net.bioclipse.seneca.views.BestStructureView.java Source code

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Here is the source code for net.bioclipse.seneca.views.BestStructureView.java

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/*******************************************************************************
 * Copyright (c) 2005-2007 Bioclipse Project
 * All rights reserved. This program and the accompanying materials
 * are made available under the terms of the Eclipse Public License v1.0
 * which accompanies this distribution, and is available at
 * http://www.eclipse.org/legal/epl-v10.html
 *
 * Contributors:
 *     Ola Spjuth - core API and implementation
 *     Egon Willighagen - tuned for SENECA
 *******************************************************************************/
package net.bioclipse.seneca.views;

import java.awt.Frame;
import java.util.ArrayList;
import java.util.List;

import net.bioclipse.cdk.jchempaint.widgets.JChemPaintEditorWidget;

import org.eclipse.swt.SWT;
import org.eclipse.swt.awt.SWT_AWT;
import org.eclipse.swt.custom.SashForm;
import org.eclipse.swt.layout.FillLayout;
import org.eclipse.swt.widgets.Composite;
import org.eclipse.ui.part.ViewPart;
import org.jfree.chart.ChartFactory;
import org.jfree.chart.ChartPanel;
import org.jfree.chart.JFreeChart;
import org.jfree.chart.plot.PlotOrientation;
import org.jfree.chart.plot.XYPlot;
import org.jfree.chart.renderer.xy.StandardXYItemRenderer;
import org.jfree.data.xy.XYDataset;
import org.jfree.data.xy.XYSeries;
import org.jfree.data.xy.XYSeriesCollection;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.layout.StructureDiagramGenerator;
import org.openscience.cdk.renderer.AtomContainerRenderer;
import org.openscience.cdk.renderer.font.SWTFontManager;
import org.openscience.cdk.renderer.generators.AtomNumberGenerator.WillDrawAtomNumbers;
import org.openscience.cdk.renderer.generators.BasicAtomGenerator;
import org.openscience.cdk.renderer.generators.BasicAtomGenerator.CompactAtom;
import org.openscience.cdk.renderer.generators.BasicBondGenerator;
import org.openscience.cdk.renderer.generators.BasicSceneGenerator;
import org.openscience.cdk.renderer.generators.IGenerator;

public class BestStructureView extends ViewPart {

    public static final String ID = "net.bioclipse.seneca.views.BestStructureView";

    private AtomContainerRenderer renderer;
    private JChemPaintEditorWidget jcpwidget;

    private IMolecule bestMolecule = null;
    private Frame fileTableFrame;

    List<Double> temps = new ArrayList<Double>();
    List<Double> scores = new ArrayList<Double>();
    JFreeChart continuousChart;

    private int maxSteps;

    private final static StructureDiagramGenerator sdg = new StructureDiagramGenerator();

    public BestStructureView() {
        List<IGenerator<IAtomContainer>> generators = makeGenerators();
        renderer = new AtomContainerRenderer(generators, new SWTFontManager(null));
        renderer.getRenderer2DModel().getParameter(CompactAtom.class).setValue(true);
        renderer.getRenderer2DModel().getParameter(WillDrawAtomNumbers.class).setValue(false);
    }

    public void createPartControl(Composite parent) {
        SashForm sash = new SashForm(parent, SWT.VERTICAL);
        jcpwidget = new JChemPaintEditorWidget(sash, SWT.PUSH);
        Composite contChartcomposite = new Composite(sash, SWT.EMBEDDED);
        FillLayout layout = new FillLayout(SWT.VERTICAL);
        contChartcomposite.setLayout(layout);
        fileTableFrame = SWT_AWT.new_Frame(contChartcomposite);

        String xAxisLabel = "Steps";
        String yAxisLabel = "Temperature/Score";
        String title = "Annealing progress";
        XYSeries series = new XYSeries("Signal");
        for (int i = 0; i < (maxSteps != 0 ? maxSteps : temps.size()); i++) {
            if (i < temps.size())
                series.add(i, temps.get(i));
            else
                series.add(i, 0);
        }

        XYDataset xyDataset = new XYSeriesCollection(series);
        continuousChart = ChartFactory.createXYAreaChart(title, xAxisLabel, yAxisLabel, xyDataset,
                PlotOrientation.VERTICAL, false, true, false);
        continuousChart.setAntiAlias(false);

        XYPlot continuousPlot = continuousChart.getXYPlot();

        continuousPlot.setRenderer(new StandardXYItemRenderer());
        ChartPanel chart = new ChartPanel(continuousChart);
        fileTableFrame.add(chart);
        //fileTableFrame.validate();
        //fileTableFrame.repaint();

    }

    public void setFocus() {
        // nothing to do
    }

    public void setBestStructure(IMolecule molecule) {
        this.bestMolecule = molecule;
        this.updateView();
    }

    private List<IGenerator<IAtomContainer>> makeGenerators() {
        List<IGenerator<IAtomContainer>> generators = new ArrayList<IGenerator<IAtomContainer>>();
        generators.add(new BasicSceneGenerator());
        generators.add(new BasicBondGenerator());
        generators.add(new BasicAtomGenerator());
        return generators;
    }

    private void updateView() {
        try {
            sdg.setMolecule((IMolecule) bestMolecule.clone());
            sdg.generateCoordinates();
            this.bestMolecule = sdg.getMolecule();
            this.getViewSite().getShell().getDisplay().syncExec(new Runnable() {
                public void run() {
                    jcpwidget.setAtomContainer(bestMolecule);
                }
            });
        } catch (Exception exception) {
            System.out.println("Error: " + exception.getMessage());
            exception.printStackTrace();
        }
    }

    public void updateViewTemp() {
        XYSeries series = new XYSeries("Temp");
        for (int i = 0; i < (maxSteps != 0 ? maxSteps : temps.size()); i++) {
            if (i < temps.size())
                series.add(i, temps.get(i));
            else
                series.add(i, 0);
        }

        XYSeriesCollection xyDataset = new XYSeriesCollection(series);
        XYSeries scoreseries = new XYSeries("Score");
        for (int i = 0; i < (maxSteps != 0 ? maxSteps : temps.size()); i++) {
            if (i < temps.size())
                scoreseries.add(i, scores.get(i));
            else
                scoreseries.add(i, 0);
        }
        xyDataset.addSeries(scoreseries);
        continuousChart.getXYPlot().setDataset(xyDataset);

    }

    public void addTemperatureValue(double temp, double score) {
        temps.add(temp);
        scores.add(score);
        updateViewTemp();
    }

    public void setMaxSteps(int maxSteps) {
        this.maxSteps = maxSteps;
    }

    public void reset() {
        temps = new ArrayList<Double>();
        scores = new ArrayList<Double>();
        updateViewTemp();
    }
}