org.biojava.bio.program.hmmer
Class FullHmmerProfileHMM

java.lang.Object
  |
  +--org.biojava.utils.AbstractChangeable
        |
        +--org.biojava.bio.dp.SimpleMarkovModel
              |
              +--org.biojava.bio.program.hmmer.FullHmmerProfileHMM

All Implemented Interfaces:

Changeable, MarkovModel, java.io.Serializable

public class FullHmmerProfileHMM

extends SimpleMarkovModel

This is a class for representing the full HMMER generated Profile HMM (including loop states N and C terminal looping states).

Since:

1.3

Author:

Lachlan Coin

See Also:

Serialized Form

Nested Class Summary

Nested classes inherited from class org.biojava.bio.dp.MarkovModel

MarkovModel.DistributionForwarder

Field Summary

Fields inherited from class org.biojava.bio.dp.SimpleMarkovModel

serialVersionUID

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

ARCHITECTURE, PARAMETER

Method Summary

EmissionState	cState() Gets the c loop state
ModelInState	hmm() Gets the inner HmmerProfileHMM state
EmissionState	jState() Gets the J loop state
EmissionState	nState() Gets the n loop state

Methods inherited from class org.biojava.bio.dp.SimpleMarkovModel

addState, containsTransition, createTransition, destroyTransition, emissionAlphabet, getChangeSupport, getWeights, heads, magicalState, removeState, setWeights, stateAlphabet, transitionsFrom, transitionsTo

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, hasListeners, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Method Detail

jState

public EmissionState jState()

Gets the J loop state

cState

public EmissionState cState()

Gets the c loop state

nState

public EmissionState nState()

Gets the n loop state

hmm

public ModelInState hmm()

Gets the inner HmmerProfileHMM state