org.biojava.bio.dist
Class OrderNDistributionFactory
java.lang.Object
org.biojava.bio.dist.OrderNDistributionFactory
- All Implemented Interfaces:
- DistributionFactory
public class OrderNDistributionFactory
- extends Object
- implements DistributionFactory
Default factory for Order-N distributions.
- Since:
- 1.1
- Author:
- Thomas Down, Mark Schreiber
Field Summary |
static DistributionFactory |
DEFAULT
Factory which used DistributionFactory.DEFAULT to create conditioned
distributions. |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
DEFAULT
public static final DistributionFactory DEFAULT
- Factory which used DistributionFactory.DEFAULT to create conditioned
distributions.
OrderNDistributionFactory
public OrderNDistributionFactory(DistributionFactory df)
- Construct a new OrderNDistributionFactory with a specified factory
for conditioned distributions.
- Parameters:
df
- The DistributionFactory used for construction new conditioned
distributions.
createDistribution
public Distribution createDistribution(Alphabet alpha)
throws IllegalAlphabetException
- Creates an OrderNDistribution of the appropriate type.
- Specified by:
createDistribution
in interface DistributionFactory
- Parameters:
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
.
- Returns:
- An OrderNDistribution
- Throws:
IllegalAlphabetException
- if a Distribution cannot be made with
that Alphabet
.