net.bioclipse.smartcyp.ds.SmartcypGenerator.java Source code

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Here is the source code for net.bioclipse.smartcyp.ds.SmartcypGenerator.java

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/* *****************************************************************************
 * Copyright (c) 2010 Ola Spjuth - ospjuth@users.sf.net
 * 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 - initial API and implementation
 ******************************************************************************/
package net.bioclipse.smartcyp.ds;

import java.awt.Color;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
import java.util.Map;

import net.bioclipse.ds.Activator;
import net.bioclipse.ds.DSConstants;
import net.bioclipse.ds.DSPrefs;

import org.apache.log4j.Logger;
import org.eclipse.jface.preference.IPreferenceStore;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.renderer.RendererModel;
import org.openscience.cdk.renderer.elements.ElementGroup;
import org.openscience.cdk.renderer.elements.IRenderingElement;
import org.openscience.cdk.renderer.elements.OvalElement;
import org.openscience.cdk.renderer.generators.IGenerator;
import org.openscience.cdk.renderer.generators.IGeneratorParameter;
import org.openscience.cdk.renderer.generators.parameter.AbstractGeneratorParameter;

/**
 * A generator to draw circles with color on a scale between blue > yellow > red.
 * 
 * @author ola
 *
 */
public class SmartcypGenerator implements IGenerator<IAtomContainer> {

    private static final Logger logger = Logger.getLogger(SmartcypGenerator.class);

    public SmartcypGenerator() {

    }

    /**
     * Adds the ability to turn the generator on/off via a Handler.
     * False by default.
     */
    public static class Visibility extends AbstractGeneratorParameter<Boolean> {
        public Boolean getDefault() {
            return false;
        }
    }

    private static IGeneratorParameter<Boolean> visible = new Visibility();

    public static void setVisible(Boolean visible1) {
        visible.setValue(visible1);
    }

    /**
     * Define values for per atom index for coloring
     */
    public static class AtomMap extends AbstractGeneratorParameter<Map<Integer, Number>> {
        public Map<Integer, Number> getDefault() {
            return Collections.emptyMap();
        }
    }

    private static IGeneratorParameter<Map<Integer, Number>> atomMap = new AtomMap();

    public static void setVisible(Map<Integer, Number> map) {
        atomMap.setValue(map);
    }

    /**
     * Set up the colored M2D circles based on calculated properties
     */
    public IRenderingElement generate(IAtomContainer ac, RendererModel model) {

        ElementGroup group = new ElementGroup();

        if (visible.getValue() == false)
            return group;
        //If no atommap, do not paint
        if (atomMap.getValue().size() <= 0) {
            logger.error("A SmartcypGenerator is used, but AtomMap was empty.");
            return group;
        }

        //Read prefs for rendering params and compute real values
        IPreferenceStore store = Activator.getDefault().getPreferenceStore();
        int circleRadiusPref = store.getInt(DSPrefs.CIRCLE_RADIUS);
        double circleRadius = (double) circleRadiusPref / 10;
        if (circleRadius <= 0 || circleRadius > 1)
            circleRadius = 0.6;

        for (int i = 0; i < ac.getAtomCount(); i++) { //Loop over all atoms
            IAtom atom = ac.getAtom(i);

            Color drawColor = Color.WHITE; //Error color
            double resValue = 0;

            //If we have a result value for this atom, use this
            if (atomMap.getValue().keySet().contains(i)) {
                resValue = atomMap.getValue().get(i).doubleValue();

                if (resValue == 1)
                    drawColor = new Color(240, 0, 0, DSConstants.OVAL_ALPHA);
                if (resValue == 2)
                    drawColor = new Color(200, 170, 0, DSConstants.OVAL_ALPHA);
                if (resValue == 3)
                    drawColor = new Color(0, 240, 0, DSConstants.OVAL_ALPHA);

            }

            if (drawColor != null) {
                group.add(new OvalElement(atom.getPoint2d().x, atom.getPoint2d().y, circleRadius, true, drawColor));

            }

        }

        return group;
    }

    public List<IGeneratorParameter<?>> getParameters() {
        return Arrays.asList(new IGeneratorParameter<?>[] { visible, atomMap });
    }
}