org.biojava.bio.dp
Class SimpleWeightMatrix

java.lang.Object
  extended by 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.
 boolean equals(java.lang.Object o)
           
 Alphabet getAlphabet()
          The alphabet for the sequences that this weight matrix models.
 Distribution getColumn(int column)
          Retrieve a column as an EmissionState.
 int hashCode()
           
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

SimpleWeightMatrix

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

SimpleWeightMatrix

public SimpleWeightMatrix(Distribution[] columns)
                   throws IllegalAlphabetException
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

hashCode

public int hashCode()
Overrides:
hashCode in class java.lang.Object

equals

public boolean equals(java.lang.Object o)
Overrides:
equals in class java.lang.Object