/*
 * 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.annotate

import com.antigenomics.vdjtools.misc.ExecUtil
import com.antigenomics.vdjtools.sample.Clonotype
import com.antigenomics.vdjtools.sample.Sample
import groovyx.gpars.GParsPool

class SampleAnnotator {
    final List<ClonotypeAnnotator> annotators

    SampleAnnotator(List<ClonotypeAnnotator> annotators) {
        this.annotators = annotators
    }

    void annotate(Sample sample) {
        if (sample.annotationHeader) {
            sample.annotationHeader += "\t" + annotators.collect { it.category + "." + it.name }.join("\t")
            GParsPool.withPool ExecUtil.THREADS, {
                sample.eachParallel { Clonotype clonotype ->
                    clonotype.annotation += "\t" + annotators.collect { it.annotate(clonotype) }.join("\t")
                }
            }
        } else {
            sample.annotationHeader = annotators.collect { it.category + "." + it.name }.join("\t")
            GParsPool.withPool ExecUtil.THREADS, {
                sample.eachParallel { Clonotype clonotype ->
                    clonotype.annotation = annotators.collect { it.annotate(clonotype) }.join("\t")
                }
            }
        }
    }
}
