/*
 * Copyright (c) 2015, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
 * (here and after addressed as Inventors)
 * All Rights Reserved
 *
 * Permission to use, copy, modify and distribute any part of this program for
 * educational, research and non-profit purposes, by non-profit institutions
 * only, without fee, and without a written agreement is hereby granted,
 * provided that the above copyright notice, this paragraph and the following
 * three paragraphs appear in all copies.
 *
 * Those desiring to incorporate this work into commercial products or use for
 * commercial purposes should contact the Inventors using one of the following
 * email addresses: chudakovdm@mail.ru, chudakovdm@gmail.com
 *
 * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT,
 * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS,
 * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN
 * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 *
 * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS
 * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR
 * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO
 * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT
 * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A
 * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY
 * PATENT, TRADEMARK OR OTHER RIGHTS.
 */

package com.antigenomics.vdjtools.diversity

import org.apache.commons.math3.distribution.ZipfDistribution
import org.apache.commons.math3.random.Well19937c

class FrequencyTableGenerator {
    int numberOfSpecies = 500, observedSpecies = 100
    double exponent = 3.0

    FrequencyTableGenerator() {


    }

    FrequencyTableGenerator(int numberOfSpecies, double exponent) {
        this.numberOfSpecies = numberOfSpecies
        this.exponent = exponent
    }

    public FrequencyTable create() {
        def distr = new ZipfDistribution(new Well19937c(21051102L),
                numberOfSpecies, exponent)

        def cache = new HashMap<Long, Long>()

        observedSpecies.times {
            def count = distr.sample()
            cache.put(count, (cache[count] ?: 0) + 1)
        }

        new FrequencyTable(cache)
    }
}
