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java.lang.Objectorg.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()
WeightMatrix
getAlphabet
in interface WeightMatrix
public int columns()
WeightMatrix
columns
in interface WeightMatrix
public Distribution getColumn(int column)
WeightMatrix
To find the emission probability for Symbol sym at column col use:
wm.getColumn(col).getWeight(sym)
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getColumn
in interface WeightMatrix
column
- the weight matrix column to retrieve
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