org.gersteinlab.regulation.model
Class LinearRateModel

java.lang.Object
  extended by org.gersteinlab.regulation.model.RateModel
      extended by org.gersteinlab.regulation.model.LinearRateModel

public class LinearRateModel
extends RateModel

        Providing methods for a rate model based on linear differential
        equations.
        

Version:
1.0 (September 1, 2008)
        Change History:
        1.0     - Initial version
        
Author:
Kevin Yuk-Lap Yip

Field Summary
protected  double[][] dykdt
           
protected  double[][] gyj
           
protected  double h_ha1p1
           
protected  double ha1_ha1d2p1_p1
           
protected  double ha1d2p1
           
protected  double[][][] hyj
           
protected  double[] yj
           
protected  double[][] yk
           
 
Fields inherited from class org.gersteinlab.regulation.model.RateModel
a, dykdts, h, n, t, yj0, yks
 
Constructor Summary
LinearRateModel(double[] tIn, double yj0In, double[][][] yksIn, double[][][] dykdtsIn)
           
 
Method Summary
 double[] f()
          Note: to avoid array copying, the internal cached result is returned.
 double[][] gf()
          Note: to avoid array copying, the internal cached result is returned.
 double[][][] hf()
          Note: to avoid array copying, the internal cached result is returned.
 void setParam(double[] aIn)
          Set the parameter values.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

yk

protected double[][] yk

dykdt

protected double[][] dykdt

yj

protected double[] yj

gyj

protected double[][] gyj

hyj

protected double[][][] hyj

ha1d2p1

protected double ha1d2p1

ha1_ha1d2p1_p1

protected double ha1_ha1d2p1_p1

h_ha1p1

protected double h_ha1p1
Constructor Detail

LinearRateModel

public LinearRateModel(double[] tIn,
                       double yj0In,
                       double[][][] yksIn,
                       double[][][] dykdtsIn)
See Also:
RateModel.RateModel(double[], double, double[][][], double[][][])
Method Detail

setParam

public void setParam(double[] aIn)
Set the parameter values. . a[0]: constant term . a[1]: coefficient of the target gene j . a[2..]: coefficients of the potential regulators (corresponding to yk[0..]) If the values in the array are changed, call setParam() again to clear any cached intermediate results before calling the other methods.

Overrides:
setParam in class RateModel
Parameters:
aIn - The parameter values

f

public double[] f()
Note: to avoid array copying, the internal cached result is returned. Calling methods should not modify the contents, or should call setParam() first before calling this method again.

Specified by:
f in class RateModel
Returns:
The estimated values at the specified time points
See Also:
RateModel.f()

gf

public double[][] gf()
Note: to avoid array copying, the internal cached result is returned. Calling methods should not modify the contents, or should call setParam() first before calling this method again.

Specified by:
gf in class RateModel
Returns:
The estimated gradients at the specified time points First dimension: time point Second dimension: parameter
See Also:
RateModel.gf()

hf

public double[][][] hf()
Note: to avoid array copying, the internal cached result is returned. Calling methods should not modify the contents, or should call setParam() first before calling this method again.

Specified by:
hf in class RateModel
Returns:
The estimated Hessians at the specified time points First dimension: time point Second and third dimensions: parameter
See Also:
RateModel.hf()