net.sf.mzmine.modules.visualization.threed.ThreeDPeakCells.java Source code

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Here is the source code for net.sf.mzmine.modules.visualization.threed.ThreeDPeakCells.java

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/*
 * Copyright 2006-2015 The MZmine 2 Development Team
 * 
 * This file is part of MZmine 2.
 * 
 * MZmine 2 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 2 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 2; if not, write to the Free Software Foundation, Inc., 51 Franklin St,
 * Fifth Floor, Boston, MA 02110-1301 USA
 */

package net.sf.mzmine.modules.visualization.threed;

import java.rmi.RemoteException;

import net.sf.mzmine.datamodel.Feature;
import visad.CellImpl;
import visad.ConstantMap;
import visad.Data;
import visad.DataReference;
import visad.DataReferenceImpl;
import visad.Display;
import visad.DisplayImpl;
import visad.GriddedSet;
import visad.MathType;
import visad.VisADException;
import visad.bom.PickManipulationRendererJ3D;

import com.google.common.collect.Range;

/**
 * This class represents a 3D boxes which are displayed when user shift+clicks
 * on a peak in the 3D view
 */
public class ThreeDPeakCells extends CellImpl {

    private final DisplayImpl display;
    private Feature[] peaks;
    private DataReference[] references;
    private final MathType pointTupleType;
    private final PickManipulationRendererJ3D picker;

    /**
     * Create the peak cells.
     *
     * @param display3D
     *            the parent display.
     * @param pointType
     *            the point tuple type.
     * @param pickRenderer
     *            pick renderer.
     */
    public ThreeDPeakCells(final DisplayImpl display3D, final MathType pointType,
            final PickManipulationRendererJ3D pickRenderer) {

        // Initialize.
        display = display3D;
        pointTupleType = pointType;
        picker = pickRenderer;
        peaks = null;
        references = null;
    }

    /**
     * Set the peaks.
     *
     * @param thePeaks
     *            the peaks.
     * @throws VisADException
     *             if there are VisAD problems.
     * @throws RemoteException
     *             if there are VisAD problems.
     */
    public void setPeaks(final Feature[] thePeaks) throws VisADException, RemoteException {
        synchronized (display) {

            peaks = thePeaks.clone();

            // First remove all existing data references.
            if (references != null) {
                for (final DataReference reference : references) {
                    if (reference != null) {
                        display.removeReference(reference);
                    }
                }
            }

            // Create new empty array for new data references
            references = new DataReference[peaks.length];
        }
    }

    @Override
    public void doAction() throws VisADException, RemoteException {
        synchronized (display) {

            final int index = picker.getCloseIndex();

            if (index >= 0) {

                // Is the peak box already displayed?
                if (references[index] == null) {

                    // Create the peak box reference.
                    final DataReferenceImpl reference = new DataReferenceImpl("PeakShape");
                    reference.setData(createPeakBox(peaks[index]));

                    // Add the reference to the display
                    display.addReference(reference,
                            new ConstantMap[] { new ConstantMap(0.8, Display.Red),
                                    new ConstantMap(0.2, Display.Green), new ConstantMap(0.2, Display.Blue),
                                    new ConstantMap(0.25, Display.Alpha) });

                    // Save the reference.
                    references[index] = reference;

                } else {

                    display.removeReference(references[index]);
                    references[index] = null;
                }
            }
        }
    }

    /**
     * Create a peak bounding box.
     *
     * @param peak
     *            the peak.
     * @return the bounding box as a gridded set.
     * @throws VisADException
     *             if there are VisAD problems.
     */
    private Data createPeakBox(final Feature peak) throws VisADException {

        // Get the extents.
        final Range<Double> rtRange = peak.getRawDataPointsRTRange();
        final Range<Double> mzRange = peak.getRawDataPointsMZRange();
        final float rtMin = rtRange.lowerEndpoint().floatValue();
        final float rtMax = rtRange.upperEndpoint().floatValue();
        final float mzMin = mzRange.lowerEndpoint().floatValue();
        final float mzMax = mzRange.upperEndpoint().floatValue();
        final float heightMin = 1.0f;
        final float heightMax = peak.getRawDataPointsIntensityRange().upperEndpoint().floatValue();

        // Create the box set.
        return GriddedSet.create(pointTupleType, new float[][] {
                { rtMin, rtMax, rtMin, rtMax, rtMin, rtMax, rtMin, rtMax, rtMin, rtMin, rtMin, rtMin, rtMax, rtMax,
                        rtMax, rtMax, },
                { mzMin, mzMin, mzMin, mzMin, mzMax, mzMax, mzMax, mzMax, mzMin, mzMax, mzMin, mzMax, mzMin, mzMax,
                        mzMin, mzMax },
                { heightMin, heightMin, heightMax, heightMax, heightMax, heightMax, heightMin, heightMin, heightMin,
                        heightMin, heightMax, heightMax, heightMax, heightMax, heightMin, heightMin } },
                new int[] { 2, 8 });
    }
}