Class Gene

Object

Gene

public class Gene
extends Object

An instance of the Gene class represents (1) the name of a gene (2) the reported function of the gene and (3) the gene's expression values from a set of experiments.

Constructor Summary

Constructors

Constructor and Description
Gene(String lineFromFile) Creates a Gene from a tab-delimited String.

Method Summary

Modifier and Type	Method and Description
double	distanceToExpressionVector(java.util.Vector<Double> vector) Returns the Euclidean distance between this Gene's expression values and the specified collection of expression values.
double	getExpressionInOneExperiment(int experiment) Returns the expression value of this Gene in the specified experiment.
java.util.Vector<Double>	getExpressionVector() Returns a copy of this Gene's expression values in all experiments.
String	getGeneFunction() Returns a String representation of the gene's function.
String	getGeneName() Returns a String representation of the gene's name.
String	toString() Returns a String representation of this Gene, including the gene's name and function.

Methods inherited from class Object

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

Constructor Detail

Gene

public Gene(String lineFromFile)

Creates a Gene from a tab-delimited String.

Parameters:

lineFromFile - a tab-delimited String, possibly read-in from a file

Method Detail

toString

public String toString()

Returns a String representation of this Gene, including the gene's name and function.

Overrides:

toString in class Object

Returns:

a String represenation of this Gene

getGeneName

public String getGeneName()

Returns a String representation of the gene's name.

Returns:

a String represenation of this Gene's name

getGeneFunction

public String getGeneFunction()

Returns a String representation of the gene's function.

Returns:

a String represenation of this Gene's function

getExpressionInOneExperiment

public double getExpressionInOneExperiment(int experiment)

Returns the expression value of this Gene in the specified experiment.

Parameters:

experiment - the index of a particular experiment

Returns:

a double representing this Gene's expression value

getExpressionVector

public java.util.Vector<Double> getExpressionVector()

Returns a copy of this Gene's expression values in all experiments.

Returns:

a Vector of doubles corresponding to this Gene's expression values

distanceToExpressionVector

public double distanceToExpressionVector(java.util.Vector<Double> vector)

Returns the Euclidean distance between this Gene's expression values and the specified collection of expression values.

Parameters:

vector - a collection of expression values

Returns:

a double corresponding to the distance between two sets of expression values