MsSpectrumDataSet.java

/*
 * Copyright 2006-2015 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.plots.msspectrum.datasets;

import java.text.NumberFormat;
import java.util.concurrent.ScheduledThreadPoolExecutor;

import org.jfree.data.xy.AbstractXYDataset;
import org.jfree.data.xy.XYDataset;

import com.google.common.collect.Range;

import io.github.msdk.datamodel.msspectra.MsSpectrum;
import io.github.msdk.datamodel.msspectra.MsSpectrumType;
import io.github.msdk.datamodel.rawdata.MsScan;
import io.github.msdk.spectra.splash.SplashCalculationAlgorithm;
import io.github.msdk.util.MsSpectrumUtil;
import io.github.mzmine.main.MZmineCore;
import io.github.mzmine.modules.plots.msspectrum.MsSpectrumPlotDataSet;
import io.github.mzmine.util.MsScanUtils;
import javafx.application.Platform;
import javafx.beans.property.BooleanProperty;
import javafx.beans.property.DoubleProperty;
import javafx.beans.property.IntegerProperty;
import javafx.beans.property.ObjectProperty;
import javafx.beans.property.SimpleBooleanProperty;
import javafx.beans.property.SimpleDoubleProperty;
import javafx.beans.property.SimpleIntegerProperty;
import javafx.beans.property.SimpleObjectProperty;
import javafx.beans.property.SimpleStringProperty;
import javafx.beans.property.StringProperty;
import javafx.scene.paint.Color;

/**
 * MS spectrum data set. Implements IntervalXYDataset for centroid spectra support (rendered by
 * XYBarRenderer).
 */
public class MsSpectrumDataSet extends AbstractXYDataset implements MsSpectrumPlotDataSet {

  private static final long serialVersionUID = -3188441074323131747L;

  private static final ScheduledThreadPoolExecutor threadPool = new ScheduledThreadPoolExecutor(1);

  private MsSpectrum spectrum;
  private double mzValues[];
  private float intensityValues[];
  private float topIndensity = 0f;
  private int numOfDataPoints = 0;

  private final StringProperty name = new SimpleStringProperty(this, "name", "MS spectrum");
  private final DoubleProperty intensityScale =
      new SimpleDoubleProperty(this, "intensityScale", 0.0);
  private final DoubleProperty mzShift = new SimpleDoubleProperty(this, "mzShift", 0.0);
  private final IntegerProperty lineThickness = new SimpleIntegerProperty(this, "lineThickness", 1);
  private final ObjectProperty<MsSpectrumType> renderingType =
      new SimpleObjectProperty<>(this, "renderingType", MsSpectrumType.CENTROIDED);
  private final ObjectProperty<Color> color = new SimpleObjectProperty<>(this, "color", Color.BLUE);
  private final BooleanProperty showDataPoints =
      new SimpleBooleanProperty(this, "showDataPoints", false);

  public MsSpectrumDataSet(MsSpectrum spectrum, String datasetName) {

    // Listen for property changes
    mzShift.addListener(e -> {
      fireDatasetChanged();
    });
    intensityScale.addListener(e -> {
      fireDatasetChanged();
    });
    name.addListener(e -> {
      fireDatasetChanged();
    });

    setSpectrum(spectrum, datasetName);

  }

  public void setSpectrum(MsSpectrum spectrum, String datasetName) {

    // Load the actual data in a separate thread to avoid blocking the GUI
    threadPool.execute(() -> {

      // Turn notify to off, to avoid redrawing the plot after each
      // property change
      setNotify(false);

      // Remember if the current intensity scale was modified
      boolean modifiedIntensityScale = (getIntensityScale() != this.topIndensity);

      this.spectrum = spectrum;
      this.mzValues = spectrum.getMzValues();
      this.intensityValues = spectrum.getIntensityValues();
      this.numOfDataPoints = spectrum.getNumberOfDataPoints();
      this.topIndensity = MsSpectrumUtil.getMaxIntensity(intensityValues, numOfDataPoints);

      // If the intensity scale was not modified by the user, set the new
      // scale to max intensity
      if (!modifiedIntensityScale)
        setIntensityScale((double) topIndensity);

      setName(datasetName);
      renderingType.get();
      setRenderingType(spectrum.getSpectrumType());

      // Finally, update the GUI
      Platform.runLater(() -> {
        setNotify(true);
      });

    });

  }

  public String getDescription() {
    StringBuilder sb = new StringBuilder();
    if (spectrum instanceof MsScan) {
      MsScan scan = (MsScan) spectrum;
      String scanDesc = MsScanUtils.createFullMsScanDescription(scan);
      sb.append(scanDesc);
    }

    NumberFormat intensityFormat = MZmineCore.getConfiguration().getIntensityFormat();
    NumberFormat mzFormat = MZmineCore.getConfiguration().getMZFormat();

    sb.append("Spectrum type: ");
    sb.append(spectrum.getSpectrumType());
    sb.append("\n");
    sb.append("Number of data points: ");
    sb.append(numOfDataPoints);
    sb.append("\n");
    Range<Double> mzRange = spectrum.getMzRange();
    if (mzRange != null) {
      sb.append("m/z range: ");
      sb.append(mzFormat.format(mzRange.lowerEndpoint()));
      sb.append(" - ");
      sb.append(mzFormat.format(mzRange.upperEndpoint()));
      sb.append(" m/z\n");
    }
    sb.append("Base peak intensity: ");
    sb.append(intensityFormat.format(topIndensity));
    sb.append("\n");
    sb.append("SPLASH ID: ");
    String splash = SplashCalculationAlgorithm.calculateSplash(spectrum);
    sb.append(splash);

    return sb.toString();
  }

  public MsSpectrum getSpectrum() {
    return spectrum;
  }

  public String getName() {
    return name.get();
  }

  public void setName(String newName) {
    name.set(newName);
  }

  public StringProperty nameProperty() {
    return name;
  }

  public Double getIntensityScale() {
    return intensityScale.get();
  }

  public void setIntensityScale(Double newIntensityScale) {
    intensityScale.set(newIntensityScale);
  }

  public DoubleProperty intensityScaleProperty() {
    return intensityScale;
  }

  public void resetIntensityScale() {
    setIntensityScale((double) topIndensity);
  }

  public Double getMzShift() {
    return mzShift.get();
  }

  public void setMzShift(Double newMzShift) {
    mzShift.set(newMzShift);
  }

  public DoubleProperty mzShiftProperty() {
    return mzShift;
  }

  public Integer getLineThickness() {
    return lineThickness.get();
  }

  public void setLineThickness(Integer newLineThickness) {
    lineThickness.set(newLineThickness);
  }

  public IntegerProperty lineThicknessProperty() {
    return lineThickness;
  }

  public Boolean getShowDataPoints() {
    return showDataPoints.get();
  }

  public void setShowDataPoints(Boolean newShowDataPoints) {
    showDataPoints.set(newShowDataPoints);
  }

  public BooleanProperty showDataPointsProperty() {
    return showDataPoints;
  }

  public MsSpectrumType getRenderingType() {
    return renderingType.get();
  }

  public void setRenderingType(MsSpectrumType newType) {
    renderingType.set(newType);
  }

  public ObjectProperty<MsSpectrumType> renderingTypeProperty() {
    return renderingType;
  }

  public Color getColor() {
    return color.get();
  }

  public void setColor(Color newColor) {
    color.set(newColor);
  }

  public ObjectProperty<Color> colorProperty() {
    return color;
  }

  @Override
  public int getItemCount(int series) {
    return numOfDataPoints;
  }

  @Override
  public Number getX(int series, int index) {
    return mzValues[index];
  }

  @Override
  public Number getY(int series, int index) {
    return intensityValues[index] * (getIntensityScale() / topIndensity);
  }

  @Override
  public int getSeriesCount() {
    return 1;
  }

  @Override
  public Comparable<?> getSeriesKey(int series) {
    return getName();
  }

  @Override
  public String generateLabel(XYDataset ds, int series, int index) {
    final double mz = mzValues[index] - mzShift.doubleValue();
    NumberFormat mzFormat = MZmineCore.getConfiguration().getMZFormat();
    String label = mzFormat.format(mz);
    return label;
  }

  @Override
  public String generateToolTip(XYDataset ds, int series, int index) {
    final double actualMz = mzValues[index];
    final float scaledIntensity = getY(series, index).floatValue();
    final float actualIntensity = intensityValues[index];
    NumberFormat mzFormat = MZmineCore.getConfiguration().getMZFormat();
    NumberFormat intensityFormat = MZmineCore.getConfiguration().getIntensityFormat();
    StringBuilder sb = new StringBuilder();

    if (mzShift.doubleValue() != 0.0) {
      final double displayMz = mzValues[index] - mzShift.doubleValue();
      sb.append("Display m/z: ");
      sb.append(mzFormat.format(displayMz));
      sb.append(" (shift ");
      sb.append(mzFormat.format(mzShift.doubleValue()));
      sb.append(" m/z)\n");
    }
    sb.append("Data point m/z: ");
    sb.append(mzFormat.format(actualMz));
    sb.append("\n");

    if (intensityScale.get() != topIndensity) {
      sb.append("Scaled intensity: ");
      sb.append(intensityFormat.format(scaledIntensity));
      sb.append("\n");
    }

    sb.append("Data point intensity: ");
    sb.append(intensityFormat.format(actualIntensity));
    return sb.toString();

  }

  @Override
  public Number getStartX(int series, int item) {
    return getX(series, item);
  }

  @Override
  public double getStartXValue(int series, int item) {
    return getXValue(series, item);
  }

  @Override
  public Number getEndX(int series, int item) {
    return getX(series, item);
  }

  @Override
  public double getEndXValue(int series, int item) {
    return getXValue(series, item);
  }

  @Override
  public Number getStartY(int series, int item) {
    return getY(series, item);
  }

  @Override
  public double getStartYValue(int series, int item) {
    return getYValue(series, item);
  }

  @Override
  public Number getEndY(int series, int item) {
    return getY(series, item);
  }

  @Override
  public double getEndYValue(int series, int item) {
    return getYValue(series, item);
  }

}