Package 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
    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

    Modifier and Type
    Method
    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 Details

    • 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 Details

    • 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