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java.lang.Objectorg.biojava.utils.AbstractChangeable
org.biojava.bio.dp.SimpleMarkovModel
org.biojava.bio.program.hmmer.FullHmmerProfileHMM
This is a class for representing the full HMMER generated Profile HMM (including loop states N and C terminal looping states).
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 |
public EmissionState jState()
public EmissionState cState()
public EmissionState nState()
public ModelInState hmm()
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