TableUtils.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.util;

import java.util.List;
import java.util.Map;

import io.github.msdk.datamodel.chromatograms.Chromatogram;
import io.github.msdk.datamodel.featuretables.FeatureTableRow;
import io.github.msdk.datamodel.ionannotations.IonAnnotation;
import io.github.msdk.datamodel.rawdata.ChromatographyInfo;
import javafx.collections.ObservableList;
import javafx.event.EventHandler;
import javafx.scene.control.TreeTableColumn;
import javafx.scene.control.TreeTablePosition;
import javafx.scene.control.TreeTableView;
import javafx.scene.input.Clipboard;
import javafx.scene.input.ClipboardContent;
import javafx.scene.input.KeyCode;
import javafx.scene.input.KeyCodeCombination;
import javafx.scene.input.KeyCombination;
import javafx.scene.input.KeyEvent;

public class TableUtils {

  /**
   * Add the keyboard handler.
   * 
   * @param table
   */
  public static void addCopyHandler(TreeTableView<?> table,
      Map<Integer, TreeTableColumn<FeatureTableRow, Object>> columnMap) {
    table.setOnKeyPressed(new KeyEventHandler(columnMap));
  }

  /**
   * Copy event handler.
   */
  public static class KeyEventHandler implements EventHandler<KeyEvent> {
    KeyCodeCombination keyCodeCompination =
        new KeyCodeCombination(KeyCode.C, KeyCombination.CONTROL_ANY);

    Map<Integer, TreeTableColumn<FeatureTableRow, Object>> columnMap;

    KeyEventHandler(Map<Integer, TreeTableColumn<FeatureTableRow, Object>> columnMap) {
      this.columnMap = columnMap;
    }

    public void handle(final KeyEvent keyEvent) {
      if (keyCodeCompination.match(keyEvent)) {
        if (keyEvent.getSource() instanceof TreeTableView) {
          // Copy to clipboard
          copySelectionToClipboard((TreeTableView<?>) keyEvent.getSource());

          // Event is handled, consume it
          keyEvent.consume();
        }
      }
    }

    /**
     * Get table selection and copy it to the clipboard.
     * 
     * @param <S>
     * 
     * @param table
     */
    public void copySelectionToClipboard(TreeTableView table) {
      StringBuilder clipboardString = new StringBuilder();

      ObservableList<TreeTablePosition<?, ?>> positionList =
          table.getSelectionModel().getSelectedCells();
      int prevRow = -1;

      // Add sample headers
      int hiddenColumns = 0;
      for (TreeTablePosition<?, ?> position : positionList) {
        int rowNr = position.getRow();
        int columnNr = position.getColumn() + hiddenColumns;

        // Account for hidden columns
        while (!columnMap.get(columnNr).isVisible()) {
          hiddenColumns++;
          columnNr++;
        }

        // Get the column from the map to avoid trouble with sample
        // headers
        TreeTableColumn<?, ?> column = columnMap.get(columnNr);
        Object object = (Object) column.getCellData(rowNr);

        // Skip chromatogram column
        if (object instanceof Chromatogram)
          continue;

        if (prevRow == rowNr || prevRow == -1) {
          String columnTitle;
          if (column.getParentColumn() != null) {
            columnTitle = column.getParentColumn().getText();
          } else {
            columnTitle = "";
          }

          clipboardString.append(columnTitle);
          clipboardString.append('\t');
        } else {
          break;
        }
        prevRow = rowNr;
      }
      prevRow = -1;
      clipboardString.append('\n');

      // Add column headers
      hiddenColumns = 0;
      for (TreeTablePosition<?, ?> position : positionList) {
        int rowNr = position.getRow();
        int columnNr = position.getColumn() + hiddenColumns;

        // Account for hidden columns
        while (!columnMap.get(columnNr).isVisible()) {
          hiddenColumns++;
          columnNr++;
        }

        // Get the column from the map to avoid trouble with sample
        // headers
        TreeTableColumn<?, ?> column = columnMap.get(columnNr);
        Object object = (Object) column.getCellData(rowNr);

        // Skip chromatogram column
        if (object instanceof Chromatogram)
          continue;

        // Add all columns
        if (prevRow == rowNr || prevRow == -1) {
          String columnTitle = column.getText();
          clipboardString.append(columnTitle);
          clipboardString.append('\t');
        } else {
          break;
        }
        prevRow = rowNr;
      }
      prevRow = -1;
      clipboardString.append('\n');

      // Add data
      hiddenColumns = 0;
      for (TreeTablePosition<?, ?> position : positionList) {

        int rowNr = position.getRow();
        if (prevRow != rowNr) {
          hiddenColumns = 0;
        }
        int columnNr = position.getColumn() + hiddenColumns;

        // Account for hidden columns
        while (!columnMap.get(columnNr).isVisible()) {
          hiddenColumns++;
          columnNr++;
        }

        // Get the column from the map to avoid trouble with sample
        // headers
        TreeTableColumn<?, ?> column = columnMap.get(columnNr);

        String text = null;
        Object object = (Object) column.getCellData(rowNr);
        if (object instanceof ChromatographyInfo) {
          // Format to RT1, RT2
          ChromatographyInfo chromatographyInfo = (ChromatographyInfo) object;
          Float rt1 = chromatographyInfo.getRetentionTime();
          Float rt2 = chromatographyInfo.getSecondaryRetentionTime();
          if (rt1 != null) {
            text = rt1.toString();
          }
          if (text != null && rt2 != null) {
            text = text + ", ";
          }
          if (rt2 != null) {
            text = text + rt2.toString();
          }
        } else if (object instanceof List) {
          text = "";
          List<IonAnnotation> ionAnnotations = (List<IonAnnotation>) object;
          for (IonAnnotation ionAnnotation : ionAnnotations) {
            if (text != "")
              text += ", ";
            if (ionAnnotation.getDescription() != null)
              text += ionAnnotation.getDescription();
            else
              text += ionAnnotation.getAnnotationId();
          }
        } else if (object instanceof Chromatogram) {
          continue;
        } else {
          if (object != null)
            text = object.toString();
        }

        // Are we looping over a row or column?
        if (prevRow == rowNr) {
          clipboardString.append('\t');
        } else if (prevRow != -1) {
          clipboardString.append('\n');
        }

        if (text == null || text.equals("null"))
          text = "";

        // Add new item to clipboard
        clipboardString.append(text);

        // Remember previous
        prevRow = rowNr;
      }

      // Set string to the clipboard
      final ClipboardContent clipboardContent = new ClipboardContent();
      clipboardContent.putString(clipboardString.toString());
      Clipboard.getSystemClipboard().setContent(clipboardContent);
    }
  }

}