Package org.biojava.bio.dist

Interface Count

All Superinterfaces:

Changeable

All Known Implementing Classes:

IndexedCount

public interface Count
extends Changeable

An encapsulation of a count over the Symbols within an alphabet.

A Count is effectively a vector of counts from an Alphabet.

Since:

1.1

Author:

Matthew Pocock

Field Summary

Fields

Modifier and Type	Field	Description
static ChangeType	COUNTS	Whenever a component count changes the values that would be returned by getCount, they should fire a ChangeEvent with this object as the type.

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 interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Field Detail

COUNTS

static final ChangeType COUNTS

Whenever a component count changes the values that would be returned by getCount, they should fire a ChangeEvent with this object as the type.

If the whole count changes, then the change and previous fields of the ChangeEvent should be left null. If only a single weight is modified, then change should be of the form Object[] { symbol, new Double(newVal) } and previous should be of the form Object[] { symbol, new Double(oldVal) }

Method Detail

getAlphabet

Alphabet getAlphabet()

The alphabet from which this Count is over.

Returns:

the Alphabet associated with this Count

getCount

double getCount(AtomicSymbol s)
         throws IllegalSymbolException

Return the counts for a given Symbol.

Parameters:

s - the Symbol

Returns:

the number of counts for this symbol

Throws:

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

setCount

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

Set the count for the Symbol s.

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

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

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

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

void setCounts(Count c)
        throws IllegalAlphabetException,
               ChangeVetoException

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

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

void zeroCounts()
         throws ChangeVetoException

Reset all the counts to zero.

Throws:

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