MZmineCore.java

/*
 * Copyright 2006-2016 The MZmine 3 Development Team
 * 
 * This file is part of MZmine 3.
 * 
 * MZmine 3 is free software; you can redistribute it and/or modify it under the terms of the GNU
 * General Public License as published by the Free Software Foundation; either version 2 of the
 * License, or (at your option) any later version.
 * 
 * MZmine 3 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
 * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 * General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License along with MZmine 3; if not,
 * write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301
 * USA
 */

package io.github.mzmine.main;

import java.io.InputStream;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import java.util.Properties;
import java.util.concurrent.ScheduledThreadPoolExecutor;

import javax.annotation.Nonnull;

import io.github.mzmine.gui.MZmineGUI;
import io.github.mzmine.gui.mainwindow.MainWindowController;
import io.github.mzmine.modules.MZmineModule;
import io.github.mzmine.modules.MZmineRunnableModule;
import io.github.mzmine.parameters.ParameterSet;
import io.github.mzmine.project.MZmineProject;
import io.github.mzmine.project.auditlog.AuditLogEntry;
import javafx.concurrent.Task;

/**
 * MZmine core functions for modules
 */
public final class MZmineCore {

  private static final @Nonnull MZmineConfiguration configuration = new MZmineConfiguration();

  private static final @Nonnull ScheduledThreadPoolExecutor taskExecutor =
      new ScheduledThreadPoolExecutor(2);

  private static @Nonnull MZmineProject currentProject = new MZmineProject();

  public static @Nonnull MZmineConfiguration getConfiguration() {
    return configuration;
  }

  public static @Nonnull String getMZmineVersion() {
    try {
      ClassLoader myClassLoader = MZmineCore.class.getClassLoader();
      InputStream inStream = myClassLoader
          .getResourceAsStream("META-INF/maven/io.github.mzmine/mzmine/pom.properties");
      if (inStream == null)
        return "0.0";
      Properties properties = new Properties();
      properties.load(inStream);
      String value = properties.getProperty("version");
      if (value == null)
        return "0.0";
      else
        return value;
    } catch (Exception e) {
      e.printStackTrace();
      return "0.0";
    }
  }

  public static @Nonnull MZmineProject getCurrentProject() {
    return currentProject;
  }

  public static void setCurrentProject(@Nonnull MZmineProject newProject) {
    currentProject = newProject;
  }

  public static void submitTasks(@Nonnull Collection<Task<?>> tasks) {

    for (Task<?> task : tasks) {
      MainWindowController mwc = MZmineGUI.getMainWindowController();
      if (mwc != null) {
        mwc.getTaskTable().getTasks().add(task);
      }
      taskExecutor.execute(task);
    }
  }

  public static @Nonnull ScheduledThreadPoolExecutor getTaskExecutor() {
    return taskExecutor;
  }

  public static <ModuleType extends MZmineModule> ModuleType getModuleInstance(
      Class<ModuleType> moduleClass) {
    return MZmineModuleStarter.getModuleInstance(moduleClass);
  }

  public static void runMZmineModule(@Nonnull Class<? extends MZmineRunnableModule> moduleClass,
      @Nonnull ParameterSet parameters) {

    MZmineRunnableModule module = (MZmineRunnableModule) getModuleInstance(moduleClass);

    // Usage Tracker
    GoogleAnalyticsTracker GAT =
        new GoogleAnalyticsTracker(module.getName(), "/JAVA/" + module.getName());
    Thread gatThread = new Thread(GAT);
    gatThread.setPriority(Thread.MIN_PRIORITY);
    gatThread.start();

    // Run the module
    final List<Task<?>> newTasks = new ArrayList<>();
    module.runModule(currentProject, parameters, newTasks);
    submitTasks(newTasks);

    // Log module run in audit log
    AuditLogEntry auditLogEntry = new AuditLogEntry(module, parameters, newTasks);
    currentProject.logProcessingStep(auditLogEntry);

  }

}