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+/*%0A * Copyright (C) 2014 ibnsalem%0A *%0A * This program is free software: you can redistribute it and/or modify%0A * it under the terms of the GNU General Public License as published by%0A * the Free Software Foundation, either version 3 of the License, or%0A * (at your option) any later version.%0A *%0A * This program is distributed in the hope that it will be useful,%0A * but WITHOUT ANY WARRANTY; without even the implied warranty of%0A * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the%0A * GNU General Public License for more details.%0A *%0A * You should have received a copy of the GNU General Public License%0A * along with this program.  If not, see %3Chttp://www.gnu.org/licenses/%3E.%0A */%0Apackage annotation;%0A%0Aimport genomicregions.Gene;%0Aimport genomicregions.GenomicElement;%0Aimport java.util.ArrayList;%0A%0A/**%0A * This class implements an effect mechanism annotation of a structural variant, %0A * such as deletions, duplication or inversion with respect to affected genes, %0A * enhancers and regulatory interaction between them. %0A * A structural variation (SV) or CNV might hold a list of serveral annotation %0A * object. Each annotation object is related to a gene that is affected by the SV.%0A * %0A * @author ibnsalem%0A */%0Apublic class Annotation %7B%0A    %0A    /**%0A     * The %7B@link Gene%7D that is affected by the CNV%0A     */%0A    private Gene gene;%0A    %0A    /** %0A     * A score to quantify this effect mechanism. This score should be the %0A     * Phenomatch score that quantifies the similarity of phenotypes associated%0A     * with the gene and phenotypes observed in the patient.%0A     */%0A    private Double score;%0A    %0A    /**%0A     * List of enhancers that are involved in the CNV effect mechanism%0A     */%0A    private ArrayList%3CGenomicElement%3E enhancers;%0A    %0A    /**%0A     * List of topological domain boundary elements involved in the effect mechanism%0A     */%0A    private ArrayList%3CGenomicElement%3E boundaries;%0A    %0A    /**%0A     * Interaction change between %7B@link Gene%7D and enhancers. %0A     * This String sould be %22gain%22 or %22loss%22.%0A     */%0A    private String interactionChange;%0A    %0A    /**%0A     * An indicator %7B@link String%7D for the method and or settings used to create %0A     * this annotation.%0A     */%0A    private String method;%0A    %0A%7D%0A    %0A%0A

Add Annotation.java class in package annotation