org.biojava.bio.dp

Class WMAsMM

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.dp.WMAsMM

All Implemented Interfaces:

Serializable, MarkovModel, Changeable

public class WMAsMM
extends AbstractChangeable
implements MarkovModel, Serializable

Wraps a weight matrix up so that it appears to be a very simple HMM.

Author:

Matthew Pocock

See Also:

Serialized Form

Field Summary

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

ARCHITECTURE, PARAMETER

Constructor Summary

Constructors

Constructor and Description
WMAsMM(WeightMatrix wm)

Method Summary

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.
Distribution	getWeights(State source) Get a probability Distribution over the transition from 'source'.
int	heads() The number of heads on this model.
protected int	index(State s)
MagicalState	magicalState() The MagicalState for this model.
void	registerWithTrainer(ModelTrainer modelTrainer)
void	removeState(State toAdd) Remove a state from the model.
void	setWeights(State source, Distribution dist) Set the probability distribution over the transitions from 'source'.
FiniteAlphabet	stateAlphabet() FiniteAlphabet of the states.
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, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Constructor Detail

WMAsMM

public WMAsMM(WeightMatrix wm)
       throws IllegalSymbolException

Throws:

IllegalSymbolException

Method Detail

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

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

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 ChangeVetoException

Description copied from interface: MarkovModel

Set the probability distribution over the transitions from 'source'.

This should throw an IllegalAlphabetException if the source alphabet in 'dist' is not the same alphabet as returned by transitionsFrom(source).

Specified by:

setWeights in interface MarkovModel

Parameters:

source - the source State

dist - the new distribution over transitions from 'source'

Throws:

ChangeVetoException - if for any reason the distribution can't be replaced at this time

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

registerWithTrainer

public void registerWithTrainer(ModelTrainer modelTrainer)
                         throws BioException

Throws:

BioException

createTransition

public void createTransition(State from,
                    State to)
                      throws 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:

ChangeVetoException - if creating the transition is vetoed

destroyTransition

public void destroyTransition(State from,
                     State to)
                       throws 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:

ChangeVetoException - if breaking the transition is vetoed

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 toAdd)
                 throws IllegalSymbolException,
                        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:

toAdd - the state to remove

Throws:

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

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

index

protected int index(State s)