org.biojava.bio.program.hmmer
Class FullHmmerProfileHMM

java.lang.Object
  extended byorg.biojava.utils.AbstractChangeable
      extended byorg.biojava.bio.dp.SimpleMarkovModel
          extended byorg.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