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 Summary

Methods

Modifier and Type	Method and Description
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

getAlphabet

Alphabet 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

Distribution getColumn(int column)
                       throws IndexOutOfBoundsException

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