de.jstacs.data.sequences
Class RecursiveSequence

java.lang.Object
  de.jstacs.data.Sequence
      de.jstacs.data.sequences.RecursiveSequence

All Implemented Interfaces:

Comparable<Sequence>

Direct Known Subclasses:

PermutedSequence, Sequence.CompositeSequence, Sequence.SubSequence

public abstract class RecursiveSequence
extends Sequence

This is the main class for subsequences, composite sequences, ... . All these sequences are defined on an existing Sequence.

Author:

Jens Keilwagen

Nested Class Summary

Nested classes/interfaces inherited from class de.jstacs.data.Sequence

Sequence.CompositeSequence, Sequence.SubSequence

Field Summary

protected Sequence

content The internal sequence.

Fields inherited from class de.jstacs.data.Sequence

alphabetCon, annotation, rc

Constructor Summary

RecursiveSequence(AlphabetContainer alphabet, Sequence seq)
Creates a new RecursiveSequence on the Sequence seq with the AlphabetContainer alphabet using the annotation of the given Sequence.

RecursiveSequence(AlphabetContainer alphabet, SequenceAnnotation[] annotation, Sequence seq)
Creates a new RecursiveSequence on the Sequence seq with the AlphabetContainer alphabet and the annotation annotation.

Method Summary

double	continuousVal(int pos) Returns the continuous value at position pos of the Sequence.CompositeSequence.
int	discreteVal(int pos) Returns the discrete value at position pos of the Sequence.CompositeSequence.
protected abstract int	getIndex(int pos) Returns the index in the internal sequence.

Methods inherited from class de.jstacs.data.Sequence

annotate, compareTo, complement, complement, create, create, create, equals, flatCloneWithoutAnnotation, getAlphabetContainer, getAnnotation, getCompositeSequence, getCompositeSequence, getLength, getSubSequence, getSubSequence, getSubSequence, getSubSequence, hashCode, reverse, reverse, reverseComplement, reverseComplement, toDiscrete, toString, toString, toString, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

content

protected Sequence content

The internal sequence.

Constructor Detail

RecursiveSequence

public RecursiveSequence(AlphabetContainer alphabet,
                         SequenceAnnotation[] annotation,
                         Sequence seq)

Creates a new RecursiveSequence on the Sequence seq with the AlphabetContainer alphabet and the annotation annotation.

Parameters:

alphabet - the AlphabetContainer

annotation - the annotation of the RecursiveSequence

seq - the sequence

See Also:

Sequence.Sequence(AlphabetContainer, SequenceAnnotation[])

RecursiveSequence

public RecursiveSequence(AlphabetContainer alphabet,
                         Sequence seq)

Creates a new RecursiveSequence on the Sequence seq with the AlphabetContainer alphabet using the annotation of the given Sequence.

Parameters:

alphabet - the AlphabetContainer

seq - the sequence

Method Detail

continuousVal

public double continuousVal(int pos)

Description copied from class: Sequence

Returns the continuous value at position pos of the Sequence.CompositeSequence.

Specified by:

continuousVal in class Sequence

Parameters:

pos - the position of the Sequence.CompositeSequence

Returns:

the continuous value at position pos of the Sequence.CompositeSequence

discreteVal

public int discreteVal(int pos)

Description copied from class: Sequence

Returns the discrete value at position pos of the Sequence.CompositeSequence.

Specified by:

discreteVal in class Sequence

Parameters:

pos - the position of the Sequence.CompositeSequence

Returns:

the discrete value at position pos of the Sequence.CompositeSequence

getIndex

protected abstract int getIndex(int pos)

Returns the index in the internal sequence.

Parameters:

pos - the index in the external sequence

Returns:

the index in the internal sequence