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java.lang.Objectorg.biojava.utils.AbstractChangeable
org.biojava.bio.dp.SimpleMarkovModel
org.biojava.bio.program.hmmer.FullHmmerProfileHMM
public class FullHmmerProfileHMM
This is a class for representing the full HMMER generated Profile HMM (including loop states N and C terminal looping states).
Field Summary |
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Fields inherited from class org.biojava.bio.dp.SimpleMarkovModel |
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serialVersionUID |
Fields inherited from interface org.biojava.bio.dp.MarkovModel |
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ARCHITECTURE, PARAMETER |
Method Summary | |
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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 |
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addState, advance, containsTransition, createTransition, destroyTransition, emissionAlphabet, getChangeSupport, getWeights, heads, magicalState, removeState, setWeights, stateAlphabet, toString, transitionsFrom, transitionsTo |
Methods inherited from class org.biojava.utils.AbstractChangeable |
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addChangeListener, addChangeListener, generateChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Methods inherited from interface org.biojava.utils.Changeable |
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addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener |
Method Detail |
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public EmissionState jState()
public EmissionState cState()
public EmissionState nState()
public ModelInState hmm()
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