/*
 * Copyright (C) 2009-2010 Institute for Computational Biomedicine,
 *                    Weill Medical College of Cornell University
 *
 *  This program is free software; you can redistribute it and/or modify
 *  it under the terms of the GNU 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 General Public License for more details.
 *
 *  You should have received a copy of the GNU General Public License
 *  along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */

package edu.cornell.med.icb.goby.algorithmic.algorithm;

import edu.cornell.med.icb.goby.algorithmic.data.Annotation;

/**
 * Interface for implementations that estimate counts for annotations.
 * @author Fabien Campagne
 *         Date: May 16, 2010
 *         Time: 3:48:37 PM
 */
public interface AnnotationCountInterface {

    void startPopulating();
    void populate(int startPosition, int endPosition, int queryIndex);

    void sortReads();

    float averageReadsPerPosition(int geneStart, int geneEnd);

    double countReadsPartiallyOverlappingWithInterval(int geneStart, int geneEnd);

    double countReadsStriclyWithinInterval(int geneStart, int geneEnd);

    double geneExpressionCount(Annotation annot);

    void accumulate();

    void baseCount();
}
