Decorator.java

/*
 * #%L
 * gitools-core
 * %%
 * Copyright (C) 2013 Universitat Pompeu Fabra - Biomedical Genomics group
 * %%
 * This program 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 3 of the 
 * License, or (at your option) any later version.
 * 
 * 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 General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public 
 * License along with this program.  If not, see
 * <http://www.gnu.org/licenses/gpl-3.0.html>.
 * #L%
 */
package org.gitools.heatmap.decorator;

import com.jgoodies.binding.beans.Model;
import org.gitools.api.matrix.IMatrix;
import org.gitools.api.matrix.IMatrixLayer;
import org.gitools.api.matrix.IMatrixPosition;
import org.gitools.heatmap.decorator.impl.*;
import org.gitools.matrix.MatrixUtils;
import org.gitools.utils.colorscale.INumericColorScale;
import org.gitools.utils.formatter.ITextFormatter;

import javax.xml.bind.annotation.*;
import java.util.ArrayList;
import java.util.List;

@XmlRootElement
@XmlAccessorType(XmlAccessType.FIELD)
@XmlSeeAlso({BinaryDecorator.class, LinearDecorator.class,
        PValueDecorator.class, ZScoreDecorator.class,
        CorrelationDecorator.class, CategoricalDecorator.class,
        PValueLogSumDecorator.class})
public abstract class Decorator<C extends INumericColorScale> extends Model {

    public static final String PROPERTY_SHOW_VALUE = "showValue";
    public static final String OUTSIDE_EVENTS_FUNCTION = "Outside Events";
    public static final String NON_0_EVENTS_FUNCTION = "Non-0 Events";

    @XmlAttribute
    private String name;

    @XmlElement(name = "show-value")
    private boolean showValue = false;

    @XmlTransient
    private List<NonEventToNullFunction> eventFunctions;

    public Decorator() {
        super();
    }


    public abstract void decorate(Decoration decoration, ITextFormatter textFormatter, IMatrix matrix, IMatrixLayer layer, String... identifiers);

    public abstract NonEventToNullFunction getDefaultEventFunction();

    public List<NonEventToNullFunction> getEventFunctionAlternatives() {

        if (eventFunctions == null) {
            initEventFunctions();
        }

        return eventFunctions;

    }

    protected void initEventFunctions() {
        eventFunctions = new ArrayList<>();

        eventFunctions.add(new NonEventToNullFunction<INumericColorScale>(getScale(), OUTSIDE_EVENTS_FUNCTION) {

            @Override
            public Double apply(Double value, IMatrixPosition position) {
                this.position = position;
                if (value == null) {
                    return null;
                }

                if (getColorScale().isOutsideRange(value)) {
                    return value;
                } else {
                    return null;
                }


            }

            @Override
            public String getDescription() {
                INumericColorScale scale = getColorScale();
                return "All values below " + scale.getMinValue() + "  or above " +
                        scale.getMaxValue() +
                        " of the scale are events";
            }
        });

        eventFunctions.add(new NonEventToNullFunction<INumericColorScale>(getScale(), NON_0_EVENTS_FUNCTION) {
            @Override
            public Double apply(Double value, IMatrixPosition position) {
                this.position = position;
                return (value == null || value == 0) ? null : value;
            }

            @Override
            public String getDescription() {
                return "All values not equal to 0 or 'empty' are events";
            }
        });


    }


    public void decorate(Decoration decoration, ITextFormatter textFormatter, IMatrix matrix, IMatrixLayer layer, IMatrixPosition position) {
        decorate(decoration, textFormatter, matrix, layer, position.toVector());
    }

    public abstract C getScale();

    public String getName() {
        return name;
    }

    public void setName(String name) {
        this.name = name;
    }

    public boolean isShowValue() {
        return showValue;
    }

    public void setShowValue(boolean showValue) {
        setShowValue(showValue, false);
    }

    public void setShowValue(boolean showValue, boolean avoidFirePropertyChange) {
        boolean oldValue = this.showValue;
        this.showValue = showValue;
        if (!avoidFirePropertyChange) {
            firePropertyChange(PROPERTY_SHOW_VALUE, oldValue, showValue);
        }
    }

    protected static double toDouble(Object value) {
        return MatrixUtils.doubleValue(value);
    }
}