org.biojava.bio.dist
Class SimpleDistribution
java.lang.Object
|
+--org.biojava.bio.dist.AbstractDistribution
|
+--org.biojava.bio.dist.SimpleDistribution
- public final class SimpleDistribution
- extends AbstractDistribution
- implements java.io.Serializable
A simple implementation of a distribution, which works with any finite alphabet.
- Author:
- Matthew Pocock, Thomas Down
- See Also:
- Serialized Form
Methods inherited from class java.lang.Object |
clone,
equals,
finalize,
getClass,
hashCode,
notify,
notifyAll,
toString,
wait,
wait,
wait |
SimpleDistribution
public SimpleDistribution(FiniteAlphabet alphabet)
getAlphabet
public Alphabet getAlphabet()
- Description copied from interface: Distribution
- The alphabet from which this spectrum emits symbols.
- Tags copied from interface: Distribution
- Returns:
- the Alphabet associated with this spectrum
getNullModel
public Distribution getNullModel()
- Description copied from class: AbstractDistribution
- Retrieve the null model Distribution that this Distribution recognizes.
- Overrides:
- getNullModel in class AbstractDistribution
- Tags copied from class: AbstractDistribution
- Returns:
- the apropriate null model
setNullModel
public void setNullModel(Distribution nullModel)
throws IllegalAlphabetException
- Assign a distribution to be the background null model.
- Parameters:
nullModel
- the distribution to act as the null model.
getWeight
public double getWeight(Symbol s)
throws IllegalSymbolException
- Description copied from interface: Distribution
- Return the probability that Symbol s is emited by this spectrum.
If the symbol is an AmbiguitySymbol, then it is the probability that
exactly one of the symbols matching it was emitted.
- Tags copied from interface: Distribution
- Parameters:
s
- the Symbol emitted- Returns:
- the log probability of emitting that symbol
- Throws:
- IllegalSymbolException - if s is not from this state's alphabet
setWeight
public void setWeight(Symbol s,
double w)
throws IllegalSymbolException
- Set the weight associated with the specified symbol in this distribution.
- Overrides:
- setWeight in class AbstractDistribution
- Tags copied from interface: Distribution
- Parameters:
s
- the Symbol emittedw
- the probability of emitting that symbol- Throws:
- IllegalSymbolException - if s is not from this state's alphabet, or
if it is an ambiguity symbol and the implementation can't handle
this case
- java.lang.UnsupportedOperationException - if this state does not allow weights
to be tampered with
registerWithTrainer
public void registerWithTrainer(DistributionTrainerContext dtc)
- Register a simple trainer for this distribution.
- Overrides:
- registerWithTrainer in class AbstractDistribution
- Tags copied from interface: Distribution
- Parameters:
dtc
- the DistributionTrainerContext with witch to register a trainer