All Implemented Interfaces:

Serializable, MarkovModel, Changeable

Direct Known Subclasses:

FullHmmerProfileHMM, ProfileHMM

public class SimpleMarkovModel
extends AbstractChangeable
implements MarkovModel, Serializable 

Author:

Matthew Pocock, Thomas Down, Samiul Hasan, Keith James

See Also:

Serialized Form

• Field Summary

  Fields

  Modifier and Type	Field and Description
  static long	serialVersionUID

  • Fields inherited from interface org.biojava.bio.dp.MarkovModel

    ARCHITECTURE, PARAMETER

• Constructor Summary

  Constructors

  Constructor and Description
  SimpleMarkovModel (int heads, Alphabet emissionAlpha) Deprecated.
  SimpleMarkovModel (int heads, Alphabet emissionAlpha, String name)

• Method Summary

  All Methods

  Modifier and Type	Method and Description
  void	addState (State toAdd) Adds a state to the model.
  int[]	advance () The maximum advance for this model.
  boolean	containsTransition (State from, State to) Returns wether a transition exists or not.
  void	createTransition (State from, State to) Makes a transition between two states legal.
  void	destroyTransition (State from, State to) Breaks a transition between two states legal.
  Alphabet	emissionAlphabet () Alphabet that is emitted by the emission states.
  protected ChangeSupport	getChangeSupport (ChangeType ct) Called to retrieve the ChangeSupport for this object.
  Distribution	getWeights (State source) Get a probability Distribution over the transition from 'source'.
  int	heads () The number of heads on this model.
  MagicalState	magicalState () The MagicalState for this model.
  void	removeState (State toGo) Remove a state from the model.
  void	setWeights (State source, Distribution dist) Use this methods to customize the transition probabilities.
  FiniteAlphabet	stateAlphabet () FiniteAlphabet of the states.
  String	toString ()
  FiniteAlphabet	transitionsFrom (State from) Returns the FiniteAlphabet of all states that have a transition from 'source'.
  FiniteAlphabet	transitionsTo (State to) Returns the FiniteAlphabet of all states that have a transition to 'dest'.

  • Methods inherited from class org.biojava.utils.AbstractChangeable

    addChangeListener, addChangeListener, generateChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener

  • Methods inherited from class java.lang.Object

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

  • Methods inherited from interface org.biojava.utils.Changeable

    addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

• Field Detail

  • serialVersionUID

    public static final long serialVersionUID 

    See Also:

    Constant Field Values

• Constructor Detail

  • SimpleMarkovModel

    public SimpleMarkovModel(int heads,
     Alphabet emissionAlpha,
     String name)

  • SimpleMarkovModel

    public SimpleMarkovModel(int heads,
     Alphabet emissionAlpha)

    Deprecated.

• Method Detail

  • getChangeSupport

    protected ChangeSupport getChangeSupport(ChangeType ct)

    Description copied from class: AbstractChangeable
    Called to retrieve the ChangeSupport for this object.

    Your implementation of this method should have the following structure:

     ChangeSupport cs = super.getChangeSupport(ct);
     if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
     someForwarder = new ChangeForwarder(...
     this.stateVariable.addChangeListener(someForwarder, VariableInterface.AChange);
     }
     return cs;
     

    It is usual for the forwarding listeners (someForwarder in this example) to be transient and lazily instantiated. Be sure to register & unregister the forwarder in the code that does the ChangeEvent handling in setter methods.

    Overrides:

    getChangeSupport in class AbstractChangeable

  • emissionAlphabet

    public Alphabet emissionAlphabet()

    Description copied from interface: MarkovModel
    Alphabet that is emitted by the emission states.

    Specified by:

    emissionAlphabet in interface MarkovModel

  • stateAlphabet

    public FiniteAlphabet stateAlphabet()

    Description copied from interface: MarkovModel
    FiniteAlphabet of the states.

    We are modeling a finite-state-machine, so there will be a finite set of states.

    The MagicalState returned by getMagicalState is always contained within this as the start/end state.

    Specified by:

    stateAlphabet in interface MarkovModel

    Returns:

    the alphabet over states

  • heads

    public int heads()

    Description copied from interface: MarkovModel
    The number of heads on this model.

    Each head consumes a single SymbolList. A single-head model just consumes/ emits a single sequence. A two-head model performs alignment between two sequences (e.g. smith-waterman). Models with more heads do more interesting things.

    heads() should equal advance().length.

    Specified by:

    heads in interface MarkovModel

    Returns:

    the number of heads in this model.

  • magicalState

    public MagicalState magicalState()

    Description copied from interface: MarkovModel
    The MagicalState for this model.

    Specified by:

    magicalState in interface MarkovModel

  • advance

    public int[] advance()

    Description copied from interface: MarkovModel
    The maximum advance for this model.

    Each head consumes a single SymbolList. However, the states that advance through that SymbolList may emit more than one symbol at a time. This array give the maximum advance in each direction.

    Be sure to return a new array each time this is called. This protects the internal state of the object from someone modifying the advance array. Be sure to update this as/when states modify their advance arrays and as/when states are added or removed

    Specified by:

    advance in interface MarkovModel

    Returns:

    the maximum advance of all states for all heads

  • getWeights

    public Distribution getWeights(State source)
     throws IllegalSymbolException 

    Description copied from interface: MarkovModel
    Get a probability Distribution over the transition from 'source'.

    Specified by:

    getWeights in interface MarkovModel

    Parameters:

    source - the State currently occupied

    Returns:

    the probability Distribution over the reachable states

    Throws:

    IllegalSymbolException - if from is not a legal state

  • setWeights

    public void setWeights(State source,
     Distribution dist)
     throws IllegalSymbolException,
     IllegalAlphabetException,
     ChangeVetoException 

    Use this methods to customize the transition probabilities.

    By default, the distribution P(destination | source) is a totally free distribution. This allows the different probabilities to vary. If you wish to change this behaviour (for example, to make one set of transition probabilities equal to another), then use this method to replace the Distribution with one of your own.

    Specified by:

    setWeights in interface MarkovModel

    Parameters:

    source - source State

    dist - the new Distribution over the transition probabilites from source

    Throws:

    IllegalSymbolException - if source is not a member of this model

    IllegalAlphabetException - if dist is not a distribution over the states returned by model.transitionsFrom(source)

    ChangeVetoException - if a listener vetoed this change

  • createTransition

    public void createTransition(State from,
     State to)
     throws IllegalSymbolException,
     ChangeVetoException 

    Description copied from interface: MarkovModel
    Makes a transition between two states legal.

    This should inform each TransitionListener that a transition is to be created using preCreateTransition, and if none of the listeners fire a ChangeVetoException, it should create the transition, and then inform each TransitionListener with postCreateTransition.

    Specified by:

    createTransition in interface MarkovModel

    Parameters:

    from - the State currently occupied

    to - the State to move to

    Throws:

    IllegalSymbolException - if either from or to are not legal states

    ChangeVetoException - if creating the transition is vetoed

  • destroyTransition

    public void destroyTransition(State from,
     State to)
     throws IllegalSymbolException,
     ChangeVetoException 

    Description copied from interface: MarkovModel
    Breaks a transition between two states legal.

    This should inform each TransitionListener that a transition is to be broken using preDestroyTransition, and if none of the listeners fire a ChangeVetoException, it should break the transition, and then inform each TransitionListener with postDestroyTransition.

    Specified by:

    destroyTransition in interface MarkovModel

    Parameters:

    from - the State currently occupied

    to - the State to move to

    Throws:

    IllegalSymbolException - if either from or to are not legal states

    ChangeVetoException - if breaking the transition is vetoed

  • containsTransition

    public boolean containsTransition(State from,
     State to)
     throws IllegalSymbolException 

    Description copied from interface: MarkovModel
    Returns wether a transition exists or not.

    Specified by:

    containsTransition in interface MarkovModel

    Parameters:

    from - the transitin source

    to - the transition destination

    Returns:

    true/false depending on wether this model has the transition

    Throws:

    IllegalSymbolException - if either from or to are not states in this model

  • transitionsFrom

    public FiniteAlphabet transitionsFrom(State from)
     throws IllegalSymbolException 

    Description copied from interface: MarkovModel
    Returns the FiniteAlphabet of all states that have a transition from 'source'.

    Specified by:

    transitionsFrom in interface MarkovModel

    Parameters:

    from - the source State

    Returns:

    a FiniteAlphabet of State objects that can reach from 'source'

    Throws:

    IllegalSymbolException

  • transitionsTo

    public FiniteAlphabet transitionsTo(State to)
     throws IllegalSymbolException 

    Description copied from interface: MarkovModel
    Returns the FiniteAlphabet of all states that have a transition to 'dest'.

    Specified by:

    transitionsTo in interface MarkovModel

    Parameters:

    to - the destination state

    Returns:

    a FiniteAlphabet of State objects that can reach 'dest'

    Throws:

    IllegalSymbolException

  • addState

    public void addState(State toAdd)
     throws IllegalSymbolException,
     ChangeVetoException 

    Description copied from interface: MarkovModel
    Adds a state to the model.

    Specified by:

    addState in interface MarkovModel

    Parameters:

    toAdd - the state to add

    Throws:

    IllegalSymbolException - if the state is not valid or is a MagicalState

    ChangeVetoException - if either the model does not allow states to be added, or the change was vetoed

  • removeState

    public void removeState(State toGo)
     throws IllegalSymbolException,
     IllegalTransitionException,
     ChangeVetoException 

    Description copied from interface: MarkovModel
    Remove a state from the model.

    States should not be removed untill they are involved in no transitions. This is to avoid producing corrupted models by accident.

    Specified by:

    removeState in interface MarkovModel

    Parameters:

    toGo - the state to remove

    Throws:

    IllegalSymbolException - if the symbol is not part of this model or a MagicalState

    IllegalTransitionException - if the state is currently involved in any transitions

    ChangeVetoException - if either the model does not allow states to be removed, or the change was vetoed

  • toString

    public String toString()

    Overrides:

    toString in class Object