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A log odds weight matrix.
The weight matrix uses computer-coordinates. Thus, a 10 column weight matrix has columns (0 - 9). I guess that if you try to access columns outside the logical range, the implementation may throw an IndexOutOfBoundsException.
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. |
Method Detail |
public Alphabet getAlphabet()
public int columns()
public Distribution getColumn(int column) throws java.lang.IndexOutOfBoundsException
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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