de.jstacs.clustering.distances

Class RandomSequenceScoreDistance

java.lang.Object

de.jstacs.clustering.distances.DistanceMetric<StatisticalModel>

de.jstacs.clustering.distances.SequenceScoreDistance

de.jstacs.clustering.distances.RandomSequenceScoreDistance

public class RandomSequenceScoreDistance
extends SequenceScoreDistance

Class for a distance metric between StatisticalModels based on the correlation of score profiles on random sequences. For two StatisticalModels 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.

Author:

Jan Grau

Field Summary

Fields inherited from class de.jstacs.clustering.distances.SequenceScoreDistance

exp, seqs

Constructor Summary

Constructors

Constructor and Description
RandomSequenceScoreDistance(DiscreteAlphabet alphabet, int n, boolean exp) Creates a distance using a random sequence of length .

Method Summary

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.

Methods inherited from class de.jstacs.clustering.distances.SequenceScoreDistance

getDistance, getDistance, getDistance, getPairwiseDistanceMatrix

Methods inherited from class de.jstacs.clustering.distances.DistanceMetric

getPairwiseDistanceMatrix

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

RandomSequenceScoreDistance

public RandomSequenceScoreDistance(DiscreteAlphabet alphabet,
                                   int n,
                                   boolean exp)
                            throws WrongAlphabetException,
                                   WrongSequenceTypeException

Creates a distance using a random sequence of length .

Parameters:

alphabet - the alphabet

n - the exponent of the sequence length

exp - if exponential profiles should be computed

Throws:

WrongAlphabetException - if the alphabet does not match

WrongSequenceTypeException - if the sequence could not be created for this alphabet

Method Detail

getProfile

public double[][] getProfile(StatisticalModel o,
                             boolean rc)
                      throws Exception

Description copied from class: SequenceScoreDistance

Returns the score profile for the model.

Overrides:

getProfile in class SequenceScoreDistance

Parameters:

o - the mode

rc - if the reverse complement should be considered

Returns:

the score profile

Throws:

Exception - if the score could not be computed

createSequences

public static CyclicSequenceAdaptor[] createSequences(DiscreteAlphabet alphabet,
                                                      int n)
                                               throws WrongAlphabetException,
                                                      WrongSequenceTypeException

Creates a new random sequence of the given length and alphabet.

Parameters:

alphabet - the alphabet

n - the exponent of the sequence length (see above)

Returns:

the sequence

Throws:

WrongAlphabetException - if the alphabet does not match

WrongSequenceTypeException - if the sequence could not be created for this alphabet