org.gersteinlab.regulation.model
Class SigmoidalRateModel
java.lang.Object
org.gersteinlab.regulation.model.RateModel
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
|
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 |
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
SigmoidalRateModel
public SigmoidalRateModel(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]: 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()