org.gersteinlab.regulation.model
Class MultiplicativeRateModel
java.lang.Object
org.gersteinlab.regulation.model.RateModel
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
|
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 |
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
MultiplicativeRateModel
public MultiplicativeRateModel(double[] tIn,
double yj0In,
double[][][] yksIn,
double[][][] dykdtsIn)
- See Also:
RateModel.RateModel(double[], double, double[][][], double[][][])
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()