/*
 * The Exomiser - A tool to annotate and prioritize genomic variants
 *
 * Copyright (c) 2016-2018 Queen Mary University of London.
 * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd.
 *
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU Affero 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 Affero General Public License for more details.
 *
 * You should have received a copy of the GNU Affero General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */

/*
 * To change this license header, choose License Headers in Project Properties.
 * To change this template file, choose Tools | Templates
 * and open the template in the editor.
 */
package org.monarchinitiative.exomiser.core.analysis.util;

import org.monarchinitiative.exomiser.core.model.Gene;
import org.monarchinitiative.exomiser.core.model.GeneScore;

import java.util.Collections;
import java.util.List;
import java.util.function.Function;

/**
 *
 * @author Jules Jacobsen <jules.jacobsen@sanger.ac.uk>
 */
@FunctionalInterface
public interface GeneScorer {

    public Function<Gene, List<GeneScore>> scoreGene();

    default List<Gene> scoreGenes(List<Gene> genes) {
        //TODO! FIX THIS
        genes.forEach(gene -> {
            List<GeneScore> geneScores = scoreGene().apply(gene);
            for (GeneScore score : geneScores) {
                gene.addGeneScore(score);
            }
        });
        Collections.sort(genes);
        return genes;
    }
}
/*
 * The Exomiser - A tool to annotate and prioritize genomic variants
 *
 * Copyright (c) 2016-2018 Queen Mary University of London.
 * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd.
 *
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU Affero 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 Affero General Public License for more details.
 *
 * You should have received a copy of the GNU Affero General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */

/*
 * To change this license header, choose License Headers in Project Properties.
 * To change this template file, choose Tools | Templates
 * and open the template in the editor.
 */
package org.monarchinitiative.exomiser.core.analysis.util;

import org.monarchinitiative.exomiser.core.model.Gene;
import org.monarchinitiative.exomiser.core.model.GeneScore;

import java.util.Collections;
import java.util.List;
import java.util.function.Function;

/**
 *
 * @author Jules Jacobsen <jules.jacobsen@sanger.ac.uk>
 */
@FunctionalInterface
public interface GeneScorer {

    public Function<Gene, List<GeneScore>> scoreGene();

    default List<Gene> scoreGenes(List<Gene> genes) {
        genes.forEach(gene -> {
            List<GeneScore> geneScores = scoreGene().apply(gene);
            for (GeneScore score : geneScores) {
                gene.addGeneScore(score);
            }
        });
        Collections.sort(genes);
        return genes;
    }
}
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