Transcript.java

/*
 * Copyright (c) 2006-2008 Genome Research Limited.
 *
 * This program is free software; you can redistribute it and/or modify
 * it under the terms of the GNU Library General Public License as published
 * by  the Free Software Foundation; either version 2 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 Library General Public License for more details.
 *
 * You should have received a copy of the GNU Library General Public License
 * along with this program; see the file COPYING.LIB.  If not, write to
 * the Free Software Foundation Inc., 59 Temple Place - Suite 330,
 * Boston, MA  02111-1307 USA
 */

package org.genedb.db.domain.objects;

import java.awt.Color;
import java.io.Serializable;
import java.util.List;
import java.util.Set;
import java.util.SortedSet;
import java.util.TreeSet;

import org.gmod.schema.mapped.Feature;
import org.gmod.schema.mapped.FeatureProp;

public class Transcript extends LocatedFeature implements Serializable {
    private transient Feature protein;
    private String name;
    private Integer colourId; // May be null
    private BasicGene gene;
    private SortedSet<TranscriptComponent> components;
    private List<String> products;
    private int fmin, fmax;

    @Override
    public String getUniqueName() {
        return name;
    }
    public void setUniqueName(String name) {
        this.name = name;
    }

    @Override
    public int getFmin() {
        return fmin;
    }
    public void setFmin(int fmin) {
        this.fmin = fmin;
    }

    @Override
    public int getFmax() {
        return fmax;
    }
    public void setFmax(int fmax) {
        this.fmax = fmax;
    }

    public SortedSet<TranscriptComponent> getComponents() {
        return components;
    }
    public void setComponents(SortedSet<TranscriptComponent> components) {
        this.components = components;
    }
    public void setComponents(Set<TranscriptComponent> components) {
        this.components = new TreeSet<TranscriptComponent> (components);
    }

    public Integer getColourId() {
        return colourId;
    }
    public void setColourId(Integer colourId) {
        this.colourId = colourId;
    }

    private static Color[] artemisColours = new Color[] {
        new Color(255, 255, 255),
        new Color(100, 100, 100),
        new Color(255, 0, 0),
        new Color(0, 255, 0),
        new Color(0, 0, 255),
        new Color(0, 255, 255),
        new Color(255, 0, 255),
        new Color(224, 208, 0), // previously: new Color(245, 245, 0),
        new Color(152, 251, 152),
        new Color(135, 206, 250),
        new Color(255, 165, 0),
        new Color(200, 150, 100),
        new Color(255, 200, 200),
        new Color(170, 170, 170),
        new Color(0, 0, 0),
        new Color(255, 63,  63),
        new Color(255, 127, 127),
        new Color(255, 191, 191),
    };

    @Override
    public Color getColor() {
        if (colourId == null || colourId >= artemisColours.length) {
            return null;
        }
        return artemisColours[colourId];
    }

    public Feature getProtein() {
        return protein;
    }

    /**
     * Sets the protein property, and also updates the colourId from the protein.
     *
     * @param protein
     */
    public void setProtein(Feature protein) {
        this.protein = protein;
        for (FeatureProp proteinProp: protein.getFeatureProps()) {
            if (proteinProp.getType().getName().equals("colour"))
                setColourId(Integer.parseInt(proteinProp.getValue()));
        }
    }

    public BasicGene getGene() {
        return gene;
    }
    public void setGene(BasicGene gene) {
        this.gene = gene;
    }
    public List<String> getProducts() {
        return products;
    }
    public void setProducts(List<String> products) {
        this.products = products;
    }
}