Field Summary

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

  ARCHITECTURE, PARAMETER

Constructor Summary

Method Summary

• 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

Field Detail

• serialVersionUID

  public static final long serialVersionUID

  See Also:

  Constant Field Values

Constructor Detail

• SimpleMarkovModel

  public SimpleMarkovModel​(int heads,
                           Alphabet emissionAlpha,
                           String name)

• SimpleMarkovModel

  public SimpleMarkovModel​(int heads,
                           Alphabet emissionAlpha)

  Deprecated.

Method Detail

• getChangeSupport

  protected ChangeSupport getChangeSupport​(ChangeType ct)

  Called to retrieve the ChangeSupport for this object.

  Your implementation of this method should have the following structure:

   ChangeSupport cs = super.getChangeSupport(ct);
  
   if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
     someForwarder = new ChangeForwarder(...
  
     this.stateVariable.addChangeListener(someForwarder, VariableInterface.AChange);
   }
  
   return cs;
   

  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.

  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.

  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

• 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

• 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,
                         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 interface MarkovModel

  Parameters:

  source - source State

  dist - the new Distribution over the transition probabilites from source

  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)

  ChangeVetoException - if a listener vetoed this change

• 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:

  IllegalSymbolException - if either from or to are not legal states

  ChangeVetoException - if creating the transition is vetoed

• 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:

  IllegalSymbolException - if either from or to are not legal states

  ChangeVetoException - if breaking the transition is 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

• 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

• 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 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

  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

• toString

  public String toString()

  Overrides:

  toString in class Object