Package org.biojava.bio.dp
Class SimpleWeightMatrix
java.lang.Object
org.biojava.bio.dp.SimpleWeightMatrix
- All Implemented Interfaces:
Serializable
,WeightMatrix
- Author:
- Matthew Pocock
- See Also:
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Constructor Summary
ConstructorsConstructorDescriptionSimpleWeightMatrix
(Distribution[] columns) SimpleWeightMatrix
(Alphabet alpha, int columns, DistributionFactory dFact) -
Method Summary
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Constructor Details
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SimpleWeightMatrix
public SimpleWeightMatrix(Alphabet alpha, int columns, DistributionFactory dFact) throws IllegalAlphabetException - Throws:
IllegalAlphabetException
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SimpleWeightMatrix
- Throws:
IllegalAlphabetException
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Method Details
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getAlphabet
Description copied from interface:WeightMatrix
The alphabet for the sequences that this weight matrix models.- Specified by:
getAlphabet
in interfaceWeightMatrix
- Returns:
- the Alphabet
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columns
Description copied from interface:WeightMatrix
The number of columns modeled by the weight matrix.- Specified by:
columns
in interfaceWeightMatrix
- Returns:
- the number of columns
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getColumn
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 interfaceWeightMatrix
- Parameters:
column
- the weight matrix column to retrieve- Returns:
- the EmissionState that represents the individual column
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hashCode
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equals
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