org.biojava.bio.dp

Interface MarkovModel

All Superinterfaces:

Changeable

All Known Implementing Classes:

FullHmmerProfileHMM, HmmerProfileHMM, ProfileHMM, SimpleMarkovModel, WMAsMM

public interface MarkovModel
extends Changeable

A markov model.

All probablities are in log space.

This interface models a subset of hidden markov models with an explicit start and end state. In principle, these can be combined together, so that a state within one model may be an entire model in its own right, wired via container->start and end->container. For the sample methods to work, the log scores must be probabilities (sum to 1).

Field Summary

Fields

Modifier and Type	Field and Description
static ChangeType	ARCHITECTURE Signals that the architecture of the model is changing.
static ChangeType	PARAMETER Signals that one or more parameters have altered.

Method Summary

Methods

Modifier and Type	Method and Description
void	addState(State newState) 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() Deprecated. use advance().length
MagicalState	magicalState() The MagicalState for this model.
void	removeState(State toGo) 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 source) Returns the FiniteAlphabet of all states that have a transition from 'source'.
FiniteAlphabet	transitionsTo(State dest) Returns the FiniteAlphabet of all states that have a transition to 'dest'.

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Field Detail

ARCHITECTURE

static final ChangeType ARCHITECTURE

Signals that the architecture of the model is changing.

For a transition creation, the changed field should be a two element array containing the source and destination states of the new transition, and the previous field should be null. Likewise for the removal of a transition, the previos should hold the array, and changed should be null.

PARAMETER

static final ChangeType PARAMETER

Signals that one or more parameters have altered.

If it is clear which parameter has changed, then this should be in the current and/or previous field. Otherwise, these should be null.

Method Detail

emissionAlphabet

Alphabet emissionAlphabet()

Alphabet that is emitted by the emission states.

stateAlphabet

FiniteAlphabet stateAlphabet()

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.

Returns:

the alphabet over states

magicalState

MagicalState magicalState()

The MagicalState for this model.

heads

int heads()

Deprecated. use advance().length

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.

Returns:

the number of heads in this model.

advance

int[] advance()

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

Returns:

the maximum advance of all states for all heads

getWeights

Distribution getWeights(State source)
                        throws IllegalSymbolException

Get a probability Distribution over the transition from 'source'.

Parameters:

source - the State currently occupied

Returns:

the probability Distribution over the reachable states

Throws:

IllegalSymbolException - if from is not a legal state

setWeights

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

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).

Parameters:

source - the source State

dist - the new distribution over transitions from 'source'

Throws:

IllegalSymbolException - if source is not a state in this model

IllegalAlphabetException - if the distribution has the wrong source alphabet

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

transitionsFrom

FiniteAlphabet transitionsFrom(State source)
                               throws IllegalSymbolException

Returns the FiniteAlphabet of all states that have a transition from 'source'.

Parameters:

source - the source State

Returns:

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

Throws:

IllegalSymbolException

transitionsTo

FiniteAlphabet transitionsTo(State dest)
                             throws IllegalSymbolException

Returns the FiniteAlphabet of all states that have a transition to 'dest'.

Parameters:

dest - the destination state

Returns:

a FiniteAlphabet of State objects that can reach 'dest'

Throws:

IllegalSymbolException

containsTransition

boolean containsTransition(State from,
                         State to)
                           throws IllegalSymbolException

Returns wether a transition exists or not.

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

createTransition

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

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.

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

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

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.

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

addState

void addState(State newState)
              throws IllegalSymbolException,
                     ChangeVetoException

Adds a state to the model.

Parameters:

newState - 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

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

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.

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