AssayDataDoseResponseHill4p.java

package gov.nih.ncgc.bard.pcparser;
// $Id: AssayDataDoseResponseHill4p.java 2278 2008-05-29 22:27:45Z nguyenda $

import java.io.IOException;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;

public class AssayDataDoseResponseHill4p extends AssayDataDoseResponse {
    private static final long serialVersionUID = 12242007L;
    private static final double ln10 = 2.30258509299404568401;

    private double hillCoef;
    private double zeroAct;
    private double infAct;
    private double ac50; // in Molar
    private double logac50;

    public AssayDataDoseResponseHill4p (int tid) {
	super (tid);
    }
    public AssayDataDoseResponseHill4p (int tid, Double[] response) {
	super (tid, response);
    }

    public void setHillCoef (double hillCoef) { this.hillCoef = hillCoef; }
    public double getHillCoef () { return hillCoef; }
    public void setZeroAct (double zeroAct) { this.zeroAct = zeroAct; }
    public double getZeroAct () { return zeroAct; }
    public void setInfAct (double infAct) { this.infAct = infAct; }
    public double getInfAct () { return infAct; }
    public void setAc50 (double ac50) { 
	this.ac50 = ac50; 
	if (ac50 != 0.) {
	    this.logac50 = Math.log10(ac50);
	}
    }
    public double getAc50 () { return ac50; }

    private double hillfn (double logx) { // x - log10 M
	if (ac50 != 0.) {
	    return zeroAct + ((infAct - zeroAct)  
			      / (1. + Math.exp(ln10 * hillCoef * 
					       (logac50 - logx))));
	}
	return 0.;
    }

    public double[][] getFittedDoseResponseCurve () { 
	double[][] curve = new double[0][];

	Double[] dose = getDose ();
	if (dose == null || dose.length == 0) {
	    ///...
	}
	else if (ac50 != 0.) {
	    double[] x = new double[dose.length];
	    //System.out.println();
	    for (int i = 0; i < x.length; ++i) {
		x[i] = Math.log10(dose[i]);
		//System.out.println(dose[i] + " " + x[i] + " " + hillfn (x[i]));
	    }
	    
	    // upsample enough time to get a smooth curve...
	    x = upsample (upsample (upsample (upsample (x))));
	    
	    curve = new double[2][x.length];
	    for (int i = 0; i < x.length; ++i) {
		curve[0][i] = hillfn (x[i]);
		curve[1][i] = x[i];
	    }
	}
	return curve;
    }

    private static double[] upsample (double[] x) {
        if (x.length == 0) {
            return new double[]{};
        }
	
        double[] x2 = new double[2*x.length-1];
        for (int i=0; i<x2.length; i++) {
            if (i%2 == 0)
                x2[i] = x[i/2];
            else
                x2[i] = 0.5*(x[(i-1)/2]+x[(i+1)/2]);
        }
        return x2;
    }
    
    /*
     * override these methods in case we make changes to the
     * class later on, so that it doesn't break old code
     */
    private void writeObject (ObjectOutputStream out) throws IOException {
	out.writeDouble(hillCoef);
	out.writeDouble(zeroAct);
	out.writeDouble(infAct);
	out.writeDouble(ac50);
    }

    private void readObject (ObjectInputStream in) 
	throws IOException, ClassNotFoundException {
	setHillCoef (in.readDouble());
	setZeroAct (in.readDouble());
	setInfAct (in.readDouble());
	setAc50 (in.readDouble());
    }
}