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## 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
`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
`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

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