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java.lang.Objectorg.biojava.utils.AbstractChangeable
org.biojava.bio.dp.SimpleMarkovModel
public class SimpleMarkovModel
Field Summary | |
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static long |
serialVersionUID
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Fields inherited from interface org.biojava.bio.dp.MarkovModel |
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ARCHITECTURE, PARAMETER |
Constructor Summary | |
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SimpleMarkovModel(int heads,
Alphabet emissionAlpha)
Deprecated. |
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SimpleMarkovModel(int heads,
Alphabet emissionAlpha,
String name)
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Method Summary | |
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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 |
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addChangeListener, addChangeListener, generateChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Methods inherited from interface org.biojava.utils.Changeable |
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addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener |
Field Detail |
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public static final long serialVersionUID
Constructor Detail |
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public SimpleMarkovModel(int heads, Alphabet emissionAlpha, String name)
public SimpleMarkovModel(int heads, Alphabet emissionAlpha)
Method Detail |
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protected ChangeSupport getChangeSupport(ChangeType ct)
AbstractChangeable
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 & unregister the
forwarder in the code that does the ChangeEvent handling in setter methods.
ChangeSupport cs = super.getChangeSupport(ct);
if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
someForwarder = new ChangeForwarder(...
this.stateVariable.addChangeListener(someForwarder, VariableInterface.AChange);
}
return cs;
getChangeSupport
in class AbstractChangeable
public Alphabet emissionAlphabet()
MarkovModel
emissionAlphabet
in interface MarkovModel
public FiniteAlphabet stateAlphabet()
MarkovModel
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.
stateAlphabet
in interface MarkovModel
public int heads()
MarkovModel
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
.
heads
in interface MarkovModel
public MagicalState magicalState()
MarkovModel
magicalState
in interface MarkovModel
public int[] advance()
MarkovModel
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
advance
in interface MarkovModel
public Distribution getWeights(State source) throws IllegalSymbolException
MarkovModel
getWeights
in interface MarkovModel
source
- the State currently occupied
IllegalSymbolException
- if from is not a legal statepublic void setWeights(State source, Distribution dist) throws IllegalSymbolException, IllegalAlphabetException, ChangeVetoException
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.
setWeights
in interface MarkovModel
source
- source Statedist
- the new Distribution over the transition probabilites from source
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 changepublic void createTransition(State from, State to) throws IllegalSymbolException, ChangeVetoException
MarkovModel
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.
createTransition
in interface MarkovModel
from
- the State currently occupiedto
- the State to move to
IllegalSymbolException
- if either from or to are not legal states
ChangeVetoException
- if creating the transition is vetoedpublic void destroyTransition(State from, State to) throws IllegalSymbolException, ChangeVetoException
MarkovModel
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.
destroyTransition
in interface MarkovModel
from
- the State currently occupiedto
- the State to move to
IllegalSymbolException
- if either from or to are not legal states
ChangeVetoException
- if breaking the transition is vetoedpublic boolean containsTransition(State from, State to) throws IllegalSymbolException
MarkovModel
containsTransition
in interface MarkovModel
from
- the transitin sourceto
- the transition destination
IllegalSymbolException
- if either from or to are not states in this
modelpublic FiniteAlphabet transitionsFrom(State from) throws IllegalSymbolException
MarkovModel
transitionsFrom
in interface MarkovModel
from
- the source State
IllegalSymbolException
public FiniteAlphabet transitionsTo(State to) throws IllegalSymbolException
MarkovModel
transitionsTo
in interface MarkovModel
to
- the destination state
IllegalSymbolException
public void addState(State toAdd) throws IllegalSymbolException, ChangeVetoException
MarkovModel
addState
in interface MarkovModel
toAdd
- the state to add
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 vetoedpublic void removeState(State toGo) throws IllegalSymbolException, IllegalTransitionException, ChangeVetoException
MarkovModel
States should not be removed untill they are involved in no transitions. This is to avoid producing corrupted models by accident.
removeState
in interface MarkovModel
toGo
- the state to remove
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 vetoedpublic String toString()
toString
in class Object
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