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)
This constructor creates a recursive sequence using the annotation of the given sequence.

RecursiveSequence(AlphabetContainer alphabet, SequenceAnnotation[] annotation, Sequence seq)
This constructor creates a recursive sequence.

Method Summary

double	continuousVal(int pos) Returns the continuous value of position pos.
int	discreteVal(int pos) Returns the discrete value of position pos.
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)

This constructor creates a recursive sequence.

Parameters:

alphabet - the AlphabetContainer

annotation - the annotation of the recursive sequence

seq - the sequence

RecursiveSequence

public RecursiveSequence(AlphabetContainer alphabet,
                         Sequence seq)

This constructor creates a recursive sequence using the annotation of the given sequence.

Parameters:

alphabet - the AlphabetContainer

seq - the sequence

Method Detail

continuousVal

public final double continuousVal(int pos)

Description copied from class: Sequence

Returns the continuous value of position pos.

Specified by:

continuousVal in class Sequence

Parameters:

pos - the position

Returns:

the continuous value of position pos

discreteVal

public final int discreteVal(int pos)

Description copied from class: Sequence

Returns the discrete value of position pos.

Specified by:

discreteVal in class Sequence

Parameters:

pos - the position

Returns:

the discrete value of position pos

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