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:
- Changeable, MarkovModel, java.io.Serializable
- public class HmmerProfileHMM
- extends ProfileHMM
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 <-> 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:
- Serialized Form
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 java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
HmmerProfileHMM
protected HmmerProfileHMM(Alphabet alpha,
int columns,
DistributionFactory matchFactory,
DistributionFactory insertFactory,
java.lang.String name)
throws IllegalSymbolException,
IllegalTransitionException,
IllegalAlphabetException
connectModel
protected void connectModel()
throws ChangeVetoException,
IllegalSymbolException,
IllegalTransitionException,
IllegalAlphabetException
- This is called by constructor in setting up the allowed transitions in the model
- Overrides:
connectModel
in class ProfileHMM
- Throws:
ChangeVetoException
IllegalSymbolException
IllegalTransitionException
IllegalAlphabetException
transScore
public double transScore(State from,
State to,
Symbol symFrom,
Symbol symTo)
throws IllegalSymbolException
- Throws:
IllegalSymbolException
log2
protected static double log2(double x)
makeNewInsertState
protected EmissionState makeNewInsertState(java.lang.String str,
Annotation ann,
int[] adv,
Distribution dis)
makeNewMatchState
protected EmissionState makeNewMatchState(java.lang.String str,
Annotation ann,
int[] adv,
Distribution dis)