org.csml.tommo.sugar.heatmap.AbsoluteDiffOperation.java Source code

Introduction

Here is the source code for org.csml.tommo.sugar.heatmap.AbsoluteDiffOperation.java

Source

/**
 *    Copyright Masao Nagasaki
 *    Nagasaki Lab
 *    Laboratory of Biomedical Information Analysis,
 *    Department of Integrative Genomics,
 *    Tohoku Medical Megabank Organization, Tohoku University 
 *    @since 2013
 *
 *    This file is part of SUGAR (Subtile-based GUI-Assisted Refiner).
 *    SUGAR is an extension of FastQC (copyright 2010-12 Simon Andrews)
 *
 *    SUGAR 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.
 *
 *    SUGAR 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 SUGAR; if not, write to the Free Software
 *    Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
 */
package org.csml.tommo.sugar.heatmap;

import org.csml.tommo.sugar.modules.QualityHeatMapsPerTileAndBase;
import org.jfree.chart.renderer.PaintScale;

public class AbsoluteDiffOperation extends DiffOperation {

    public AbsoluteDiffOperation() {
        super();
    }

    public AbsoluteDiffOperation(double param) {
        super(param);
    }

    @Override
    public double mix(double topValue, double bottomValue) {
        return Math.abs(super.mix(topValue, bottomValue));
    }

    @Override
    public PaintScale getPaintScale() {
        return new TemperaturePaintScale(0d, QualityHeatMapsPerTileAndBase.MAX_LOWQ_READS_RATIO);
    }
}