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 Details
- 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 Details
- 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

Class IndexedCount

Field Summary

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

Constructor Summary

Method Summary

Methods inherited from class org.biojava.utils.AbstractChangeable

Methods inherited from class java.lang.Object

Methods inherited from interface org.biojava.utils.Changeable

Constructor Details

IndexedCount

IndexedCount

Method Details

getAlphabet

getCount

setCount

increaseCount

setCounts

zeroCounts