org.gersteinlab.regulation.model
Class SigmoidalRateModel

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

public class SigmoidalRateModel
extends RateModel

        Providing methods for a rate model based on sigmoidal 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[] expTerms
           
protected  double[][] gyj
           
protected  double hha0a1
           
protected  double hha1a1d2mha1p1
           
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
SigmoidalRateModel(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

expTerms

protected double[] expTerms

hha1a1d2mha1p1

protected double hha1a1d2mha1p1

hha0a1

protected double hha0a1
Constructor Detail

SigmoidalRateModel

public SigmoidalRateModel(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]: b_{j1}, maximum rate of expression . a[1]: b_{j2}, degradation rate . a[3]: a_{j0}, constant term in the linear part . a[4..]: a_{jk}, coefficients of the regulators in the lienar part (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()