org.biojava.bio.dp
Class SimpleWeightMatrix
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
SimpleWeightMatrix
public SimpleWeightMatrix(Alphabet alpha,
int columns,
DistributionFactory dFact)
throws IllegalAlphabetException
- Throws:
IllegalAlphabetException
SimpleWeightMatrix
public SimpleWeightMatrix(Distribution[] columns)
throws IllegalAlphabetException
- Throws:
IllegalAlphabetException
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