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java.lang.Objectorg.biojava.bio.dist.OrderNDistributionFactory
public class OrderNDistributionFactory
Default factory for Order-N distributions.
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biojava.bio.dist.DistributionFactory |
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DistributionFactory.DefaultDistributionFactory |
Field Summary | |
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static DistributionFactory |
DEFAULT
Factory which used DistributionFactory.DEFAULT to create conditioned distributions. |
Constructor Summary | |
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OrderNDistributionFactory(DistributionFactory df)
Construct a new OrderNDistributionFactory with a specified factory for conditioned distributions. |
Method Summary | |
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Distribution |
createDistribution(Alphabet alpha)
Creates an OrderNDistribution of the appropriate type. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public static final DistributionFactory DEFAULT
Constructor Detail |
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public OrderNDistributionFactory(DistributionFactory df)
df
- The DistributionFactory used for construction new conditioned
distributions.Method Detail |
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public Distribution createDistribution(Alphabet alpha) throws IllegalAlphabetException
createDistribution
in interface DistributionFactory
alpha
- the Alphabet should be in a form that clearly indicates the
conditioning and the conditioned alphabet unless it is very obvious. For
example (DNA x DNA) is obvious, ((DNA x DNA x DNA) x DNA) indicates that
(DNA x DNA x DNA) is the conditioning Alphabet
and DNA is the
conditioned Alphabet
. (DNA x DNA x DNA x DNA) doesn't but
for compatibility with biojava 1.2 this is allowed in the constructor.
As from biojava 1.2.3 or greater this will be internally converted to
((DNA x DNA x DNA) x DNA) which was the convention implied by biojava 1.2
Calls to the returned Distribution
s getAlphabet()
method will return the converted Alphabet
.
IllegalAlphabetException
- if a Distribution cannot be made with
that Alphabet
.
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