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java.lang.Object | +--org.biojava.bio.dp.SimpleWeightMatrix
Constructor Summary | |
SimpleWeightMatrix(Alphabet alpha,
int columns,
DistributionFactory dFact)
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SimpleWeightMatrix(Distribution[] columns)
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Method Summary | |
int |
columns()
The number of columns modeled by the weight matrix. |
Alphabet |
getAlphabet()
The alphabet for the sequences that this weight matrix models. |
Distribution |
getColumn(int column)
Retrieve a column as an EmissionState. |
Methods inherited from class java.lang.Object |
clone,
equals,
finalize,
getClass,
hashCode,
notify,
notifyAll,
toString,
wait,
wait,
wait |
Constructor Detail |
public SimpleWeightMatrix(Alphabet alpha, int columns, DistributionFactory dFact) throws IllegalAlphabetException
public SimpleWeightMatrix(Distribution[] columns) throws IllegalAlphabetException
Method Detail |
public Alphabet getAlphabet()
public int columns()
public Distribution getColumn(int column)
To find the emission probability for Symbol sym at column col use:
wm.getColumn(col).getWeight(sym)
.
column
- the weight matrix column to retrieve
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