MZmineGUI.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.gui;

import java.io.IOException;
import java.net.URL;
import java.util.ArrayList;
import java.util.List;
import java.util.Optional;

import javax.annotation.Nonnull;

import org.controlsfx.control.StatusBar;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import io.github.msdk.datamodel.featuretables.FeatureTable;
import io.github.msdk.datamodel.rawdata.RawDataFile;
import io.github.mzmine.gui.mainwindow.MainWindowController;
import io.github.mzmine.main.MZmineCore;
import io.github.mzmine.main.NewVersionCheck;
import io.github.mzmine.main.NewVersionCheck.CheckType;
import io.github.mzmine.modules.MZmineRunnableModule;
import io.github.mzmine.parameters.ParameterSet;
import io.github.mzmine.project.MZmineGUIProject;
import javafx.application.Application;
import javafx.application.Platform;
import javafx.fxml.FXMLLoader;
import javafx.scene.Node;
import javafx.scene.Scene;
import javafx.scene.control.Alert;
import javafx.scene.control.Alert.AlertType;
import javafx.scene.control.ButtonType;
import javafx.scene.control.Dialog;
import javafx.scene.control.TreeItem;
import javafx.scene.control.TreeView;
import javafx.scene.image.Image;
import javafx.scene.layout.BorderPane;
import javafx.stage.Stage;

/**
 * MZmine JavaFX Application class
 */
public final class MZmineGUI extends Application {

  private final Logger logger = LoggerFactory.getLogger(this.getClass());

  private static final Image mzMineIcon = new Image("file:icon/mzmine-icon.png");
  private static final String mzMineFXML = "file:conf/MainWindow.fxml";

  private static MainWindowController mainWindowController;

  private static Scene rootScene;

  public void start(Stage stage) {

    try {
      // Load the main window
      URL mainFXML = new URL(mzMineFXML);
      FXMLLoader loader = new FXMLLoader(mainFXML);

      rootScene = loader.load();
      mainWindowController = loader.getController();
      stage.setScene(rootScene);

    } catch (IOException e) {
      e.printStackTrace();
      logger.error("Error loading MZmine GUI from FXML: " + e);
      Platform.exit();
    }

    stage.setTitle("MZmine " + MZmineCore.getMZmineVersion());
    stage.setMinWidth(300);
    stage.setMinHeight(300);

    // Set application icon
    stage.getIcons().setAll(mzMineIcon);

    stage.setOnCloseRequest(e -> {
      requestQuit();
      e.consume();
    });

    // Activate new GUI-supported project
    MZmineGUIProject project = new MZmineGUIProject();
    MZmineGUI.activateProject(project);

    stage.show();

    // Check for new version of MZmine
    NewVersionCheck NVC = new NewVersionCheck(CheckType.DESKTOP);
    Thread nvcThread = new Thread(NVC);
    nvcThread.setPriority(Thread.MIN_PRIORITY);
    nvcThread.start();
  }

  public static void requestQuit() {
    Alert alert = new Alert(AlertType.CONFIRMATION);
    Stage stage = (Stage) alert.getDialogPane().getScene().getWindow();
    stage.getIcons().add(mzMineIcon);
    alert.setTitle("Confirmation");
    alert.setHeaderText("Exit MZmine");
    String s = "Are you sure you want to exit?";
    alert.setContentText(s);
    Optional<ButtonType> result = alert.showAndWait();

    if ((result.isPresent()) && (result.get() == ButtonType.OK)) {
      Platform.exit();
      System.exit(0);
    }
  }

  public static void closeProject() {
    Alert alert = new Alert(AlertType.CONFIRMATION);
    Stage stage = (Stage) alert.getDialogPane().getScene().getWindow();
    stage.getIcons().add(mzMineIcon);
    alert.setTitle("Confirmation");
    alert.setHeaderText("Close project");
    String s = "Are you sure you want to close the current project?";
    alert.setContentText(s);
    Optional<ButtonType> result = alert.showAndWait();

    if ((result.isPresent()) && (result.get() == ButtonType.OK)) {
      MZmineGUIProject newProject = new MZmineGUIProject();
      activateProject(newProject);
      setStatusBarMessage("");
    }
  }

  public static void displayMessage(String msg) {
    Platform.runLater(() -> {
      Dialog<ButtonType> dialog = new Dialog<>();
      Stage stage = (Stage) dialog.getDialogPane().getScene().getWindow();
      stage.getIcons().add(mzMineIcon);
      dialog.setTitle("Warning");
      dialog.setContentText(msg);
      dialog.getDialogPane().getButtonTypes().add(ButtonType.OK);
      dialog.showAndWait();
    });
  }

  public static void setStatusBarMessage(String message) {
    Platform.runLater(() -> {
      StatusBar statusBar = mainWindowController.getStatusBar();
      statusBar.setText(message);
    });
  }

  public static MainWindowController getMainWindowController() {
    return mainWindowController;
  }

  public static void addWindow(Node node, String title) {

    BorderPane parent = new BorderPane();
    parent.setCenter(node);
    Scene newScene = new Scene(parent);

    // Copy CSS styles
    newScene.getStylesheets().addAll(rootScene.getStylesheets());

    Stage newStage = new Stage();
    newStage.setTitle(title);
    newStage.getIcons().add(mzMineIcon);
    newStage.setScene(newScene);
    newStage.show();

  }

  public static void activateProject(MZmineGUIProject project) {
    MZmineCore.setCurrentProject(project);

    TreeView<Object> rawDataTree = mainWindowController.getRawDataTree();
    rawDataTree.setRoot(project.getRawDataRootItem());

    TreeView<Object> featureTree = mainWindowController.getFeatureTree();
    featureTree.setRoot(project.getFeatureTableRootItem());

  }

  public static @Nonnull List<RawDataFile> getSelectedRawDataFiles() {

    final ArrayList<RawDataFile> list = new ArrayList<>();
    final TreeView<Object> rawDataTree = mainWindowController.getRawDataTree();
    for (TreeItem<Object> item : rawDataTree.getSelectionModel().getSelectedItems()) {
      if (!(item.getValue() instanceof RawDataFile))
        continue;
      RawDataFile file = (RawDataFile) item.getValue();
      list.add(file);
    }

    return list;

  }

  public static @Nonnull List<FeatureTable> getSelectedFeatureTables() {

    final ArrayList<FeatureTable> list = new ArrayList<>();
    final TreeView<Object> featureTableTree = mainWindowController.getFeatureTree();
    for (TreeItem<Object> item : featureTableTree.getSelectionModel().getSelectedItems()) {
      if (!(item.getValue() instanceof FeatureTable))
        continue;
      FeatureTable ft = (FeatureTable) item.getValue();
      list.add(ft);
    }

    return list;

  }

  public static <ModuleType extends MZmineRunnableModule> void setupAndRunModule(
      @Nonnull Class<ModuleType> moduleClass) {

    final ParameterSet moduleParameters =
        MZmineCore.getConfiguration().getModuleParameters(moduleClass);
    ButtonType result = moduleParameters.showSetupDialog(null);
    if (result == ButtonType.OK) {
      MZmineCore.runMZmineModule(moduleClass, moduleParameters);
    }

  }

}