org.biojava.bio.dp
Class SimpleMarkovModel

java.lang.Object
  |
  +--org.biojava.utils.AbstractChangeable
        |
        +--org.biojava.bio.dp.SimpleMarkovModel

All Implemented Interfaces:

Changeable, MarkovModel, java.io.Serializable

Direct Known Subclasses:

FullHmmerProfileHMM, ProfileHMM

public class SimpleMarkovModel

extends AbstractChangeable

implements MarkovModel, java.io.Serializable

Author:

Matthew Pocock, Thomas Down, Samiul Hasan, Keith James

See Also:

Serialized Form

Nested Class Summary

Nested classes inherited from class org.biojava.bio.dp.MarkovModel

MarkovModel.DistributionForwarder

Field Summary

static long

serialVersionUID

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

ARCHITECTURE, PARAMETER

Constructor Summary

SimpleMarkovModel(int heads, Alphabet emissionAlpha)
Deprecated.

SimpleMarkovModel(int heads, Alphabet emissionAlpha, java.lang.String name)

Method Summary

void	addState(State toAdd) Adds a state to the 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.
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, 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

Field Detail

serialVersionUID

public static final long serialVersionUID

See Also:

Constant Field Values

Constructor Detail

SimpleMarkovModel

public SimpleMarkovModel(int heads,
                         Alphabet emissionAlpha,
                         java.lang.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

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.

Specified by:

heads in interface MarkovModel

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 IllegalSymbolException,
                       IllegalAlphabetException

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:

dist - the new Distribution over the transition probabilites from source

source - the source State

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)

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:

ChangeVetoException - if creating the transition is vetoed

IllegalSymbolException - if either from or to are not legal states

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:

ChangeVetoException - if breaking the transition is vetoed

IllegalSymbolException - if either from or to are not legal states

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'

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'

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:

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

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

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

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

IllegalTransitionException - if the state is currently involved in any transitions