public class RandomSequenceScoreDistance extends SequenceScoreDistance
StatisticalModel
s based on the correlation of score
profiles on random sequences.
For two StatisticalModel
s and , we compute the score profiles
and on a random sequence of length .
The distance is then defined based on the Pearson correlation as between these score profiles,
maximizing over suitable shifts of the score profiles and both strand orientations.exp, seqs
Constructor and Description |
---|
RandomSequenceScoreDistance(DiscreteAlphabet alphabet,
int n,
boolean exp)
Creates a distance using a random sequence of length .
|
Modifier and Type | Method and Description |
---|---|
static CyclicSequenceAdaptor[] |
createSequences(DiscreteAlphabet alphabet,
int n)
Creates a new random sequence of the given length and alphabet.
|
double[][] |
getProfile(StatisticalModel o,
boolean rc)
Returns the score profile for the model.
|
getDistance, getDistance, getDistance, getPairwiseDistanceMatrix
getPairwiseDistanceMatrix
public RandomSequenceScoreDistance(DiscreteAlphabet alphabet, int n, boolean exp) throws WrongAlphabetException, WrongSequenceTypeException
alphabet
- the alphabetn
- the exponent of the sequence lengthexp
- if exponential profiles should be computedWrongAlphabetException
- if the alphabet does not matchWrongSequenceTypeException
- if the sequence could not be created for this alphabetpublic double[][] getProfile(StatisticalModel o, boolean rc) throws Exception
SequenceScoreDistance
getProfile
in class SequenceScoreDistance
o
- the moderc
- if the reverse complement should be consideredException
- if the score could not be computedpublic static CyclicSequenceAdaptor[] createSequences(DiscreteAlphabet alphabet, int n) throws WrongAlphabetException, WrongSequenceTypeException
alphabet
- the alphabetn
- the exponent of the sequence length (see above)WrongAlphabetException
- if the alphabet does not matchWrongSequenceTypeException
- if the sequence could not be created for this alphabet