Package org.biojava.bio.dp

Class ProfileHMM

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.dp.SimpleMarkovModel

org.biojava.bio.dp.ProfileHMM

All Implemented Interfaces:

Serializable, MarkovModel, Changeable

Direct Known Subclasses:

HmmerProfileHMM

public class ProfileHMM
extends SimpleMarkovModel

Author:

Matthew Pocock, 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

Constructor	Description
ProfileHMM(Alphabet alpha, int columns, DistributionFactory matchFactory, DistributionFactory insertFactory)	Deprecated.
ProfileHMM(Alphabet alpha, int columns, DistributionFactory matchFactory, DistributionFactory insertFactory, String name)	Create a new ProfileHMM.

Method Summary

Modifier and Type	Method	Description
int	columns()	Retrieve the number of columns in the model.
protected void	connectModel()	This is called by constructor in setting up the allowed transitions in the model
DotState	getDelete(int indx)	Retrieves the delete state for column indx.
EmissionState	getInsert(int indx)	Retrieves the insert state at column indx.
EmissionState	getMatch(int indx)	Retrieve the match state at column indx.

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

ProfileHMM

public ProfileHMM(Alphabet alpha,
                  int columns,
                  DistributionFactory matchFactory,
                  DistributionFactory insertFactory)
           throws IllegalSymbolException,
                  IllegalTransitionException,
                  IllegalAlphabetException

Deprecated.

Throws:

IllegalSymbolException

IllegalTransitionException

IllegalAlphabetException

ProfileHMM

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

Create a new ProfileHMM.

The profile will be over the Alphabet alpha. It will have 'columns' match states, 'columns' delete states and 'columns'+1 insert states. The match states will be created by matchFactory, and the insert states will be created by insertFactory. This gives you great freedom for changing how the states are implemented. For example, insertFactory may always return views onto a single underlying probability distribution in which case all insert states will emit the same type of stuff - or it may create an individual state for each insert state, in which case each insert can be a different type of thing. You could make the insert state a view onto your null model, or onto a protein-specific distribution.

Parameters:

alpha - the Alphabet that the profile hmm will emit

columns - the number of match states

matchFactory - the StateFactory to use for creating the match states

insertFactory - the stateFactory to use for creating the insert states

Throws:

IllegalSymbolException

IllegalTransitionException

IllegalAlphabetException

Method Detail

columns

public int columns()

Retrieve the number of columns in the model.

Returns:

the number of columns

getMatch

public EmissionState getMatch(int indx)
                       throws IndexOutOfBoundsException

Retrieve the match state at column indx.

The first match state is at index 1, and the last match state is at column columns(). The states at index 0 and columns()+1 are both the magical state. This is so that the whole model backbone can be addressed without writing lots of special-case code.

Parameters:

indx - the index of the column to retrieve the match state for

Returns:

the match state for column indx

Throws:

IndexOutOfBoundsException - if indx is negative or above columns()+1

getInsert

public EmissionState getInsert(int indx)
                        throws IndexOutOfBoundsException

Retrieves the insert state at column indx.

Insert_0 is the insert that is accessible directly from the magical state. Insert_1..columns() are 'above' each propper match state. There is no insert state above the magical state at the end of the model, as insert_columns already models trailing inserts.

Parameters:

indx - the index of the column to retrieve the insert state for

Returns:

the insert state for column indx

Throws:

IndexOutOfBoundsException - if indx is negative or above columns()

getDelete

public DotState getDelete(int indx)
                   throws IndexOutOfBoundsException

Retrieves the delete state for column indx.

Delete states are 'above' the match state that they delete. There is no delete state for the magical state at either the beginning or end of the model, so the delete state indx can range within (1..columns()).

Parameters:

indx - the index of the column to retrieve the insert state for

Returns:

the insert state for column indx

Throws:

IndexOutOfBoundsException - if indx is negative or above columns()

connectModel

protected void connectModel()
                     throws ChangeVetoException,
                            IllegalSymbolException,
                            IllegalTransitionException,
                            IllegalAlphabetException

This is called by constructor in setting up the allowed transitions in the model

Throws:

ChangeVetoException

IllegalSymbolException

IllegalTransitionException

IllegalAlphabetException