Package org.biojava.bio.program.hmmer
Class HmmerProfileHMM
java.lang.Object
org.biojava.utils.AbstractChangeable
org.biojava.bio.dp.SimpleMarkovModel
org.biojava.bio.dp.ProfileHMM
org.biojava.bio.program.hmmer.HmmerProfileHMM
- All Implemented Interfaces:
Serializable
,MarkovModel
,Changeable
This is a class for representing HMMER generated Profile HMM.
It differs from the normal ProfileHMM only in the states which are connected:
- there are no insert invalid input: '<'-> delete transitions allowed
- there is no iO initial insert state (between begin and initial match states)
- there is not iN final insert state (between final match state and end state)
- 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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Constructor Summary
ConstructorsModifierConstructorDescriptionprotected
HmmerProfileHMM
(Alphabet alpha, int columns, DistributionFactory matchFactory, DistributionFactory insertFactory, String name) -
Method Summary
Modifier and TypeMethodDescriptionprotected void
This is called by constructor in setting up the allowed transitions in the modelprotected static double
log2
(double x) protected EmissionState
makeNewInsertState
(String str, Annotation ann, int[] adv, Distribution dis) protected EmissionState
makeNewMatchState
(String str, Annotation ann, int[] adv, Distribution dis) double
transScore
(State from, State to, Symbol symFrom, Symbol symTo) Methods inherited from class org.biojava.bio.dp.ProfileHMM
columns, getDelete, getInsert, getMatch
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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Constructor Details
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HmmerProfileHMM
protected HmmerProfileHMM(Alphabet alpha, int columns, DistributionFactory matchFactory, DistributionFactory insertFactory, String name) throws IllegalSymbolException, IllegalTransitionException, IllegalAlphabetException
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Method Details
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connectModel
protected void connectModel() throws ChangeVetoException, IllegalSymbolException, IllegalTransitionException, IllegalAlphabetExceptionThis is called by constructor in setting up the allowed transitions in the model- Overrides:
connectModel
in classProfileHMM
- Throws:
ChangeVetoException
IllegalSymbolException
IllegalTransitionException
IllegalAlphabetException
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transScore
public double transScore(State from, State to, Symbol symFrom, Symbol symTo) throws IllegalSymbolException - Throws:
IllegalSymbolException
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log2
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makeNewInsertState
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makeNewMatchState
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