org.gersteinlab.regulation.model
Class MultiplicativeRateModel

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

public class MultiplicativeRateModel
extends RateModel

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

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

Field Summary
protected  double[] bigProduct
           
protected  double[][] dykdt
           
protected  double[][] dyldt
           
protected  double[][] gyj
           
protected  double[][][] hyj
           
protected  int kCount
           
protected  int lCount
           
protected  double[] yj
           
protected  double[][] yk
           
protected  double[][] yl
           
 
Fields inherited from class org.gersteinlab.regulation.model.RateModel
a, dykdts, h, n, t, yj0, yks
 
Constructor Summary
MultiplicativeRateModel(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

yl

protected double[][] yl

dyldt

protected double[][] dyldt

kCount

protected int kCount

lCount

protected int lCount

yj

protected double[] yj

gyj

protected double[][] gyj

hyj

protected double[][][] hyj

bigProduct

protected double[] bigProduct
Constructor Detail

MultiplicativeRateModel

public MultiplicativeRateModel(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]: a_{j0}, basal expression rate . a[1]: a_{j1}, degradation rate . a[2,4,...,2x]: b_{jk}, rate constant of inhibitor k . a[3,5,...,2x+1]: c_{jk}, sigmoidal constant of inhibitor k . a[2x+2,2x+4,...]: b_{jl}, rate constant of enhancer l . a[2x+3,2x+5,...]: c_{jl}, sigmoidal constant of enhancer l 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()