java.lang.Object

org.biojava.bio.dp.SimpleWeightMatrix

All Implemented Interfaces:: Serializable, WeightMatrix

public class SimpleWeightMatrix extends Object implements WeightMatrix, Serializable

Author:

Matthew Pocock

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor

Description

SimpleWeightMatrix(Distribution[] columns)

SimpleWeightMatrix(Alphabet alpha, int columns, DistributionFactory dFact)
Method Summary

Modifier and Type

Method

Description

int

columns()

The number of columns modeled by the weight matrix.

boolean

equals(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 Details
- SimpleWeightMatrix
  
  public SimpleWeightMatrix(Alphabet alpha, int columns, DistributionFactory dFact) throws IllegalAlphabetException
  
  Throws:
  
  IllegalAlphabetException
- SimpleWeightMatrix
  
  public SimpleWeightMatrix(Distribution[] columns) throws IllegalAlphabetException
  
  Throws:
  
  IllegalAlphabetException
Method Details
- 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 Object
- equals
  
  public boolean equals(Object o)
  
  Overrides:
  
  equals in class Object

Class SimpleWeightMatrix

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Details

SimpleWeightMatrix

SimpleWeightMatrix

Method Details

getAlphabet

columns

getColumn

hashCode

equals