public class ProfileHMM extends SimpleMarkovModel
serialVersionUIDARCHITECTURE, PARAMETER| Constructor and Description |
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ProfileHMM(Alphabet alpha,
int columns,
DistributionFactory matchFactory,
DistributionFactory insertFactory)
Deprecated.
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ProfileHMM(Alphabet alpha,
int columns,
DistributionFactory matchFactory,
DistributionFactory insertFactory,
String name)
Create a new ProfileHMM.
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| Modifier and Type | Method and Description |
|---|---|
int |
columns()
Retrieve the number of columns in the model.
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protected void |
connectModel()
This is called by constructor in setting up the allowed transitions in the model
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DotState |
getDelete(int indx)
Retrieves the delete state for column indx.
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EmissionState |
getInsert(int indx)
Retrieves the insert state at column indx.
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EmissionState |
getMatch(int indx)
Retrieve the match state at column indx.
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addState, advance, containsTransition, createTransition, destroyTransition, emissionAlphabet, getChangeSupport, getWeights, heads, magicalState, removeState, setWeights, stateAlphabet, toString, transitionsFrom, transitionsToaddChangeListener, addChangeListener, generateChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListenerclone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, waitaddChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListenerpublic ProfileHMM(Alphabet alpha, int columns, DistributionFactory matchFactory, DistributionFactory insertFactory) throws IllegalSymbolException, IllegalTransitionException, IllegalAlphabetException
public ProfileHMM(Alphabet alpha, int columns, DistributionFactory matchFactory, DistributionFactory insertFactory, String name) throws IllegalSymbolException, IllegalTransitionException, IllegalAlphabetException
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.
alpha - the Alphabet that the profile hmm will emitcolumns - the number of match statesmatchFactory - the StateFactory to use for creating the match statesinsertFactory - the stateFactory to use for creating the insert statesIllegalSymbolExceptionIllegalTransitionExceptionIllegalAlphabetExceptionpublic int columns()
public EmissionState getMatch(int indx) throws IndexOutOfBoundsException
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.
indx - the index of the column to retrieve the match state forIndexOutOfBoundsException - if indx is negative or above columns()+1public EmissionState getInsert(int indx) throws IndexOutOfBoundsException
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.
indx - the index of the column to retrieve the insert state forIndexOutOfBoundsException - if indx is negative or above columns()public DotState getDelete(int indx) throws IndexOutOfBoundsException
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()).
indx - the index of the column to retrieve the insert state forIndexOutOfBoundsException - if indx is negative or above columns()protected void connectModel() throws ChangeVetoException, IllegalSymbolException, IllegalTransitionException, IllegalAlphabetException
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