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
Methods inherited from class java.lang.Object |
clone,
equals,
finalize,
getClass,
hashCode,
notify,
notifyAll,
toString,
wait,
wait,
wait |
UniformDistribution
public UniformDistribution(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 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