaProj = new PCA(rawData, numComponents);
            projectionStatus = pcaProj.getProjectionStatus();
            double[][] pcaResult = pcaProj.getState();
            if (status == TaskStatus.CANCELED) {
                return;
            }
            component1Coords = pcaResult[xAxisDimension - 1];
            component2Coords = pcaResult[yAxisDimension - 1];
        } else if (result.getVisualizationType() == VisualizationType.SAMMONS) {
            // Scale data and do Sammon's mapping
            Preprocess.scaleToUnityVariance(rawData);
            Sammons sammonsProj = new Sammons(rawData);
            projectionStatus = sammonsProj.getProjectionStatus();
            sammonsProj.iterate(100);
            double[][] sammonsResult = sammonsProj.getState();
            if (status == TaskStatus.CANCELED) {
                return;
            }
            component1Coords = sammonsResult[xAxisDimension - 1];
            component2Coords = sammonsResult[yAxisDimension - 1];
        }
        ProjectionPlotWindow newFrame = new ProjectionPlotWindow(desktop.getSelectedPeakLists()[0], this, parameters);
        newFrame.setVisible(true);
    }
    status = TaskStatus.FINISHED;
    logger.info("Finished computing Clustering visualization.");
}

Example 27 with ParameterSet

use of net.sf.mzmine.parameters.ParameterSet in project mzmine2 by mzmine.

the class BatchQueue method clone.

@Override
public BatchQueue clone() {
    // Clone the parameters.
    final BatchQueue clonedQueue = new BatchQueue();
    for (final MZmineProcessingStep<MZmineProcessingModule> step : this) {
        final ParameterSet parameters = step.getParameterSet();
        final MZmineProcessingStepImpl<MZmineProcessingModule> stepCopy = new MZmineProcessingStepImpl<MZmineProcessingModule>(step.getModule(), parameters.cloneParameterSet());
        clonedQueue.add(stepCopy);
    }
    return clonedQueue;
}

Example 28 with ParameterSet

use of net.sf.mzmine.parameters.ParameterSet in project mzmine2 by mzmine.

the class BatchQueue method saveToXml.

/**
 * Serialize to XML.
 *
 * @param xmlElement the XML element to append to.
 */
public void saveToXml(final Element xmlElement) {
    final Document document = xmlElement.getOwnerDocument();
    // Process each step.
    for (final MZmineProcessingStep<?> step : this) {
        // Append a new batch step element.
        final Element stepElement = document.createElement(BATCH_STEP_ELEMENT);
        stepElement.setAttribute(METHOD_ELEMENT, step.getModule().getClass().getName());
        xmlElement.appendChild(stepElement);
        // Save parameters.
        final ParameterSet parameters = step.getParameterSet();
        if (parameters != null) {
            parameters.saveValuesToXML(stepElement);
        }
    }
}

Example 29 with ParameterSet

use of net.sf.mzmine.parameters.ParameterSet in project mzmine2 by mzmine.

the class BatchModeModule method runBatch.

public static ExitCode runBatch(@Nonnull MZmineProject project, File batchFile) {
    logger.info("Running batch from file " + batchFile);
    try {
        DocumentBuilder docBuilder = DocumentBuilderFactory.newInstance().newDocumentBuilder();
        Document parsedBatchXML = docBuilder.parse(batchFile);
        BatchQueue newQueue = BatchQueue.loadFromXml(parsedBatchXML.getDocumentElement());
        ParameterSet parameters = new BatchModeParameters();
        parameters.getParameter(BatchModeParameters.batchQueue).setValue(newQueue);
        Task batchTask = new BatchTask(project, parameters);
        batchTask.run();
        if (batchTask.getStatus() == TaskStatus.FINISHED)
            return ExitCode.OK;
        else
            return ExitCode.ERROR;
    } catch (Throwable e) {
        logger.log(Level.SEVERE, "Error while running batch", e);
        e.printStackTrace();
        return ExitCode.ERROR;
    }
}

Example 30 with ParameterSet

use of net.sf.mzmine.parameters.ParameterSet in project mzmine2 by mzmine.

the class MZmineCore method main.

/**
 * Main method
 */
@SuppressWarnings("unchecked")
public static void main(String[] args) {
    // In the beginning, set the default locale to English, to avoid
    // problems with conversion of numbers etc. (e.g. decimal separator may
    // be . or , depending on the locale)
    Locale.setDefault(new Locale("en", "US"));
    logger.info("Starting MZmine " + getMZmineVersion());
    // Remove old temporary files, if we find any
    TmpFileCleanup.removeOldTemporaryFiles();
    logger.fine("Loading core classes..");
    // create instance of configuration
    configuration = new MZmineConfigurationImpl();
    // create instances of core modules
    projectManager = new ProjectManagerImpl();
    taskController = new TaskControllerImpl();
    logger.fine("Initializing core classes..");
    projectManager.initModule();
    taskController.initModule();
    logger.fine("Loading modules");
    for (Class<?> moduleClass : MZmineModulesList.MODULES) {
        try {
            logger.finest("Loading module " + moduleClass.getName());
            // Create instance and init module
            MZmineModule moduleInstance = (MZmineModule) moduleClass.newInstance();
            // Add to the module list
            initializedModules.put(moduleClass, moduleInstance);
            // Create an instance of parameter set
            Class<? extends ParameterSet> parameterSetClass = moduleInstance.getParameterSetClass();
            ParameterSet parameterSetInstance = parameterSetClass.newInstance();
            // Add the parameter set to the configuration
            configuration.setModuleParameters((Class<MZmineModule>) moduleClass, parameterSetInstance);
        } catch (Throwable e) {
            logger.log(Level.SEVERE, "Could not load module " + moduleClass, e);
            e.printStackTrace();
            continue;
        }
    }
    // If we have no arguments, run in GUI mode, otherwise run in batch mode
    if (args.length == 0) {
        // Create the Swing GUI in the event-dispatching thread, as is
        // generally recommended
        Runnable desktopInit = new Runnable() {

            @Override
            public void run() {
                logger.fine("Initializing GUI");
                MainWindow mainWindow = new MainWindow();
                desktop = mainWindow;
                mainWindow.initModule();
                // Activate project - bind it to the desktop's project tree
                MZmineProjectImpl currentProject = (MZmineProjectImpl) projectManager.getCurrentProject();
                currentProject.activateProject();
                // add desktop menu icon
                for (Class<?> moduleClass : MZmineModulesList.MODULES) {
                    MZmineModule module = initializedModules.get(moduleClass);
                    if (module instanceof MZmineRunnableModule) {
                        mainWindow.getMainMenu().addMenuItemForModule((MZmineRunnableModule) module);
                    }
                }
            }
        };
        try {
            SwingUtilities.invokeAndWait(desktopInit);
        } catch (Exception e) {
            logger.log(Level.SEVERE, "Could not initialize GUI", e);
            e.printStackTrace();
            System.exit(1);
        }
    } else {
        desktop = new HeadLessDesktop();
    }
    // load configuration
    if (MZmineConfiguration.CONFIG_FILE.exists() && MZmineConfiguration.CONFIG_FILE.canRead()) {
        try {
            configuration.loadConfiguration(MZmineConfiguration.CONFIG_FILE);
        } catch (Exception e) {
            e.printStackTrace();
        }
    }
    // if we have GUI, show it now
    if (desktop.getMainWindow() != null && !(desktop instanceof HeadLessDesktop)) {
        // update the size and position of the main window
        ParameterSet paramSet = configuration.getPreferences();
        WindowSettingsParameter settings = paramSet.getParameter(MZminePreferences.windowSetttings);
        settings.applySettingsToWindow(desktop.getMainWindow());
        // add last project menu items
        if (desktop instanceof MainWindow) {
            ((MainWindow) desktop).createLastUsedProjectsMenu(configuration.getLastProjects());
            // listen for changes
            configuration.getLastProjectsParameter().addFileListChangedListener(list -> {
                // new list of last used projects
                Desktop desk = getDesktop();
                if (desk instanceof MainWindow) {
                    ((MainWindow) desk).createLastUsedProjectsMenu(list);
                }
            });
        }
        // show the GUI
        logger.info("Showing main window");
        desktop.getMainWindow().setVisible(true);
        // show the welcome message
        desktop.setStatusBarText("Welcome to MZmine 2!");
        // Check for updated version
        NewVersionCheck NVC = new NewVersionCheck(CheckType.DESKTOP);
        Thread nvcThread = new Thread(NVC);
        nvcThread.setPriority(Thread.MIN_PRIORITY);
        nvcThread.start();
        // Tracker
        GoogleAnalyticsTracker GAT = new GoogleAnalyticsTracker("MZmine Loaded (GUI mode)", "/JAVA/Main/GUI");
        Thread gatThread = new Thread(GAT);
        gatThread.setPriority(Thread.MIN_PRIORITY);
        gatThread.start();
        // register shutdown hook only if we have GUI - we don't want to
        // save configuration on exit if we only run a batch
        ShutDownHook shutDownHook = new ShutDownHook();
        Runtime.getRuntime().addShutdownHook(shutDownHook);
    }
    // mode
    if (args.length > 0 && desktop instanceof HeadLessDesktop) {
        // Tracker
        GoogleAnalyticsTracker GAT = new GoogleAnalyticsTracker("MZmine Loaded (Headless mode)", "/JAVA/Main/GUI");
        Thread gatThread = new Thread(GAT);
        gatThread.setPriority(Thread.MIN_PRIORITY);
        gatThread.start();
        File batchFile = new File(args[0]);
        if ((!batchFile.exists()) || (!batchFile.canRead())) {
            logger.severe("Cannot read batch file " + batchFile);
            System.exit(1);
        }
        ExitCode exitCode = BatchModeModule.runBatch(projectManager.getCurrentProject(), batchFile);
        if (exitCode == ExitCode.OK)
            System.exit(0);
        else
            System.exit(1);
    }
}