org.gersteinlab.regulation
Class TrajectoryProfile

java.lang.Object
  org.gersteinlab.regulation.TrajectoryProfile

public class TrajectoryProfile
extends java.lang.Object

        A class for storing the trajectory profile of all genes read from a
        file.
        

Version:

1.0 (August 20, 2008)

        Change History:
        1.0     - Initial version
        

Author:

Kevin Yuk-Lap Yip

Field Summary

protected double[][][]	dydt
protected int	expCount
protected int	geneCount
protected java.lang.String[]	geneNames
protected int	pointCount
protected int	polyDeg
protected double[][][]	profile
protected double[][][]	profile2
protected double[]	t
protected double[]	xs
protected double[][][]	y

Constructor Summary

protected

TrajectoryProfile(java.io.Reader r, int polyDegIn) Constructor.

Method Summary

double	getResidual(int j, int[][] ks, java.lang.Class<? extends RateModel> modelClass, double[] a0) 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.
double	getResidual(int j, int[][] ks, java.lang.Class<? extends RateModel> modelClass, double[] aStar, int iter, double[] mins, double[] maxs) 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.
static TrajectoryProfile	readProfile(java.io.Reader r, int polyDegIn) Read and return the profile in a file.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

geneCount

protected int geneCount

geneNames

protected java.lang.String[] geneNames

expCount

protected int expCount

pointCount

protected int pointCount

profile

protected double[][][] profile

polyDeg

protected int polyDeg

profile2

protected double[][][] profile2

xs

protected double[] xs

t

protected double[] t

y

protected double[][][] y

dydt

protected double[][][] dydt

Constructor Detail

TrajectoryProfile

protected TrajectoryProfile(java.io.Reader r,
                            int polyDegIn)
                     throws java.io.IOException

Constructor.

Parameters:

r - The reader of the file

polyDegIn - Degree of polynomial for smoothing the trajectories

Throws:

java.io.IOException

Method Detail

readProfile

public static TrajectoryProfile readProfile(java.io.Reader r,
                                            int polyDegIn)
                                     throws java.io.IOException

Read and return the profile in a file.

Parameters:

r - The reader of the file

polyDegIn - Degree of polynomial for smoothing the trajectories

Returns:

The profile

Throws:

java.io.IOException

getResidual

public double getResidual(int j,
                          int[][] ks,
                          java.lang.Class<? extends RateModel> modelClass,
                          double[] aStar,
                          int iter,
                          double[] mins,
                          double[] maxs)
                   throws java.lang.InstantiationException,
                          java.lang.IllegalAccessException,
                          java.lang.IllegalArgumentException,
                          java.lang.reflect.InvocationTargetException,
                          java.lang.NoSuchMethodException

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.

Parameters:

j - The gene whose expression is to be predicted

ks - The genes to be used to make the predictions First dimension: predictor set Second dimension: predictors

modelClass - The class of the rate model

aStar - For specifying the number of parameters and storing the final parameter values

iter - The number of random initial parameter sets to try

mins - Minimum of parameter values

maxs - Maximum of parameter values

Throws:

java.lang.InstantiationException

java.lang.IllegalAccessException

java.lang.IllegalArgumentException

java.lang.reflect.InvocationTargetException

java.lang.NoSuchMethodException

getResidual

public double getResidual(int j,
                          int[][] ks,
                          java.lang.Class<? extends RateModel> modelClass,
                          double[] a0)
                   throws java.lang.InstantiationException,
                          java.lang.IllegalAccessException,
                          java.lang.IllegalArgumentException,
                          java.lang.reflect.InvocationTargetException,
                          java.lang.NoSuchMethodException

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.

Parameters:

j - The gene whose expression is to be predicted

ks - The genes to be used to make the predictions First dimension: predictor set Second dimension: predictors

modelClass - The class of the rate model

a0 - The initial parameter values. The final values will be stored back to this array.

Throws:

java.lang.InstantiationException

java.lang.IllegalAccessException

java.lang.IllegalArgumentException

java.lang.reflect.InvocationTargetException

java.lang.NoSuchMethodException