org.eurocarbdb.application.glycoworkbench.plugin.PeakAnnotationReportPanel.java Source code

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Here is the source code for org.eurocarbdb.application.glycoworkbench.plugin.PeakAnnotationReportPanel.java

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/*
*   EuroCarbDB, a framework for carbohydrate bioinformatics
*
*   Copyright (c) 2006-2009, Eurocarb project, or third-party contributors as
*   indicated by the @author tags or express copyright attribution
*   statements applied by the authors.  
*
*   This copyrighted material is made available to anyone wishing to use, modify,
*   copy, or redistribute it subject to the terms and conditions of the GNU
*   Lesser General Public License, as published by the Free Software Foundation.
*   A copy of this license accompanies this distribution in the file LICENSE.txt.
*
*   This program 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 Lesser General Public License
*   for more details.
*
*   Last commit: $Rev: 1930 $ by $Author: david@nixbioinf.org $ on $Date:: 2010-07-29 #$  
*/
/**
   @author Alessio Ceroni (a.ceroni@imperial.ac.uk)
*/

package org.eurocarbdb.application.glycoworkbench.plugin;

import org.eurocarbdb.application.glycanbuilder.*;

import org.eurocarbdb.application.glycoworkbench.*;

import java.io.File;
import java.awt.*;
import java.awt.event.*;
import java.util.*;
import javax.swing.*;
import java.awt.print.*;
import org.jfree.chart.JFreeChart;
import org.jfree.chart.ChartPanel;
import org.jfree.chart.plot.XYPlot;
import org.jfree.data.category.DefaultCategoryDataset;
import org.jfree.data.xy.DefaultXYDataset;
import org.jfree.data.xy.XYBarDataset;
import org.jfree.chart.renderer.xy.StandardXYItemRenderer;

public class PeakAnnotationReportPanel extends DocumentPanel<AnnotatedPeakList> implements ActionListener {

    // components   
    protected DefaultXYDataset theDataset;
    protected XYPlot thePlot;
    protected JFreeChart theChart;
    protected ChartPanel theChartPanel;

    protected JToolBar theToolBar;

    //

    public PeakAnnotationReportPanel() {
        super();
    }

    protected void initComponents() {
        setLayout(new BorderLayout());

        // create chart
        theDataset = new DefaultXYDataset();
        theChart = org.jfree.chart.ChartFactory.createScatterPlot("Annotation", "Count", "Intensity", theDataset,
                org.jfree.chart.plot.PlotOrientation.VERTICAL, true, false, false);
        thePlot = (XYPlot) theChart.getPlot();
        thePlot.setRenderer(new StandardXYItemRenderer(StandardXYItemRenderer.LINES));

        theChartPanel = new ChartPanel(theChart);
        theChartPanel.setDomainZoomable(true);
        theChartPanel.setRangeZoomable(false);
        //theChartPanel.setPopupMenu(null);
        add(theChartPanel, BorderLayout.CENTER);

        // create toolbar
        theToolBar = createToolBar();
        add(theToolBar, BorderLayout.SOUTH);
    }

    public AnnotatedPeakList getDocumentFromWorkspace(GlycanWorkspace workspace) {
        return (workspace != null) ? workspace.getAnnotatedPeakList() : null;
    }

    public void setDocumentFromWorkspace(GlycanWorkspace workspace) {
        if (theDocument != null)
            theDocument.removeDocumentChangeListener(this);

        theDocument = getDocumentFromWorkspace(workspace);
        if (theDocument == null)
            theDocument = new AnnotatedPeakList();

        theDocument.addDocumentChangeListener(this);

        updateView();
        updateActions();
    }

    protected void createActions() {

        theActionManager.add("new", FileUtils.defaultThemeManager.getImageIcon("new"), "Clear", KeyEvent.VK_N, "",
                this);
        theActionManager.add("print", FileUtils.defaultThemeManager.getImageIcon("print"), "Print...",
                KeyEvent.VK_P, "", this);
    }

    protected void updateActions() {
    }

    private JToolBar createToolBar() {
        JToolBar toolbar = new JToolBar();
        toolbar.setFloatable(false);

        toolbar.add(theActionManager.get("new"));

        toolbar.addSeparator();

        toolbar.add(theActionManager.get("print"));

        return toolbar;
    }

    //-----------
    // Visualization

    protected void updateData() {
    }

    protected void updateView() {
        // clear
        //for( int i=1; i<theDataset.getSeriesCount(); i++ )
        //theDataset.removeSeries(theDataset.getSeriesKey(i-1));

        for (int l = 0; l < theDocument.getNoStructures(); l++)
            theDataset.removeSeries("series" + l);

        for (int l = 0; l < theDocument.getNoStructures(); l++) {

            double[][] data = new double[2][];
            data[0] = new double[theDocument.getNoPeaks()];
            data[1] = new double[theDocument.getNoPeaks()];

            // get intensities and order them
            LinkedList<Double> sortedList = new LinkedList<Double>();
            for (int i = 0; i < theDocument.getNoPeaks(); i++) {
                double intensity = theDocument.getPeak(i).getIntensity();
                if (theDocument.getAnnotations(i, l).size() == 0)
                    intensity = 0.;

                int index = Collections.binarySearch(sortedList, intensity);
                if (index < 0)
                    index = -index - 1;
                sortedList.add(index, intensity);
            }

            // set data
            for (int i = 0; i < theDocument.getNoPeaks(); i++) {
                data[0][i] = i;
                data[1][i] = sortedList.get(theDocument.getNoPeaks() - i - 1);
            }
            theDataset.addSeries("series" + l, data);
        }
    }

    //-----------------
    // actions    

    public void onPrint() {
        PrinterJob pj = theWorkspace.getPrinterJob();
        if (pj == null)
            return;

        try {
            pj.setPrintable(theChartPanel);
            if (pj.printDialog())
                pj.print();
        } catch (Exception e) {
            LogUtils.report(e);
        }
    }

    //-----------
    // listeners

    public void actionPerformed(ActionEvent e) {

        String action = e.getActionCommand();

        if (action.equals("new"))
            theApplication.onNew(theDocument);

        else if (action.equals("print"))
            onPrint();

        updateActions();
    }

}