FullHmmerProfileHMM (biojava-legacy 1.9.7 API)

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.dp.SimpleMarkovModel

org.biojava.bio.program.hmmer.FullHmmerProfileHMM

All Implemented Interfaces:: Serializable, MarkovModel, Changeable

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

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

Modifier and Type

Method

Description

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

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

Method Details
- 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