Class SimpleMarkovModel
- All Implemented Interfaces:
Serializable
,MarkovModel
,Changeable
- Direct Known Subclasses:
FullHmmerProfileHMM
,ProfileHMM
- Author:
- Matthew Pocock, Thomas Down, Samiul Hasan, Keith James
- See Also:
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Field Summary
FieldsFields inherited from interface org.biojava.bio.dp.MarkovModel
ARCHITECTURE, PARAMETER
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Constructor Summary
ConstructorsConstructorDescriptionSimpleMarkovModel
(int heads, Alphabet emissionAlpha) Deprecated.SimpleMarkovModel
(int heads, Alphabet emissionAlpha, String name) -
Method Summary
Modifier and TypeMethodDescriptionvoid
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 that is emitted by the emission states.protected ChangeSupport
Called to retrieve the ChangeSupport for this object.getWeights
(State source) Get a probability Distribution over the transition from 'source'.int
heads()
The number of heads on this model.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 of the states.toString()
transitionsFrom
(State from) Returns the FiniteAlphabet of all states that have a transition from 'source'.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
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Field Details
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serialVersionUID
- See Also:
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Constructor Details
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SimpleMarkovModel
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SimpleMarkovModel
Deprecated.
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Method Details
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getChangeSupport
Description copied from class:AbstractChangeable
Called to retrieve the ChangeSupport for this object.Your implementation of this method should have the following structure:
It is usual for the forwarding listeners (someForwarder in this example) to be transient and lazily instantiated. Be sure to register invalid input: '&' unregister the forwarder in the code that does the ChangeEvent handling in setter methods.ChangeSupport cs = super.getChangeSupport(ct); if(someForwarder == null invalid input: '&'invalid input: '&' ct.isMatching(SomeInterface.SomeChangeType)) { someForwarder = new ChangeForwarder(... this.stateVariable.addChangeListener(someForwarder, VariableInterface.AChange); } return cs;
- Overrides:
getChangeSupport
in classAbstractChangeable
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emissionAlphabet
Description copied from interface:MarkovModel
Alphabet that is emitted by the emission states.- Specified by:
emissionAlphabet
in interfaceMarkovModel
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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 interfaceMarkovModel
- Returns:
- the alphabet over states
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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 equaladvance().length
.- Specified by:
heads
in interfaceMarkovModel
- Returns:
- the number of heads in this model.
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magicalState
Description copied from interface:MarkovModel
The MagicalState for this model.- Specified by:
magicalState
in interfaceMarkovModel
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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 interfaceMarkovModel
- Returns:
- the maximum advance of all states for all heads
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getWeights
Description copied from interface:MarkovModel
Get a probability Distribution over the transition from 'source'.- Specified by:
getWeights
in interfaceMarkovModel
- Parameters:
source
- the State currently occupied- Returns:
- the probability Distribution over the reachable states
- Throws:
IllegalSymbolException
- if from is not a legal state
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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 interfaceMarkovModel
- Parameters:
source
- source Statedist
- the new Distribution over the transition probabilites from source- Throws:
IllegalSymbolException
- if source is not a member of this modelIllegalAlphabetException
- if dist is not a distribution over the states returned by model.transitionsFrom(source)ChangeVetoException
- if a listener vetoed this change
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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 interfaceMarkovModel
- Parameters:
from
- the State currently occupiedto
- the State to move to- Throws:
IllegalSymbolException
- if either from or to are not legal statesChangeVetoException
- if creating the transition is vetoed
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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 interfaceMarkovModel
- Parameters:
from
- the State currently occupiedto
- the State to move to- Throws:
IllegalSymbolException
- if either from or to are not legal statesChangeVetoException
- if breaking the transition is vetoed
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containsTransition
Description copied from interface:MarkovModel
Returns wether a transition exists or not.- Specified by:
containsTransition
in interfaceMarkovModel
- Parameters:
from
- the transitin sourceto
- 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
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transitionsFrom
Description copied from interface:MarkovModel
Returns the FiniteAlphabet of all states that have a transition from 'source'.- Specified by:
transitionsFrom
in interfaceMarkovModel
- Parameters:
from
- the source State- Returns:
- a FiniteAlphabet of State objects that can reach from 'source'
- Throws:
IllegalSymbolException
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transitionsTo
Description copied from interface:MarkovModel
Returns the FiniteAlphabet of all states that have a transition to 'dest'.- Specified by:
transitionsTo
in interfaceMarkovModel
- Parameters:
to
- the destination state- Returns:
- a FiniteAlphabet of State objects that can reach 'dest'
- Throws:
IllegalSymbolException
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addState
Description copied from interface:MarkovModel
Adds a state to the model.- Specified by:
addState
in interfaceMarkovModel
- Parameters:
toAdd
- the state to add- Throws:
IllegalSymbolException
- if the state is not valid or is a MagicalStateChangeVetoException
- if either the model does not allow states to be added, or the change was vetoed
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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 interfaceMarkovModel
- Parameters:
toGo
- the state to remove- Throws:
IllegalSymbolException
- if the symbol is not part of this model or a MagicalStateIllegalTransitionException
- if the state is currently involved in any transitionsChangeVetoException
- if either the model does not allow states to be removed, or the change was vetoed
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toString
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