Class State

Object

State

public class State
extends Object

An instance of the State class represents a single state in a hidden Markov model, including the state's name, a collection of all characters that the state can output, and the probability of outputting each character.

Constructor Summary

Constructors

Constructor and Description
State(String line) Construct a new State based on information in a tab-delimited line read-in from a file.

Method Summary

Methods

Modifier and Type	Method and Description
int	getEmissionLength() Returns the length of the characters that this State can output (all characters output by a State are the same length).
double	getEmissionProbability(String s) Returns the probability that this State emits the specified character s, or 0.0 if this State cannot emit character s.
String	getName() Returns the name of this State.
static void	main(String[] args) The main method creates a new State, for testing purposes, and prints out this newly created State to the screen.
String	toString() Returns a String representation of this State.

Methods inherited from class Object

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

Constructor Detail

State

public State(String line)

Construct a new State based on information in a tab-delimited line read-in from a file. The name of the state, the alphabet of characters, and the emission probabilities should be tab-delimited. The different characters in the alphabet should be comma-delimited. The different emission probabilities should be comma-delimited. For example:
Intergenic A,C,G,T 0.2,0.3,0.3,0.2
StartCodon ATG,GTG 0.92,0.08
StopCodon TGA,TAG,TAA 0.28,0.07,0.65


Parameters:

line - a tab-delimited line containing name, character, and emission probability information

Method Detail

getName

public String getName()

Returns the name of this State.

Returns:

a String representing the name of this State

getEmissionProbability

public double getEmissionProbability(String s)

Returns the probability that this State emits the specified character s, or 0.0 if this State cannot emit character s.

Parameters:

s - a character that this State may output

Returns:

the probability that this State outputs character s

getEmissionLength

public int getEmissionLength()

Returns the length of the characters that this State can output (all characters output by a State are the same length).

Returns:

the length of any character output by this State

toString

public String toString()

Returns a String representation of this State. The String representation includes the name of the State, the set of characters output by the State, and the probability of outputting each of these characters.

Overrides:

toString in class Object

Returns:

a String representation of this State

main

public static void main(String[] args)

The main method creates a new State, for testing purposes, and prints out this newly created State to the screen.

Parameters:

args - an array of Strings representing any command line arguments