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Library allowing generation of plots and data from proteomics and metabolomics mass spectrometry data through the use of R and java methods.

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package uk.ac.liv.pgb.analytica.lib;

import java.io.File;
import java.util.LinkedList;
import java.util.List;
import java.util.Optional;
import uk.ac.liv.pgb.analytica.lib.wrappedr.RSourceFile;
import uk.ac.liv.pgb.analytica.lib.wrappedr.RSourceScanner;


/**
 * Manages all available tasks.
 * @author sperkins
 */
public final class TaskManager {
    /**
     * The singleton instance of this class.
     */
    private static final TaskManager INSTANCE = new TaskManager();

    /**
     * The singleton instance for managing R source files.
     */
    private final RSourceScanner rSources = RSourceScanner.getInstance();

    /**
     * Tasks that have been registered.
     */
    private final List registeredTasks = new LinkedList<>();

    /**
     * The graphics policy that has been registered.
     */
    private GraphicsPolicy graphicsPolicy = null;

    /**
     * Private constructor to prevent external instantiation.
     */
    private TaskManager() {
        registerRTasks();
    }

    /**
     * Gets the singleton instance of this class.
     * @return The singleton instance of this class.
     */
    public static TaskManager getInstance() {
        return INSTANCE;
    }

    /**
     * Registers the given graphics policy with this class.
     * @param policy The graphics policy.
     */
    public void registerGraphicsPolicy(final GraphicsPolicy policy) {
        this.graphicsPolicy = policy;
    }

    /**
     * Finds a task given the name.
     * @param taskName The task name.
     * @return The found task.
     */
    public Task findTask(final String taskName) {
        Optional taskOptional = registeredTasks.stream().filter(p -> p.getName().equalsIgnoreCase(taskName)).findFirst();
        return taskOptional.isPresent() ? taskOptional.get() : null;
    }

    /**
     * Executes the given task with the given file.
     * @param task The task.
     * @param file The input file.
     */
    public void executeTask(final Task task, final File file) {
        task.execute(file, graphicsPolicy != null ? graphicsPolicy : new GraphicsPolicy());
    }

    /**
     * Registers all available R tasks from the R source scanner.
     */
    private void registerRTasks() {
        List sources = rSources.getScannedFiles();
        for (RSourceFile source : sources) {
            if (source.hasManifest()) {
                RTaskWithManifest task = new RTaskWithManifest(source);
                registeredTasks.add(task);
            } else {
                RTaskWithoutManifest task = new RTaskWithoutManifest();
                registeredTasks.add(task);
            }
        }
    }
}