org.biojava.bio.dist
Class PairDistribution

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

public class PairDistribution
extends AbstractDistribution
implements java.io.Serializable

Class for pairing up two unique distributions.

See Also:
Serialized Form

Constructor Summary
PairDistribution(Distribution first, Distribution second)
           
 
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 sym)
          Return the probability that Symbol s is emited by this spectrum.
 void registerWithTrainer(ModelTrainer trainer)
          Register this paired distribution with a model trainer.
 void setNullModel(Distribution nullModel)
          Set a null background distribution.
 
Methods inherited from class org.biojava.bio.dist.AbstractDistribution
getAmbiguityWeight, registerWithTrainer, sampleSymbol, setWeight
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

PairDistribution

public PairDistribution(Distribution first,
                        Distribution second)
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
Set a null background distribution.
Parameters:
nullModel - the distribution to act as the background distribution.

registerWithTrainer

public void registerWithTrainer(ModelTrainer trainer)
Register this paired distribution with a model trainer.
Parameters:
trainer - the trainer to register this distribution with.

getWeight

public double getWeight(Symbol sym)
                 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