Package 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:
Serializable
,MarkovModel
,Changeable
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:
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Field Summary
Fields inherited from class org.biojava.bio.dp.SimpleMarkovModel
serialVersionUID
Fields inherited from interface org.biojava.bio.dp.MarkovModel
ARCHITECTURE, PARAMETER
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Method Summary
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
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Method Details
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jState
Gets the J loop state -
cState
Gets the c loop state -
nState
Gets the n loop state -
hmm
Gets the inner HmmerProfileHMM state
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