org.biojava.bio.dist
Class UniformDistribution

java.lang.Object
  |
  +--org.biojava.bio.dist.AbstractDistribution
        |
        +--org.biojava.bio.dist.UniformDistribution

public class UniformDistribution
extends AbstractDistribution
implements java.io.Serializable

An implementation of an uniform distribution

See Also:
Serialized Form

Constructor Summary
UniformDistribution(FiniteAlphabet alphabet)
           
 
Method Summary
 Alphabet getAlphabet()
          The alphabet from which this spectrum emits symbols.
 Distribution getNullModel()
          Retrieve the null model Distribution that this Distribution recognizes.
 double getWeight(Symbol s)
          Return the probability that Symbol s is emited by this spectrum.
 void registerWithTrainer(DistributionTrainerContext dtc)
          Register an IgnoreCountsTrainer instance as the trainer for this distribution.
 void setNullModel(Distribution nullModel)
          Assign a background distribution
 
Methods inherited from class org.biojava.bio.dist.AbstractDistribution
getAmbiguityWeight, sampleSymbol, setWeight
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

UniformDistribution

public UniformDistribution(FiniteAlphabet alphabet)
Method Detail

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 background distribution
Parameters:
nullModel - the background distribution to assign

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

registerWithTrainer

public void registerWithTrainer(DistributionTrainerContext dtc)
Description copied from class: AbstractDistribution
Register an IgnoreCountsTrainer instance as the trainer for this distribution. Override this if you wish to implement a trainable distribution.
Overrides:
registerWithTrainer in class AbstractDistribution
Tags copied from interface: Distribution
Parameters:
dtc - the DistributionTrainerContext with witch to register a trainer