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
 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

public Alphabet getAlphabet()
The alphabet for the sequences that this weight matrix models.

Returns:
the Alphabet

columns

public int columns()
The number of columns modeled by the weight matrix.

Returns:
the number of columns

getColumn

public Distribution getColumn(int column)
                       throws java.lang.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:
java.lang.IndexOutOfBoundsException - if column is not between 0 and columns()-1