Package org.biojava.bio.dp

Class WMAsMM

java.lang.Object
org.biojava.utils.AbstractChangeable
org.biojava.bio.dp.WMAsMM
All Implemented Interfaces:
Serializable, MarkovModel, Changeable
public class WMAsMM extends AbstractChangeable implements MarkovModel, Serializable
Wraps a weight matrix up so that it appears to be a very simple HMM.
Author:
Matthew Pocock
See Also:

  • Constructor Details

  • Method Details

    • 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

    • 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

    • 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 ChangeVetoException
      Description copied from interface: MarkovModel
      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).

      Specified by:
      setWeights in interface MarkovModel
      Parameters:
      source - the source State
      dist - the new distribution over transitions from 'source'
      Throws:
      ChangeVetoException - if for any reason the distribution can't be replaced at this time

    • 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

    • registerWithTrainer

      public void registerWithTrainer(ModelTrainer modelTrainer) throws BioException
      Throws:
      BioException

    • createTransition

      public void createTransition(State from, State to) throws 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

    • destroyTransition

      public void destroyTransition(State from, State to) throws 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

    • 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 toAdd) throws IllegalSymbolException, 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:
      toAdd - 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

    • 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

    • index

      protected int index(State s)