Package org.biojava.bio.dp
Interface WeightMatrix
- All Known Implementing Classes:
SimpleWeightMatrix
public interface WeightMatrix
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.
- Author:
- Matthew Pocock
-
Method Details
-
getAlphabet
The alphabet for the sequences that this weight matrix models.- Returns:
- the Alphabet
-
columns
int columns()The number of columns modeled by the weight matrix.- Returns:
- the number of columns
-
getColumn
Retrieve a column as an EmissionState.To find the emission probability for Symbol sym at column col use:
wm.getColumn(col).getWeight(sym)
.- Parameters:
column
- the weight matrix column to retrieve- Returns:
- the EmissionState that represents the individual column
- Throws:
IndexOutOfBoundsException
- if column is not between 0 and columns()-1
-