bide.core.par.Spot.java Source code

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Here is the source code for bide.core.par.Spot.java

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/*******************************************************************************
 * Spot.java
 * 
 * This file is part of BIDE-2D
 * 
 * Copyright (C) 2012 Steven Wu
 * 
 * BIDE-2D 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.
 * 
 * BIDE-2D 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 BIDE-2D.  If not, see <http://www.gnu.org/licenses/>.
 ******************************************************************************/
package bide.core.par;

import java.util.ArrayList;
import java.util.Arrays;

import org.apache.commons.lang3.ArrayUtils;
import org.apache.commons.math3.random.JDKRandomGenerator;
import org.apache.commons.math3.stat.StatUtils;

import com.google.common.primitives.Doubles;

public class Spot {

    private static JDKRandomGenerator rand = new JDKRandomGenerator();
    //   private static NormalDistribution nd = new NormalDistribution(0, 1);
    private String names;
    private double[] controlSpot;
    private double[] caseSpot;
    private double[] expressControlSpot;
    private double[] expressCaseSpot;
    private int numberOfSpot;
    private int numberOfCase;
    private int numberOfControl;

    public Spot() {
    }

    /**
     * numberOfSpot = totalNumberOfCase = totalNumberOfControl
     * @param s
     */
    public Spot(String s) {
        //str format  spotNo\tCO1\tCO2\t...\tCA1\tCA2
        //String[] oneSpot = s.replaceAll("NA","NaN").replaceAll("\t0.0","\tNaN").split("\t");
        String[] oneSpot = s.replaceAll("NA", "NaN").split("\t");

        numberOfSpot = oneSpot.length / 2;
        controlSpot = new double[numberOfSpot];
        caseSpot = new double[numberOfSpot];
        int n1 = numberOfSpot + 1;
        names = oneSpot[0];
        for (int i = 0; i < numberOfSpot; i++) {
            controlSpot[i] = Double.parseDouble(oneSpot[i + 1]);
            caseSpot[i] = Double.parseDouble(oneSpot[i + n1]);

        }
        expressControlSpot = formatSpot(controlSpot);
        expressCaseSpot = formatSpot(caseSpot);
        numberOfControl = expressControlSpot.length;
        numberOfCase = expressCaseSpot.length;

    }

    private double[] formatSpot(double[] spot) {

        int express = 0;
        ArrayList<Double> expressSpot = new ArrayList<Double>();
        for (int i = 0; i < spot.length; i++) {
            if (!Double.isNaN(spot[i])) {
                express++;
                expressSpot.add(spot[i]);
            }
        }
        double[] expSpot = ArrayUtils.toPrimitive(expressSpot.toArray(new Double[express]));
        return expSpot;
    }

    public void randomInit(int n, String string) {

        numberOfSpot = n;

        controlSpot = new double[numberOfSpot];
        caseSpot = new double[numberOfSpot];
        //      int n1 = numberOfSpot+1;
        names = string;
        for (int i = 0; i < numberOfSpot; i++) {
            controlSpot[i] = generateRandomValue();
            caseSpot[i] = generateRandomValue(); //nd.randomDist();
        }
        expressControlSpot = formatSpot(controlSpot);
        expressCaseSpot = formatSpot(caseSpot);
        numberOfControl = expressControlSpot.length;
        numberOfCase = expressCaseSpot.length;

    }

    private double generateRandomValue() {

        boolean isNa = rand.nextBoolean();
        if (isNa) {
            return Double.NaN;
        } else {
            return rand.nextGaussian();
        }
    }

    public double[] getCase() {
        return caseSpot;
    }

    public double[] getControl() {
        return controlSpot;
    }

    public int getNumberOfSpot() {
        return numberOfSpot;
    }

    public String getName() {
        return names;
    }

    public double findMin() {
        return StatUtils.min(Doubles.concat(controlSpot, caseSpot));
        //      return StatUtils.min(ArrayUtils.addAll(controlSpot,caseSpot));

    }

    @Override
    public String toString() {

        StringBuilder sb = new StringBuilder();
        sb.append("SpotNumber: ").append(names).append("\n").append("Control: ")
                .append(Arrays.toString(controlSpot)).append("\n").append("Case:    ")
                .append(Arrays.toString(caseSpot)).append("\n");
        return sb.toString();
    }

    /**
     * @return Returns the expressCaseSpot.
     */
    public double[] getExpressCaseSpot() {
        return expressCaseSpot;
    }

    /**
     * @return Returns the expressControlSpot.
     */
    public double[] getExpressControlSpot() {
        return expressControlSpot;
    }

    /**
     * @return Returns the numberOfCase.
     */
    public int getNumberOfCase() {
        return numberOfCase;
    }

    /**
     * @return Returns the numberOfControl.
     */
    public int getNumberOfControl() {
        return numberOfControl;
    }

    public static ArrayList<Spot> generateList(int totalSpot, int spotPerGel) {
        ArrayList<Spot> allSpots = new ArrayList<Spot>();
        for (int i = 0; i < totalSpot; i++) {
            Spot s = new Spot();
            s.randomInit(spotPerGel, "" + i);
            s.randomInit(spotPerGel, Integer.toString(i));
            allSpots.add(s);
        }
        return allSpots;
    }
}