A B C D E F G H K L M N O P R S T U V X Y

A

a - Variable in class org.gersteinlab.regulation.model.RateModel
 
ALPHA - Static variable in class org.gersteinlab.regulation.numeric.DescentMethod
 
Analyzer - Class in org.gersteinlab.regulation
A class for analyzing the prediction results.
Analyzer() - Constructor for class org.gersteinlab.regulation.Analyzer
 
armijo(double[], double[], double, double) - Method in class org.gersteinlab.regulation.numeric.DescentMethod
The backtracking line search method (Armijo rule) for determining step size at a point towards a descent direction.
armijo(double[], double, double[], double[], double, double) - Method in class org.gersteinlab.regulation.numeric.DescentMethod
The backtracking line search method (Armijo rule) for determining step size at a point towards a descent direction, with precomputed function value and gradient.

B

BETA - Static variable in class org.gersteinlab.regulation.numeric.DescentMethod
 
bigProduct - Variable in class org.gersteinlab.regulation.model.MultiplicativeRateModel
 
buffer - Variable in class org.gersteinlab.regulation.util.StringTokenizer2
Data buffer

C

coefs - Variable in class org.gersteinlab.regulation.model.Polynomial
 
computeStats() - Method in class org.gersteinlab.regulation.DeletionProfile
1.
coSort(double[], Object[]) - Static method in class org.gersteinlab.regulation.util.Util
Sort an array of numbers in ascending order, and arrange the entries in a second array accordingly.
coSort(double[], Object[], boolean) - Static method in class org.gersteinlab.regulation.util.Util
Sort an array of numbers, and arrange the entries in a second array accordingly.
coSort(double[], Object[], boolean, int, int) - Static method in class org.gersteinlab.regulation.util.Util
Sort a continuous subarray of an array of numbers, and arrange the entries in a second array accordingly.
countTokens() - Method in class org.gersteinlab.regulation.util.StringTokenizer2
 

D

d2Coefs - Variable in class org.gersteinlab.regulation.model.Polynomial
 
d2f(double) - Method in class org.gersteinlab.regulation.model.Polynomial
 
d2f(double) - Method in class org.gersteinlab.regulation.numeric.DoublyDifferentiableFunction
Evaluate the second derivative of the function at a point.
d2f() - Method in class org.gersteinlab.regulation.numeric.DoublyDifferentiableFunction
Evaluate the second derivative of the function at the stored point.
dCoefs - Variable in class org.gersteinlab.regulation.model.Polynomial
 
DeletionProfile - Class in org.gersteinlab.regulation
A class for storing the deletion profile of all genes read from a file.
DeletionProfile() - Constructor for class org.gersteinlab.regulation.DeletionProfile
 
delim - Variable in class org.gersteinlab.regulation.util.StringTokenizer2
The delimiters
DescentMethod - Class in org.gersteinlab.regulation.numeric
A class for minimizing a differentiable multivariate real function using a descent method.
DescentMethod() - Constructor for class org.gersteinlab.regulation.numeric.DescentMethod
 
df(double) - Method in class org.gersteinlab.regulation.model.Polynomial
 
df(double) - Method in class org.gersteinlab.regulation.numeric.DifferentiableFunction
Evaluate the first derivative of the function at a point.
df() - Method in class org.gersteinlab.regulation.numeric.DifferentiableFunction
Evaluate the first derivative of the function at the stored point.
DifferentiableFunction - Class in org.gersteinlab.regulation.numeric
A class that represents a differentiable univariate real function.
DifferentiableFunction() - Constructor for class org.gersteinlab.regulation.numeric.DifferentiableFunction
 
DifferentiableMultivariateFunction - Class in org.gersteinlab.regulation.numeric
A class that represents a differentiable multivariate real function.
DifferentiableMultivariateFunction() - Constructor for class org.gersteinlab.regulation.numeric.DifferentiableMultivariateFunction
 
DoublyDifferentiableFunction - Class in org.gersteinlab.regulation.numeric
A class that represents a doubly differentiable univariate real function.
DoublyDifferentiableFunction() - Constructor for class org.gersteinlab.regulation.numeric.DoublyDifferentiableFunction
 
DoublyDifferentiableMultivariateFunction - Class in org.gersteinlab.regulation.numeric
A class that represents a doubly differentiable multivariate real function.
DoublyDifferentiableMultivariateFunction() - Constructor for class org.gersteinlab.regulation.numeric.DoublyDifferentiableMultivariateFunction
 
dydt - Variable in class org.gersteinlab.regulation.TrajectoryProfile
 
dykdt - Variable in class org.gersteinlab.regulation.model.LinearRateModel
 
dykdt - Variable in class org.gersteinlab.regulation.model.MultiplicativeRateModel
 
dykdt - Variable in class org.gersteinlab.regulation.model.SigmoidalRateModel
 
dykdts - Variable in class org.gersteinlab.regulation.model.RateModel
 
dyldt - Variable in class org.gersteinlab.regulation.model.MultiplicativeRateModel
 

E

eMean - Variable in class org.gersteinlab.regulation.DeletionProfile
 
EPSILON - Static variable in class org.gersteinlab.regulation.numeric.NewtonMethod
 
eSD - Variable in class org.gersteinlab.regulation.DeletionProfile
 
ETA - Static variable in class org.gersteinlab.regulation.numeric.GradientDescent
 
expCount - Variable in class org.gersteinlab.regulation.TrajectoryProfile
 
expTerms - Variable in class org.gersteinlab.regulation.model.SigmoidalRateModel
 

F

f() - Method in class org.gersteinlab.regulation.model.LinearRateModel
Note: to avoid array copying, the internal cached result is returned.
f() - Method in class org.gersteinlab.regulation.model.MultiplicativeRateModel
Note: to avoid array copying, the internal cached result is returned.
f(double) - Method in class org.gersteinlab.regulation.model.Polynomial
 
f(double[]) - Method in class org.gersteinlab.regulation.model.PolynomialSqrDiff
Evaluate the total squared difference at a point (i.e., a set of polynomial coefficients).
f() - Method in class org.gersteinlab.regulation.model.RateModel
Return the estimated values at the specified time points.
f() - Method in class org.gersteinlab.regulation.model.RateModelSqrDiff
Evaluate the total squared difference at the specified parameter values.
f() - Method in class org.gersteinlab.regulation.model.SigmoidalRateModel
Note: to avoid array copying, the internal cached result is returned.
f(double) - Method in class org.gersteinlab.regulation.numeric.Function
Evaluate the value of the function at a point.
f() - Method in class org.gersteinlab.regulation.numeric.Function
Evaluate the value of the function at the last stored point.
f(double[]) - Method in class org.gersteinlab.regulation.numeric.MultivariateFunction
Evaluate the value of the function at a point.
f() - Method in class org.gersteinlab.regulation.numeric.MultivariateFunction
Evaluate the value of the function at the last stored point.
Function - Class in org.gersteinlab.regulation.numeric
A class that represents a univariate real function.
Function() - Constructor for class org.gersteinlab.regulation.numeric.Function
 

G

geneCount - Variable in class org.gersteinlab.regulation.DeletionProfile
 
geneCount - Variable in class org.gersteinlab.regulation.TrajectoryProfile
 
geneNames - Variable in class org.gersteinlab.regulation.DeletionProfile
 
geneNames - Variable in class org.gersteinlab.regulation.TrajectoryProfile
 
getMean(double[]) - Static method in class org.gersteinlab.regulation.util.SimpleStats
Compute the mean of a vector.
getReactionProbs() - Method in class org.gersteinlab.regulation.DeletionProfile
 
getResidual(int, int[][], Class<? extends RateModel>, double[], int, double[], double[]) - Method in class org.gersteinlab.regulation.TrajectoryProfile
Get the residual when using some genes k to predict the expression of a gene j based on the best fit of a rate model starting from random parameter values.
getResidual(int, int[][], Class<? extends RateModel>, double[]) - Method in class org.gersteinlab.regulation.TrajectoryProfile
Get the residual when using some genes k to predict the expression of a gene j based on the best fit of a rate model starting from an initial set of parameter values.
getSD(double[]) - Static method in class org.gersteinlab.regulation.util.SimpleStats
Compute the standard deviation of a vector.
gf() - Method in class org.gersteinlab.regulation.model.LinearRateModel
Note: to avoid array copying, the internal cached result is returned.
gf() - Method in class org.gersteinlab.regulation.model.MultiplicativeRateModel
Note: to avoid array copying, the internal cached result is returned.
gf(double[]) - Method in class org.gersteinlab.regulation.model.PolynomialSqrDiff
Evaluate the gradient of the function at a point (i.e., a set of polynomial coefficients).
gf() - Method in class org.gersteinlab.regulation.model.RateModel
Return the estimated gradients at the specified time points with respect to the parameters.
gf() - Method in class org.gersteinlab.regulation.model.RateModelSqrDiff
Evaluate the gradient of the function at the specified parameter values.
gf() - Method in class org.gersteinlab.regulation.model.SigmoidalRateModel
Note: to avoid array copying, the internal cached result is returned.
gf(double[]) - Method in class org.gersteinlab.regulation.numeric.DifferentiableMultivariateFunction
Evaluate the gradient of the function at a point.
gf() - Method in class org.gersteinlab.regulation.numeric.DifferentiableMultivariateFunction
Evaluate the gradient of the function at the stored point.
GradientDescent - Class in org.gersteinlab.regulation.numeric
A class for minimizing a differentiable multivariate real function using gradient descent.
GradientDescent(DifferentiableMultivariateFunction) - Constructor for class org.gersteinlab.regulation.numeric.GradientDescent
Construct an instance for a function.
gyj - Variable in class org.gersteinlab.regulation.model.LinearRateModel
 
gyj - Variable in class org.gersteinlab.regulation.model.MultiplicativeRateModel
 
gyj - Variable in class org.gersteinlab.regulation.model.SigmoidalRateModel
 

H

h - Variable in class org.gersteinlab.regulation.model.RateModel
 
h_ha1p1 - Variable in class org.gersteinlab.regulation.model.LinearRateModel
 
ha1_ha1d2p1_p1 - Variable in class org.gersteinlab.regulation.model.LinearRateModel
 
ha1d2p1 - Variable in class org.gersteinlab.regulation.model.LinearRateModel
 
hasMoreElements() - Method in class org.gersteinlab.regulation.util.StringTokenizer2
 
hasMoreTokens() - Method in class org.gersteinlab.regulation.util.StringTokenizer2
 
hf() - Method in class org.gersteinlab.regulation.model.LinearRateModel
Note: to avoid array copying, the internal cached result is returned.
hf() - Method in class org.gersteinlab.regulation.model.MultiplicativeRateModel
Note: to avoid array copying, the internal cached result is returned.
hf(double[]) - Method in class org.gersteinlab.regulation.model.PolynomialSqrDiff
Evaluate the Hessian of the function at a point (i.e., a set of polynomial coefficients).
hf() - Method in class org.gersteinlab.regulation.model.RateModel
Return the estimated Hessians at the specified time points with respect to the parameters.
hf() - Method in class org.gersteinlab.regulation.model.RateModelSqrDiff
Evaluate the Hessian of the function at the specified parameter values.
hf() - Method in class org.gersteinlab.regulation.model.SigmoidalRateModel
Note: to avoid array copying, the internal cached result is returned.
hf(double[]) - Method in class org.gersteinlab.regulation.numeric.DoublyDifferentiableMultivariateFunction
Evaluate the Hessian of the function at a point.
hf() - Method in class org.gersteinlab.regulation.numeric.DoublyDifferentiableMultivariateFunction
Evaluate the Hessian of the function at the stored point.
hha0a1 - Variable in class org.gersteinlab.regulation.model.SigmoidalRateModel
 
hha1a1d2mha1p1 - Variable in class org.gersteinlab.regulation.model.SigmoidalRateModel
 
hyj - Variable in class org.gersteinlab.regulation.model.LinearRateModel
 
hyj - Variable in class org.gersteinlab.regulation.model.MultiplicativeRateModel
 
hyj - Variable in class org.gersteinlab.regulation.model.SigmoidalRateModel
 

K

kCount - Variable in class org.gersteinlab.regulation.model.MultiplicativeRateModel
 

L

lambda2(double[]) - Method in class org.gersteinlab.regulation.numeric.NewtonMethod
Get the error estimate, lambda^2, at a point.
lambda2(double[], double[][]) - Method in class org.gersteinlab.regulation.numeric.NewtonMethod
Get the error estimate, lambda^2, at a point, with precomputed Newton's direction and Hessian.
lastIsDelim - Variable in class org.gersteinlab.regulation.util.StringTokenizer2
Whether the last element read from st is a delimiter
lCount - Variable in class org.gersteinlab.regulation.model.MultiplicativeRateModel
 
LinearRateModel - Class in org.gersteinlab.regulation.model
Providing methods for a rate model based on linear differential equations.
LinearRateModel(double[], double, double[][][], double[][][]) - Constructor for class org.gersteinlab.regulation.model.LinearRateModel
 

M

main(String[]) - Static method in class org.gersteinlab.regulation.Analyzer
 
Main - Class in org.gersteinlab.regulation
The main predictor class.
Main() - Constructor for class org.gersteinlab.regulation.Main
 
main(String[]) - Static method in class org.gersteinlab.regulation.Main
 
minimize(double[]) - Method in class org.gersteinlab.regulation.numeric.DescentMethod
Perform the minimization using default parameters.
minimize(double[]) - Method in class org.gersteinlab.regulation.numeric.GradientDescent
Perform the minimization using default parameters.
minimize(double[], double, double, double) - Method in class org.gersteinlab.regulation.numeric.GradientDescent
Perform the minimization.
minimize(double[]) - Method in class org.gersteinlab.regulation.numeric.NewtonMethod
Perform the minimization using default parameters.
minimize(double[], double, double, double) - Method in class org.gersteinlab.regulation.numeric.NewtonMethod
Perform the minimization.
MultiplicativeRateModel - Class in org.gersteinlab.regulation.model
Providing methods for a rate model based on multiplicative differential equations.
MultiplicativeRateModel(double[], double, double[][][], double[][][]) - Constructor for class org.gersteinlab.regulation.model.MultiplicativeRateModel
 
MultivariateFunction - Class in org.gersteinlab.regulation.numeric
A class that represents a multivariate real function.
MultivariateFunction() - Constructor for class org.gersteinlab.regulation.numeric.MultivariateFunction
 

N

n - Variable in class org.gersteinlab.regulation.model.RateModel
 
nd(double[]) - Method in class org.gersteinlab.regulation.numeric.NewtonMethod
Get the standard Newton's direction at a point.
nd(double[], double[][]) - Method in class org.gersteinlab.regulation.numeric.NewtonMethod
Get the standard Newton's direction at a point, with precomputed gradient and Hessian.
NewtonMethod - Class in org.gersteinlab.regulation.numeric
A class for minimizing a doubly differentiable multivariate real function using the Newton's method.
NewtonMethod(DoublyDifferentiableMultivariateFunction) - Constructor for class org.gersteinlab.regulation.numeric.NewtonMethod
Construct an instance for a function.
nextElement() - Method in class org.gersteinlab.regulation.util.StringTokenizer2
 
nextToken() - Method in class org.gersteinlab.regulation.util.StringTokenizer2
 

O

org.gersteinlab.regulation - package org.gersteinlab.regulation
 
org.gersteinlab.regulation.model - package org.gersteinlab.regulation.model
 
org.gersteinlab.regulation.numeric - package org.gersteinlab.regulation.numeric
 
org.gersteinlab.regulation.util - package org.gersteinlab.regulation.util
 

P

pointCount - Variable in class org.gersteinlab.regulation.TrajectoryProfile
 
polyDeg - Variable in class org.gersteinlab.regulation.TrajectoryProfile
 
Polynomial - Class in org.gersteinlab.regulation.model
A class that represents a polynomial.
Polynomial(double[]) - Constructor for class org.gersteinlab.regulation.model.Polynomial
Create a polynomial with a set of coefficients.
PolynomialSqrDiff - Class in org.gersteinlab.regulation.model
A function that equals the total squared difference between a polynomial and some target values at a set of points, treating the coefficients of the polynomial as the variables.
PolynomialSqrDiff(double[], double[]) - Constructor for class org.gersteinlab.regulation.model.PolynomialSqrDiff
Create the function with the given set of points and target values.
predictIntersection(double[][][], List<String>, int[][], int, boolean) - Static method in class org.gersteinlab.regulation.Main
Make predictions from the intersection of multiple models.
predictUnion(double[][][], List<String>, int[][], int, boolean) - Static method in class org.gersteinlab.regulation.Main
Make predictions from the union of multiple models.
profile - Variable in class org.gersteinlab.regulation.DeletionProfile
 
profile - Variable in class org.gersteinlab.regulation.TrajectoryProfile
 
profile2 - Variable in class org.gersteinlab.regulation.TrajectoryProfile
 

R

RateModel - Class in org.gersteinlab.regulation.model
Providing methods for a rate model based on differential equations.
RateModel(double[], double, double[][][], double[][][]) - Constructor for class org.gersteinlab.regulation.model.RateModel
Create the model with the given set of time points and target values and differentials.
RateModelSqrDiff - Class in org.gersteinlab.regulation.model
A function that equals the total squared difference between the predicted value of a differential equation rate model and some target values at a set of time points, treating the parameters of the model as the variables.
RateModelSqrDiff(double[], double[][], double[][][][], double[][][][], Class<? extends RateModel>) - Constructor for class org.gersteinlab.regulation.model.RateModelSqrDiff
Create the function with the given set of points and target values and differentials.
readProfile(Reader) - Static method in class org.gersteinlab.regulation.DeletionProfile
Read and return the profile in a file.
readProfile(Reader, int) - Static method in class org.gersteinlab.regulation.TrajectoryProfile
Read and return the profile in a file.
returnDelims - Variable in class org.gersteinlab.regulation.util.StringTokenizer2
Whether to return delimiters

S

SEARCH_ITER - Static variable in class org.gersteinlab.regulation.Main
 
set(double[]) - Method in class org.gersteinlab.regulation.model.RateModelSqrDiff
Set the parameter values of the model.
set(double) - Method in class org.gersteinlab.regulation.numeric.Function
Store the next point to be evaluated.
set(double[]) - Method in class org.gersteinlab.regulation.numeric.MultivariateFunction
Store the next point to be evaluated.
setParam(double[]) - Method in class org.gersteinlab.regulation.model.LinearRateModel
Set the parameter values.
setParam(double[]) - Method in class org.gersteinlab.regulation.model.MultiplicativeRateModel
Set the parameter values.
setParam(double[]) - Method in class org.gersteinlab.regulation.model.RateModel
Set the parameter values.
setParam(double[]) - Method in class org.gersteinlab.regulation.model.SigmoidalRateModel
Set the parameter values.
SigmoidalRateModel - Class in org.gersteinlab.regulation.model
Providing methods for a rate model based on sigmoidal differential equations.
SigmoidalRateModel(double[], double, double[][][], double[][][]) - Constructor for class org.gersteinlab.regulation.model.SigmoidalRateModel
 
SimpleStats - Class in org.gersteinlab.regulation.util
This class provides functions for computing some simple statistics.
SimpleStats() - Constructor for class org.gersteinlab.regulation.util.SimpleStats
 
st - Variable in class org.gersteinlab.regulation.util.StringTokenizer2
The underlying string tokenizer
StringTokenizer2 - Class in org.gersteinlab.regulation.util
This class represents a modified version of StringTokenizer that returns an empty string between two consecutive delimiters.
StringTokenizer2(String) - Constructor for class org.gersteinlab.regulation.util.StringTokenizer2
 
StringTokenizer2(String, String) - Constructor for class org.gersteinlab.regulation.util.StringTokenizer2
 
StringTokenizer2(String, String, boolean) - Constructor for class org.gersteinlab.regulation.util.StringTokenizer2
 

T

t - Variable in class org.gersteinlab.regulation.model.RateModel
 
t - Variable in class org.gersteinlab.regulation.TrajectoryProfile
 
TEAM_NAME - Static variable in class org.gersteinlab.regulation.Main
 
TrajectoryProfile - Class in org.gersteinlab.regulation
A class for storing the trajectory profile of all genes read from a file.
TrajectoryProfile(Reader, int) - Constructor for class org.gersteinlab.regulation.TrajectoryProfile
Constructor.

U

Util - Class in org.gersteinlab.regulation.util
This class provides some utility functions.
Util() - Constructor for class org.gersteinlab.regulation.util.Util
 

V

vMeans - Variable in class org.gersteinlab.regulation.DeletionProfile
 

X

xs - Variable in class org.gersteinlab.regulation.TrajectoryProfile
 
xStored - Variable in class org.gersteinlab.regulation.numeric.Function
 
xStored - Variable in class org.gersteinlab.regulation.numeric.MultivariateFunction
 

Y

y - Variable in class org.gersteinlab.regulation.TrajectoryProfile
 
yj - Variable in class org.gersteinlab.regulation.model.LinearRateModel
 
yj - Variable in class org.gersteinlab.regulation.model.MultiplicativeRateModel
 
yj - Variable in class org.gersteinlab.regulation.model.SigmoidalRateModel
 
yj0 - Variable in class org.gersteinlab.regulation.model.RateModel
 
yk - Variable in class org.gersteinlab.regulation.model.LinearRateModel
 
yk - Variable in class org.gersteinlab.regulation.model.MultiplicativeRateModel
 
yk - Variable in class org.gersteinlab.regulation.model.SigmoidalRateModel
 
yks - Variable in class org.gersteinlab.regulation.model.RateModel
 
yl - Variable in class org.gersteinlab.regulation.model.MultiplicativeRateModel
 

A B C D E F G H K L M N O P R S T U V X Y