// Path: src/main/java/uk/ac/tgac/rampart/stage/analyse/asm/stats/Scaling.java
// public class Scaling {
// 
//     public static double min(double[] a) {
// 
//         double min = 0.0;
// 
//         for(double v : a) {
//             min = Math.min(v, min);
//         }
// 
//         return min;
//     }
// 
//     public static double max(double[] a) {
// 
//         double max = 0.0;
// 
//         for(double v : a) {
//             max = Math.max(v, max);
//         }
// 
//         return max;
//     }
// 
//     public static void clear(double[] a) {
//         for(int i = 0; i < a.length; i++) {
//             a[i] = 0;
//         }
//     }
// 
//     public static void weight(double[] a, double weight) {
//         for(int i = 0; i < a.length; i++) {
//             a[i] *= weight;
//         }
//     }
// 
//     public static void standardScale(double[] a, boolean invert) {
// 
//         double min = min(a);
//         double max = max(a);
// 
//         for (int i = 0; i < a.length; i++) {
// 
//             double delta = a[i] - min;
// 
//             double diff = max - min;
// 
//             double norm = delta / diff;
// 
//             double newVal = diff == 0.0 ? 0.5 : norm;
// 
//             a[i] = invert ? 1.0 - newVal : newVal;
//         }
//     }
// 
//     public static void deviationScale(double[] a, double mean) {
// 
//         double max = 0.0;
// 
//         for (int i = 0; i < a.length; i++) {
// 
//             double dev = Math.abs(a[i] - mean);
// 
//             max = Math.max(max, dev);
//         }
// 
//         for (int i = 0; i < a.length; i++) {
// 
//             double dev = Math.abs(a[i] - mean);
// 
//             double norm = 1.0 - (dev / max);
// 
//             a[i] = 1.0 - norm;
//         }
//     }
// 
//     public static void percentageScale(double[] a, boolean invert) {
// 
//         for (int i = 0; i < a.length; i++) {
// 
//             double norm = a[i] / 100.0;
// 
//             a[i] = invert ? 1.0 - norm : norm;
//         }
//     }
// }


import static org.junit.Assert.assertTrue;
import org.junit.Test;
import uk.ac.tgac.rampart.stage.analyse.asm.stats.Scaling;
import java.io.IOException;
/*
 * RAMPART - Robust Automatic MultiPle AssembleR Toolkit
 * Copyright (C) 2015  Daniel Mapleson - TGAC
 *
 * 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 uk.ac.tgac.rampart.stage.analyse.asm.selector;




/**
 * User: maplesod
 * Date: 26/04/13
 * Time: 10:57
 */
public class ScalingTest {

    @Test
    public void testStandardNormalise() throws IOException {

        double[] a = new double[] {
                851620,
                746981,
                637136,
                581571,
                521126,
                485352
        };

        Scaling.standardScale(a, true);

        assertTrue(a[0] == 0.0);
    }

    @Test
    public void testDeviationNormalise0() throws IOException {

        double[] a = new double[] {
                399155917,
                400283582,
// Path: src/main/java/uk/ac/tgac/rampart/stage/analyse/asm/stats/Scaling.java
// public class Scaling {
// 
//     public static double min(double[] a) {
// 
//         double min = 0.0;
// 
//         for(double v : a) {
//             min = Math.min(v, min);
//         }
// 
//         return min;
//     }
// 
//     public static double max(double[] a) {
// 
//         double max = 0.0;
// 
//         for(double v : a) {
//             max = Math.max(v, max);
//         }
// 
//         return max;
//     }
// 
//     public static void clear(double[] a) {
//         for(int i = 0; i < a.length; i++) {
//             a[i] = 0;
//         }
//     }
// 
//     public static void weight(double[] a, double weight) {
//         for(int i = 0; i < a.length; i++) {
//             a[i] *= weight;
//         }
//     }
// 
//     public static void standardScale(double[] a, boolean invert) {
// 
//         double min = min(a);
//         double max = max(a);
// 
//         for (int i = 0; i < a.length; i++) {
// 
//             double delta = a[i] - min;
// 
//             double diff = max - min;
// 
//             double norm = delta / diff;
// 
//             double newVal = diff == 0.0 ? 0.5 : norm;
// 
//             a[i] = invert ? 1.0 - newVal : newVal;
//         }
//     }
// 
//     public static void deviationScale(double[] a, double mean) {
// 
//         double max = 0.0;
// 
//         for (int i = 0; i < a.length; i++) {
// 
//             double dev = Math.abs(a[i] - mean);
// 
//             max = Math.max(max, dev);
//         }
// 
//         for (int i = 0; i < a.length; i++) {
// 
//             double dev = Math.abs(a[i] - mean);
// 
//             double norm = 1.0 - (dev / max);
// 
//             a[i] = 1.0 - norm;
//         }
//     }
// 
//     public static void percentageScale(double[] a, boolean invert) {
// 
//         for (int i = 0; i < a.length; i++) {
// 
//             double norm = a[i] / 100.0;
// 
//             a[i] = invert ? 1.0 - norm : norm;
//         }
//     }
// }


// Path: src/test/java/uk/ac/tgac/rampart/stage/analyse/asm/selector/ScalingTest.java
import static org.junit.Assert.assertTrue;
import org.junit.Test;
import uk.ac.tgac.rampart.stage.analyse.asm.stats.Scaling;
import java.io.IOException;

/*
 * RAMPART - Robust Automatic MultiPle AssembleR Toolkit
 * Copyright (C) 2015  Daniel Mapleson - TGAC
 *
 * 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 uk.ac.tgac.rampart.stage.analyse.asm.selector;




/**
 * User: maplesod
 * Date: 26/04/13
 * Time: 10:57
 */
public class ScalingTest {

    @Test
    public void testStandardNormalise() throws IOException {

        double[] a = new double[] {
                851620,
                746981,
                637136,
                581571,
                521126,
                485352
        };

        Scaling.standardScale(a, true);

        assertTrue(a[0] == 0.0);
    }

    @Test
    public void testDeviationNormalise0() throws IOException {

        double[] a = new double[] {
                399155917,
                400283582,
                402925744,