Package org.biojava.bio.dist

Class IndexedCount

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.dist.IndexedCount

All Implemented Interfaces:

Serializable, Count, Changeable

public final class IndexedCount
extends AbstractChangeable
implements Count, Serializable

An encapsulation of a count over the Symbols within a FiniteAlphabet using an AlphabetIndex object.

Since:

1.1

Author:

Matthew Pocock, Mark Schreiber (serialization), Thomas Down (more serialization...)

See Also:

Serialized Form

Field Summary

Fields inherited from interface org.biojava.bio.dist.Count

COUNTS

Constructor Summary

Constructors

Constructor	Description
IndexedCount(AlphabetIndex indexer)	Get a new InexedCount for an alphabet indexer.
IndexedCount(FiniteAlphabet fa)	Get a new IdexedCount for an alphabet using the default indexer.

Method Summary

Modifier and Type	Method	Description
Alphabet	getAlphabet()	The alphabet from which this Count is over.
double	getCount(AtomicSymbol s)	Return the counts for a given Symbol.
void	increaseCount(AtomicSymbol s, double c)	Set the probability or odds that Symbol s is emitted by this state.
void	setCount(AtomicSymbol s, double c)	Set the count for the Symbol s.
void	setCounts(Count c)	Set the counts in this Counts to be equal to the counts in c.
void	zeroCounts()	Reset all the counts to zero.

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Constructor Detail

IndexedCount

public IndexedCount(FiniteAlphabet fa)

Get a new IdexedCount for an alphabet using the default indexer.

Parameters:

fa - the FiniteAlphabet to count

IndexedCount

public IndexedCount(AlphabetIndex indexer)

Get a new InexedCount for an alphabet indexer.

Parameters:

indexer - the AlphabetIndex used to map between symbols and indecies

Method Detail

getAlphabet

public Alphabet getAlphabet()

Description copied from interface: Count

The alphabet from which this Count is over.

Specified by:

getAlphabet in interface Count

Returns:

the Alphabet associated with this Count

getCount

public double getCount(AtomicSymbol s)
                throws IllegalSymbolException

Description copied from interface: Count

Return the counts for a given Symbol.

Specified by:

getCount in interface Count

Parameters:

s - the Symbol

Returns:

the number of counts for this symbol

Throws:

IllegalSymbolException - if s is not from this Count's alphabet

setCount

public void setCount(AtomicSymbol s,
                     double c)
              throws IllegalSymbolException,
                     ChangeVetoException

Description copied from interface: Count

Set the count for the Symbol s.

Specified by:

setCount in interface Count

Parameters:

s - the Symbol emitted

c - the new count for the Symbol

Throws:

IllegalSymbolException - if s is not from this state's alphabet, or if it is an ambiguity symbol and the implementation can't handle this case

ChangeVetoException - if this distribution does not allow counts to be tampered with, or if one of the listeners vetoed this change

increaseCount

public void increaseCount(AtomicSymbol s,
                          double c)
                   throws IllegalSymbolException,
                          ChangeVetoException

Description copied from interface: Count

Set the probability or odds that Symbol s is emitted by this state.

Specified by:

increaseCount in interface Count

Parameters:

s - the Symbol emitted

c - the delta to add to the count for the Symbol

Throws:

IllegalSymbolException - if s is not from this state's alphabet, or if it is an ambiguity symbol and the implementation can't handle this case

ChangeVetoException - if this Count does not allow counts to be tampered with, or if one of the listeners vetoed this change

setCounts

public void setCounts(Count c)
               throws IllegalAlphabetException,
                      ChangeVetoException

Description copied from interface: Count

Set the counts in this Counts to be equal to the counts in c.

Specified by:

setCounts in interface Count

Parameters:

c - the Count object to copy the counts from

Throws:

IllegalAlphabetException - if c has a different Alphabet to this Count

ChangeVetoException - if this Count does not allow the counts to be tampered with, or if one of the listeners vetoed this change

zeroCounts

public void zeroCounts()
                throws ChangeVetoException

Description copied from interface: Count

Reset all the counts to zero.

Specified by:

zeroCounts in interface Count

Throws:

ChangeVetoException - if this Count does not allow the counts to be tampered with, or if one of the listeners vetoed this change