ChromatogramRenderer.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.modules.featuretable.renderers;

import io.github.msdk.datamodel.chromatograms.Chromatogram;
import io.github.msdk.datamodel.featuretables.FeatureTableRow;
import io.github.msdk.datamodel.rawdata.ChromatographyInfo;
import javafx.scene.chart.LineChart;
import javafx.scene.chart.NumberAxis;
import javafx.scene.chart.XYChart;
import javafx.scene.control.TreeTableCell;
import javafx.scene.control.TreeTableColumn;
import javafx.util.Callback;

public class ChromatogramRenderer implements
    Callback<TreeTableColumn<FeatureTableRow, Object>, TreeTableCell<FeatureTableRow, Object>> {

  @Override
  public TreeTableCell<FeatureTableRow, Object> call(TreeTableColumn<FeatureTableRow, Object> p) {
    return new TreeTableCell<FeatureTableRow, Object>() {
      @Override
      public void updateItem(Object object, boolean empty) {
        super.updateItem(object, empty);
        setStyle(
            "-fx-border-color: transparent -fx-table-cell-border-color -fx-table-cell-border-color transparent;");
        if (object == null) {
          setText(null);
        } else {

          Chromatogram chromatogram = (Chromatogram) object;

          ChromatographyInfo[] chromatographyInfoValues = chromatogram.getRetentionTimes();
          float[] intensityValues = chromatogram.getIntensityValues();
          int numOfDataPoints = chromatogram.getNumberOfDataPoints();

          // x-axis
          NumberAxis xAxis = new NumberAxis();
          xAxis.setTickLabelsVisible(false);
          xAxis.setOpacity(0);
          xAxis.setAutoRanging(false);
          xAxis.setLowerBound(chromatogram.getRtRange().lowerEndpoint().getRetentionTime());
          xAxis.setUpperBound(chromatogram.getRtRange().upperEndpoint().getRetentionTime());

          // y-axis
          NumberAxis yAxis = new NumberAxis();
          yAxis.setTickLabelsVisible(false);
          yAxis.setOpacity(0);

          // Chart line
          final LineChart<Number, Number> lineChart = new LineChart<Number, Number>(xAxis, yAxis);
          XYChart.Series series = new XYChart.Series();
          for (int i = 1; i < numOfDataPoints; i++) {
            series.getData().add(new XYChart.Data(chromatographyInfoValues[i].getRetentionTime(),
                intensityValues[i]));
          }

          // Chart
          lineChart.getData().addAll(series);
          lineChart.setLegendVisible(false);
          lineChart.setCreateSymbols(false);
          lineChart.setMinSize(0, 0);
          lineChart.setPrefHeight(75);
          lineChart.setPrefWidth(100);

          setGraphic(lineChart);
        }
      }
    };
  }

}