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

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

Field Summary

Fields inherited from class org.biojava.bio.dp.SimpleMarkovModel

serialVersionUID

Fields inherited from interface org.biojava.bio.dp.MarkovModel

ARCHITECTURE, PARAMETER

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	HmmerProfileHMM(Alphabet alpha, int columns, DistributionFactory matchFactory, DistributionFactory insertFactory, String name)

Method Summary

Modifier and Type	Method	Description
protected void	connectModel()	This is called by constructor in setting up the allowed transitions in the model
protected 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

Constructor Detail

HmmerProfileHMM

protected HmmerProfileHMM(Alphabet alpha,
                          int columns,
                          DistributionFactory matchFactory,
                          DistributionFactory insertFactory,
                          String name)
                   throws IllegalSymbolException,
                          IllegalTransitionException,
                          IllegalAlphabetException

Throws:

IllegalSymbolException

IllegalTransitionException

IllegalAlphabetException

Method Detail

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(String str,
                                           Annotation ann,
                                           int[] adv,
                                           Distribution dis)

makeNewMatchState

protected EmissionState makeNewMatchState(String str,
                                          Annotation ann,
                                          int[] adv,
                                          Distribution dis)