net.sf.mzmine.modules.peaklistmethods.dataanalysis.rtmzplots.RTMZPlot.java Source code

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Here is the source code for net.sf.mzmine.modules.peaklistmethods.dataanalysis.rtmzplots.RTMZPlot.java

Source

/*
 * Copyright 2006-2014 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.peaklistmethods.dataanalysis.rtmzplots;

import java.awt.BasicStroke;
import java.awt.Color;
import java.awt.Font;
import java.text.NumberFormat;

import net.sf.mzmine.main.MZmineCore;
import net.sf.mzmine.util.interpolatinglookuppaintscale.InterpolatingLookupPaintScale;

import org.jfree.chart.ChartFactory;
import org.jfree.chart.ChartPanel;
import org.jfree.chart.JFreeChart;
import org.jfree.chart.axis.NumberAxis;
import org.jfree.chart.axis.ValueAxis;
import org.jfree.chart.plot.PlotOrientation;
import org.jfree.chart.plot.XYPlot;
import org.jfree.chart.renderer.xy.XYItemRenderer;
import org.jfree.chart.title.PaintScaleLegend;
import org.jfree.chart.title.TextTitle;
import org.jfree.data.xy.AbstractXYZDataset;
import org.jfree.ui.RectangleInsets;

public class RTMZPlot extends ChartPanel {

    private static final Color gridColor = Color.lightGray;
    private static final Color crossHairColor = Color.gray;
    private static final Font titleFont = new Font("SansSerif", Font.PLAIN, 11);
    // crosshair stroke
    private static final BasicStroke crossHairStroke = new BasicStroke(1, BasicStroke.CAP_BUTT,
            BasicStroke.JOIN_BEVEL, 1.0f, new float[] { 5, 3 }, 0);

    private JFreeChart chart;
    private XYPlot plot;
    private ValueAxis paintScaleAxis;
    private PaintScaleLegend paintScaleLegend;

    private XYItemRenderer spotRenderer;

    private InterpolatingLookupPaintScale paintScale;

    public RTMZPlot(RTMZAnalyzerWindow masterFrame, AbstractXYZDataset dataset,
            InterpolatingLookupPaintScale paintScale) {
        super(null);

        this.paintScale = paintScale;

        chart = ChartFactory.createXYAreaChart("", "Retention time", "m/z", dataset, PlotOrientation.VERTICAL,
                false, false, false);
        chart.setBackgroundPaint(Color.white);
        setChart(chart);

        // title

        TextTitle chartTitle = chart.getTitle();
        chartTitle.setMargin(5, 0, 0, 0);
        chartTitle.setFont(titleFont);
        chart.removeSubtitle(chartTitle);

        // disable maximum size (we don't want scaling)
        setMaximumDrawWidth(Integer.MAX_VALUE);
        setMaximumDrawHeight(Integer.MAX_VALUE);

        // set the plot properties
        plot = chart.getXYPlot();
        plot.setBackgroundPaint(Color.white);
        plot.setAxisOffset(new RectangleInsets(5.0, 5.0, 5.0, 5.0));

        // set grid properties
        plot.setDomainGridlinePaint(gridColor);
        plot.setRangeGridlinePaint(gridColor);

        // set crosshair (selection) properties
        plot.setDomainCrosshairVisible(true);
        plot.setRangeCrosshairVisible(true);
        plot.setDomainCrosshairPaint(crossHairColor);
        plot.setRangeCrosshairPaint(crossHairColor);
        plot.setDomainCrosshairStroke(crossHairStroke);
        plot.setRangeCrosshairStroke(crossHairStroke);

        NumberFormat rtFormat = MZmineCore.getConfiguration().getRTFormat();
        NumberFormat mzFormat = MZmineCore.getConfiguration().getMZFormat();

        // set the X axis (retention time) properties
        NumberAxis xAxis = (NumberAxis) plot.getDomainAxis();
        xAxis.setNumberFormatOverride(rtFormat);
        xAxis.setUpperMargin(0.001);
        xAxis.setLowerMargin(0.001);

        // set the Y axis (intensity) properties
        NumberAxis yAxis = (NumberAxis) plot.getRangeAxis();
        yAxis.setAutoRangeIncludesZero(false);
        yAxis.setNumberFormatOverride(mzFormat);

        plot.setDataset(dataset);
        spotRenderer = new RTMZRenderer(dataset, paintScale);
        plot.setRenderer(spotRenderer);
        spotRenderer.setBaseToolTipGenerator(new RTMZToolTipGenerator());

        // Add a paintScaleLegend to chart

        paintScaleAxis = new NumberAxis("Logratio");
        paintScaleAxis.setRange(paintScale.getLowerBound(), paintScale.getUpperBound());

        paintScaleLegend = new PaintScaleLegend(paintScale, paintScaleAxis);
        paintScaleLegend.setPosition(plot.getDomainAxisEdge());
        paintScaleLegend.setMargin(5, 25, 5, 25);

        chart.addSubtitle(paintScaleLegend);

    }

    public InterpolatingLookupPaintScale getPaintScale() {
        return paintScale;
    }

    public void setPaintScale(InterpolatingLookupPaintScale paintScale) {

        RTMZRenderer renderer = (RTMZRenderer) plot.getRenderer();
        renderer.setPaintScale(paintScale);

        this.paintScale = paintScale;
        paintScaleAxis.setRange(paintScale.getLowerBound(), paintScale.getUpperBound());
        paintScaleLegend.setScale(paintScale);
    }

}