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An encapsulation of a count over the Symbols within an alphabet.
A Count is effectively a vector of counts from an Alphabet.
Field Summary | |
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 | |
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 emited 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 |
public 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 |
public Alphabet getAlphabet()
public double getCount(AtomicSymbol s) throws IllegalSymbolException
s
- the Symbol
IllegalSymbolException
- if s is not from this Count's alphabetpublic void setCount(AtomicSymbol s, double c) throws IllegalSymbolException, ChangeVetoException
s
- the Symbol emittedc
- the new count for the Symbol
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 changepublic void increaseCount(AtomicSymbol s, double c) throws IllegalSymbolException, ChangeVetoException
s
- the Symbol emittedc
- the delta to add to the count for the Symbol
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 changepublic void setCounts(Count c) throws IllegalAlphabetException, ChangeVetoException
c
- the Count object to copy the counts from
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 changepublic void zeroCounts() throws ChangeVetoException
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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