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java.lang.Object | +--org.biojava.bio.dist.AbstractDistribution | +--org.biojava.bio.dist.DNADistribution
A state in a markov process.
This implementation is optimized for DNA.
Constructor Summary | |
DNADistribution()
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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 probability distribution to the DNA distribution. |
void |
setWeight(Symbol s,
double score)
Set the weight of a given symbol in this distribution. |
Methods inherited from class org.biojava.bio.dist.AbstractDistribution |
getAmbiguityWeight,
sampleSymbol |
Methods inherited from class java.lang.Object |
clone,
equals,
finalize,
getClass,
hashCode,
notify,
notifyAll,
toString,
wait,
wait,
wait |
Constructor Detail |
public DNADistribution()
Method Detail |
public Alphabet getAlphabet()
public Distribution getNullModel()
public void setNullModel(Distribution nullModel) throws IllegalAlphabetException
nullModel
- the Distribution to be added as the background distribution.public double getWeight(Symbol s) throws IllegalSymbolException
If the symbol is an AmbiguitySymbol, then it is the probability that exactly one of the symbols matching it was emitted.
s
- the Symbol emittedpublic void setWeight(Symbol s, double score) throws IllegalSymbolException
s
- the Symbol emittedw
- the probability of emitting that symbolpublic void registerWithTrainer(DistributionTrainerContext dtc)
dtc
- the DistributionTrainerContext with witch to register a trainer
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