MainWindowController.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.mainwindow;

import java.util.Collection;

import org.controlsfx.control.StatusBar;
import org.controlsfx.control.TaskProgressView;
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.MZmineGUI;
import io.github.mzmine.main.MZmineCore;
import io.github.mzmine.modules.featuretable.FeatureTableModule;
import io.github.mzmine.modules.featuretable.FeatureTableModuleParameters;
import io.github.mzmine.modules.plots.chromatogram.ChromatogramPlotModule;
import io.github.mzmine.modules.plots.chromatogram.ChromatogramPlotParameters;
import io.github.mzmine.modules.plots.msspectrum.MsSpectrumPlotModule;
import io.github.mzmine.modules.plots.msspectrum.MsSpectrumPlotParameters;
import io.github.mzmine.parameters.ParameterSet;
import io.github.mzmine.parameters.parametertypes.selectors.FeatureTablesParameter;
import io.github.mzmine.parameters.parametertypes.selectors.FeatureTablesSelectionType;
import io.github.mzmine.parameters.parametertypes.selectors.RawDataFilesParameter;
import io.github.mzmine.parameters.parametertypes.selectors.RawDataFilesSelectionType;
import io.github.mzmine.taskcontrol.MZmineTask;
import javafx.animation.Animation;
import javafx.animation.KeyFrame;
import javafx.animation.Timeline;
import javafx.collections.ObservableList;
import javafx.concurrent.Task;
import javafx.event.ActionEvent;
import javafx.fxml.FXML;
import javafx.scene.Scene;
import javafx.scene.control.Label;
import javafx.scene.control.ProgressBar;
import javafx.scene.control.SelectionMode;
import javafx.scene.control.Tab;
import javafx.scene.control.TreeItem;
import javafx.scene.control.TreeView;
import javafx.scene.input.MouseEvent;
import javafx.scene.layout.BorderPane;
import javafx.util.Duration;

/**
 * This class controls the main window of the application
 * 
 */
public class MainWindowController {

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

  @FXML
  private Scene mainScene;

  @FXML
  private BorderPane mainWindowPane;

  @FXML
  private TreeView<Object> rawDataTree;

  @FXML
  private TreeView<Object> featureTree;

  @FXML
  private TaskProgressView<Task<?>> tasksView;

  @FXML
  private StatusBar statusBar;

  @FXML
  private ProgressBar memoryBar;

  @FXML
  private Label memoryBarLabel;

  @FXML
  public void initialize() {

    rawDataTree.getSelectionModel().setSelectionMode(SelectionMode.MULTIPLE);
    rawDataTree.setShowRoot(true);

    // Add mouse clicked event handler
    rawDataTree.setOnMouseClicked(event -> {
      if (event.getClickCount() == 2) {
        handleShowTIC(null);
      }
    });

    featureTree.getSelectionModel().setSelectionMode(SelectionMode.MULTIPLE);
    featureTree.setShowRoot(true);

    // Add mouse clicked event handler
    featureTree.setOnMouseClicked(event -> {
      if (event.getClickCount() == 2) {
        // Show feature table for selected row
        ParameterSet moduleParameters =
            MZmineCore.getConfiguration().getModuleParameters(FeatureTableModule.class);
        FeatureTablesParameter inputTablesParam =
            moduleParameters.getParameter(FeatureTableModuleParameters.featureTables);
        inputTablesParam.switchType(FeatureTablesSelectionType.GUI_SELECTED_FEATURE_TABLES);
        MZmineCore.runMZmineModule(FeatureTableModule.class, moduleParameters);
      }
    });

    statusBar.setText("Welcome to MZmine " + MZmineCore.getMZmineVersion());

    /*
     * tasksView.setGraphicFactory(task -> { return new Glyph("FontAwesome",
     * FontAwesome.Glyph.COG).size(24.0) .color(Color.BLUE); });
     */

    // Setup the Timeline to update the memory indicator periodically
    final Timeline memoryUpdater = new Timeline();
    int UPDATE_FREQUENCY = 500; // ms
    memoryUpdater.setCycleCount(Animation.INDEFINITE);
    memoryUpdater.getKeyFrames().add(new KeyFrame(Duration.millis(UPDATE_FREQUENCY), e -> {

      final long freeMemMB = Runtime.getRuntime().freeMemory() / (1024 * 1024);
      final long totalMemMB = Runtime.getRuntime().totalMemory() / (1024 * 1024);
      final double memory = ((double) (totalMemMB - freeMemMB)) / totalMemMB;

      memoryBar.setProgress(memory);
      memoryBarLabel.setText(freeMemMB + "/" + totalMemMB + " MB free");
    }));
    memoryUpdater.play();

    // Setup the Timeline to update the MZmine tasks periodically
    final Timeline msdkTaskUpdater = new Timeline();
    UPDATE_FREQUENCY = 50; // ms
    msdkTaskUpdater.setCycleCount(Animation.INDEFINITE);
    msdkTaskUpdater.getKeyFrames().add(new KeyFrame(Duration.millis(UPDATE_FREQUENCY), e -> {

      Collection<Task<?>> tasks = tasksView.getTasks();
      for (Task<?> task : tasks) {
        if (task instanceof MZmineTask) {
          MZmineTask mzmineTask = (MZmineTask) task;
          mzmineTask.refreshStatus();
        }
      }
    }));
    msdkTaskUpdater.play();
  }

  @FXML
  public void memoryBarClicked(MouseEvent e) {
    // Run garbage collector on a new thread, so it does not block the GUI
    new Thread(() -> {
      logger.info("Running garbage collector");
      System.gc();
    }).start();

  }

  public TreeView<Object> getRawDataTree() {
    return rawDataTree;
  }

  public TreeView<Object> getFeatureTree() {
    return featureTree;
  }

  public TaskProgressView<Task<?>> getTaskTable() {
    return tasksView;
  }

  public StatusBar getStatusBar() {
    return statusBar;
  }

  public void handleShowTIC(ActionEvent event) {
    logger.debug("Activated Show chromatogram menu item");
    ParameterSet chromPlotParams =
        MZmineCore.getConfiguration().getModuleParameters(ChromatogramPlotModule.class);
    RawDataFilesParameter inputFilesParam =
        chromPlotParams.getParameter(ChromatogramPlotParameters.inputFiles);
    inputFilesParam.switchType(RawDataFilesSelectionType.GUI_SELECTED_FILES);
    MZmineGUI.setupAndRunModule(ChromatogramPlotModule.class);
  }

  public void handleShowMsSpectrum(ActionEvent event) {
    logger.debug("Activated Show MS spectrum menu item");
    ParameterSet specPlotParams =
        MZmineCore.getConfiguration().getModuleParameters(MsSpectrumPlotModule.class);
    RawDataFilesParameter inputFilesParam =
        specPlotParams.getParameter(MsSpectrumPlotParameters.inputFiles);
    inputFilesParam.switchType(RawDataFilesSelectionType.GUI_SELECTED_FILES);
    MZmineGUI.setupAndRunModule(MsSpectrumPlotModule.class);
  }

  public void removeRawData(ActionEvent event) {
    // Get selected tree items
    ObservableList<TreeItem<Object>> rows = null;
    if (rawDataTree.getSelectionModel() != null) {
      rows = rawDataTree.getSelectionModel().getSelectedItems();
    }

    // Loop through all selected tree items
    if (rows != null) {
      for (int i = rows.size() - 1; i >= 0; i--) {
        TreeItem<Object> row = rows.get(i);

        if (!(row.getValue() instanceof RawDataFile))
          continue;

        // Remove feature table from current project
        RawDataFile rawDataFile = (RawDataFile) row.getValue();
        MZmineCore.getCurrentProject().removeFile(rawDataFile);

        // Remove raw data file from tree table view
        TreeItem<?> parent = row.getParent();
        if (parent == null)
          continue;
        parent.getChildren().remove(row);
      }
      rawDataTree.getSelectionModel().clearSelection();
    }
  }

  public void removeFeatureTable(ActionEvent event) {
    // Get selected tree items
    ObservableList<TreeItem<Object>> rows = null;
    if (featureTree.getSelectionModel() != null) {
      rows = featureTree.getSelectionModel().getSelectedItems();
    }

    // Loop through all selected tree items
    if (rows != null) {
      for (int i = rows.size() - 1; i >= 0; i--) {
        TreeItem<Object> row = rows.get(i);

        if (!(row.getValue() instanceof FeatureTable))
          continue;

        // Remove feature table from current project
        FeatureTable featureTable = (FeatureTable) row.getValue();
        MZmineCore.getCurrentProject().removeFeatureTable(featureTable);

        // Remove feature table from tree table view
        TreeItem<?> parent = row.getParent();
        if (parent == null)
          continue;
        parent.getChildren().remove(row);
      }
      featureTree.getSelectionModel().clearSelection();
    }
  }

  public void updateTabName(Tab tab) {
    /*
     * String title = ""; if (tab.equals(rawDataFilesTab)) { title = "Raw Data"; int rawDataFiles =
     * MZmineCore.getCurrentProject().getRawDataFiles() .size(); if (rawDataFiles > 0) title += " ("
     * + rawDataFiles + ")"; rawDataFilesTab.setText(title); return; } if
     * (tab.equals(featureTablesTab)) { title = "Feature Tables"; int featureTables =
     * MZmineCore.getCurrentProject() .getFeatureTables().size(); if (featureTables > 0) title +=
     * " (" + featureTables + ")"; featureTablesTab.setText(title); return; }
     */
  }
}