org.biojava.utils.automata

Class FiniteAutomaton

java.lang.Object

org.biojava.utils.automata.FiniteAutomaton

Direct Known Subclasses:

Nfa

public class FiniteAutomaton
extends Object

Class for modelling finite automata.

This class models basic FA behaviour. More specialised behaviour is implemented by subclassing this.

Since:

1.4

Author:

David Huen

Field Summary

Fields

Modifier and Type	Field and Description
protected org.biojava.utils.automata.FiniteAutomaton.Node	end
protected Set	nodes
protected org.biojava.utils.automata.FiniteAutomaton.Node	start
protected Set	transitions

Method Summary

Methods

Modifier and Type	Method and Description
org.biojava.utils.automata.FiniteAutomaton.Node	addNode(boolean terminal) Add a node to the FA.
org.biojava.utils.automata.FiniteAutomaton.Transition	addTransition(org.biojava.utils.automata.FiniteAutomaton.Node start, org.biojava.utils.automata.FiniteAutomaton.Node end, Symbol sym)
protected int	alphaIndex(Symbol sym)
org.biojava.utils.automata.FiniteAutomaton.NodeSet	createNodeSet()
FiniteAutomaton	getAutomaton()
org.biojava.utils.automata.FiniteAutomaton.Node	getEnd()
org.biojava.utils.automata.FiniteAutomaton.NodeSet	getNodes() get all Nodes within this instance.
org.biojava.utils.automata.FiniteAutomaton.Node	getStart()
Set	getTransitions() retrieve Set of all transitions in instance.
String	toString() dumps internal data of Nodes and Transitions that describe this FiniteAutomaton.

Methods inherited from class java.lang.Object

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

Field Detail

nodes

protected Set nodes

transitions

protected Set transitions

start

protected org.biojava.utils.automata.FiniteAutomaton.Node start

end

protected org.biojava.utils.automata.FiniteAutomaton.Node end

Method Detail

getStart

public org.biojava.utils.automata.FiniteAutomaton.Node getStart()

getEnd

public org.biojava.utils.automata.FiniteAutomaton.Node getEnd()

getAutomaton

public FiniteAutomaton getAutomaton()

addTransition

public org.biojava.utils.automata.FiniteAutomaton.Transition addTransition(org.biojava.utils.automata.FiniteAutomaton.Node start,
                                                                  org.biojava.utils.automata.FiniteAutomaton.Node end,
                                                                  Symbol sym)

addNode

public org.biojava.utils.automata.FiniteAutomaton.Node addNode(boolean terminal)

Add a node to the FA.

Parameters:

terminal - Is the Node terminal?

getNodes

public org.biojava.utils.automata.FiniteAutomaton.NodeSet getNodes()

get all Nodes within this instance.

getTransitions

public Set getTransitions()

retrieve Set of all transitions in instance.

createNodeSet

public org.biojava.utils.automata.FiniteAutomaton.NodeSet createNodeSet()

toString

public String toString()

dumps internal data of Nodes and Transitions that describe this FiniteAutomaton. It is not possible to dump it as a regex as there are FA that cannot be expressed as a regex.

Overrides:

toString in class Object

alphaIndex

protected int alphaIndex(Symbol sym)
                  throws IllegalSymbolException

Throws:

IllegalSymbolException