org.biojava.bio.dp
Class SimpleWeightMatrix

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

public class SimpleWeightMatrix
extends java.lang.Object
implements WeightMatrix, java.io.Serializable

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
Tags copied from 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
Tags copied from 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
Tags copied from interface: WeightMatrix
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