Chromosome.java

/**
 * See the NOTICE file distributed with this work for additional
 * information regarding copyright ownership.
 *
 * This is free software; you can redistribute it and/or modify it
 * under the terms of the GNU Lesser General Public License as
 * published by the Free Software Foundation; either version 2.1 of
 * the License, or (at your option) any later version.
 *
 * This software 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.
 *
 * You should have received a copy of the GNU Lesser General Public
 * License along with this software; if not, write to the Free
 * Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA
 * 02110-1301 USA, or see the FSF site: http://www.fsf.org.
 */
package org.ut.biolab.medsavant.shared.model;

import java.io.Serializable;


/**
 *
 * @author mfiume
 */
public class Chromosome implements Serializable {
    private final int centromerePos;
    private final String name;
    private final int length;

    public Chromosome(String name, int centromerePos, int length) {
        this.name = name;
        this.length = length;
        this.centromerePos = centromerePos;
    }

    public int getCentromerePos() {
        return centromerePos;
    }

    public int getLength() {
        return length;
    }

    public String getName() {
        return name;
    }

    public String getShortname() {
        return generateShortName(getName());
    }

    private String generateShortName(String name){
        return name.toLowerCase().replace("chr","").replace("contig", "").toUpperCase();
    }

    public static Chromosome[] getHG17Chromosomes(){
        return new Chromosome[] {
            new Chromosome("chr1", 125000000, 245522847),
            new Chromosome("chr2", 93300000, 243018229),
            new Chromosome("chr3", 91000000, 199505740),
            new Chromosome("chr4", 50400000, 191411218),
            new Chromosome("chr5", 48400000, 180857866),
            new Chromosome("chr6", 61000000, 170975699),
            new Chromosome("chr7", 59900000, 158628139),
            new Chromosome("chr8", 45600000, 146274826),
            new Chromosome("chr9", 49000000, 138429268),
            new Chromosome("chr10", 40200000, 135413628),
            new Chromosome("chr11", 53700000, 134452384),
            new Chromosome("chr12", 35800000, 132449811),
            new Chromosome("chr13", 17900000, 114142980),
            new Chromosome("chr14", 17600000, 106368585),
            new Chromosome("chr15", 19000000, 100338915),
            new Chromosome("chr16", 36600000, 88827254),
            new Chromosome("chr17", 24000000, 78774742),
            new Chromosome("chr18", 17200000, 76117153),
            new Chromosome("chr19", 26500000, 63811651),
            new Chromosome("chr20", 27500000, 62435964),
            new Chromosome("chr21", 13200000, 46944323),
            new Chromosome("chr22", 14700000, 49554710),
            new Chromosome("chrX", 60600000, 154824264),
            new Chromosome("chrY", 12500000, 57701691)
        };
    }

    public static Chromosome[] getHG18Chromosomes(){
        return new Chromosome[] {
            new Chromosome("chr1", 125000000, 247249719),
            new Chromosome("chr2", 93300000, 242951149),
            new Chromosome("chr3", 91000000, 199501827),
            new Chromosome("chr4", 50400000, 191273063),
            new Chromosome("chr5", 48400000, 180857866),
            new Chromosome("chr6", 61000000, 170899992),
            new Chromosome("chr7", 59900000, 158821424),
            new Chromosome("chr8", 45600000, 146274826),
            new Chromosome("chr9", 49000000, 140273252),
            new Chromosome("chr10", 40200000, 135374737),
            new Chromosome("chr11", 53700000, 134452384),
            new Chromosome("chr12", 35800000, 132349534),
            new Chromosome("chr13", 17900000, 114142980),
            new Chromosome("chr14", 17600000, 106368585),
            new Chromosome("chr15", 19000000, 100338915),
            new Chromosome("chr16", 36600000, 88827254),
            new Chromosome("chr17", 24000000, 78774742),
            new Chromosome("chr18", 17200000, 76117153),
            new Chromosome("chr19", 26500000, 63811651),
            new Chromosome("chr20", 27500000, 62435964),
            new Chromosome("chr21", 13200000, 46944323),
            new Chromosome("chr22", 14700000, 49691432),
            new Chromosome("chrX", 60600000, 154913754),
            new Chromosome("chrY", 12500000, 57772954)
        };
    }

    public static Chromosome[] getHG19Chromosomes(){
        return new Chromosome[] {
            new Chromosome("chr1", 125000000, 249250621),
            new Chromosome("chr2", 93300000, 243199373),
            new Chromosome("chr3", 91000000, 198022430),
            new Chromosome("chr4", 50400000, 191154276),
            new Chromosome("chr5", 48400000, 180915260),
            new Chromosome("chr6", 61000000, 171115067),
            new Chromosome("chr7", 59900000, 159138663),
            new Chromosome("chr8", 45600000, 146364022),
            new Chromosome("chr9", 49000000, 141213431),
            new Chromosome("chr10", 40200000, 135534747),
            new Chromosome("chr11", 53700000, 135006516),
            new Chromosome("chr12", 35800000, 133851895),
            new Chromosome("chr13", 17900000, 115169878),
            new Chromosome("chr14", 17600000, 107349540),
            new Chromosome("chr15", 19000000, 102531392),
            new Chromosome("chr16", 36600000, 90354753),
            new Chromosome("chr17", 24000000, 81195210),
            new Chromosome("chr18", 17200000, 78077248),
            new Chromosome("chr19", 26500000, 59128983),
            new Chromosome("chr20", 27500000, 63025520),
            new Chromosome("chr21", 13200000, 48129895),
            new Chromosome("chr22", 14700000, 51304566),
            new Chromosome("chrX", 60600000, 155270560),
            new Chromosome("chrY", 12500000, 59373566)
        };
    }

}