org.biojava.bio.dp
Class SimpleWeightMatrix

java.lang.Object
  |
  +--org.biojava.bio.dp.SimpleWeightMatrix

All Implemented Interfaces:

java.io.Serializable, WeightMatrix

public class SimpleWeightMatrix

extends java.lang.Object

implements WeightMatrix, java.io.Serializable

Author:

Matthew Pocock

See Also:

Serialized Form

Constructor Summary

SimpleWeightMatrix(Alphabet alpha, int columns, DistributionFactory dFact)

SimpleWeightMatrix(Distribution[] columns)

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

SimpleWeightMatrix

public SimpleWeightMatrix(Alphabet alpha,
                          int columns,
                          DistributionFactory dFact)
                   throws IllegalAlphabetException

SimpleWeightMatrix

public SimpleWeightMatrix(Distribution[] columns)
                   throws IllegalAlphabetException

Method Detail

getAlphabet

public Alphabet getAlphabet()

Description copied from interface: WeightMatrix

The alphabet for the sequences that this weight matrix models.

Specified by:

getAlphabet in interface WeightMatrix

Returns:

the Alphabet

columns

public int columns()

Description copied from interface: WeightMatrix

The number of columns modeled by the weight matrix.

Specified by:

columns in interface WeightMatrix

Returns:

the number of columns

getColumn

public Distribution getColumn(int column)

Description copied from interface: WeightMatrix

Retrieve a column as an EmissionState.

To find the emission probability for Symbol sym at column col use: wm.getColumn(col).getWeight(sym).

Specified by:

getColumn in interface WeightMatrix

Parameters:

column - the weight matrix column to retrieve

Returns:

the EmissionState that represents the individual column