com.milaboratory.core.sequence

Class Sequence<S extends Sequence<S>>

java.lang.Object

com.milaboratory.core.sequence.AbstractSeq<S>

com.milaboratory.core.sequence.Sequence<S>

Type Parameters:

S - type of sequence

All Implemented Interfaces:

HasSequence<S>, Seq<S>, Comparable<S>

Direct Known Subclasses:

AminoAcidSequence, NucleotideSequence

public abstract class Sequence<S extends Sequence<S>>
extends AbstractSeq<S>
implements Comparable<S>, HasSequence<S>

Parent class for all types of sequences. Each element of sequence (e.g. nucleotide, or amino acid) encoded in byte, so Sequence is a simple container of ordered bytes; the correspondence between byte codes and particular elements is defined in Alphabet that corresponds to this type of sequence (via getAlphabet()).

Author:

Bolotin Dmitriy (bolotin.dmitriy@gmail.com), Shugay Mikhail (mikhail.shugay@gmail.com)

See Also:

Alphabet, SequenceBuilder, NucleotideSequence, AminoAcidSequence

Constructor Summary

Constructors

Constructor and Description
Sequence()

Method Summary

Methods

Modifier and Type	Method and Description
byte[]	asArray() Returns an array of bytes that encodes this sequence.
abstract byte	codeAt(int position) Returns letter code at specified position.
int	compareTo(S o)
boolean	containWildcards()
boolean	equals(Object obj)
abstract Alphabet<S>	getAlphabet() Returns the alphabet corresponding to this type of sequence.
SequenceBuilder<S>	getBuilder() Returns a builder for corresponding seq type.
S	getSequence()
int	hashCode()
int	indexOf(S subSequence) Tests whether this sequence contains subSequence and returns position of the first matched letter in this sequence or -1 if it does not contain subSequence.
char	symbolAt(int position) Returns a character representation of element at specified position.
Motif<S>	toMotif() Converts sequnce to motif data structure efficient for exact and fuzzy wildcard-aware matching and searching of sequences.
String	toString()

Methods inherited from class com.milaboratory.core.sequence.AbstractSeq

concatenate, getRange

Methods inherited from class java.lang.Object

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

Methods inherited from interface com.milaboratory.core.sequence.Seq

getRange, size

Constructor Detail

Sequence

public Sequence()

Method Detail

codeAt

public abstract byte codeAt(int position)

Returns letter code at specified position.

Parameters:

position - position in sequence

Returns:

element at specified position

getAlphabet

public abstract Alphabet<S> getAlphabet()

Returns the alphabet corresponding to this type of sequence.

Returns:

alphabet corresponding to this type of sequence

asArray

public byte[] asArray()

Returns an array of bytes that encodes this sequence.

Returns:

array of bytes that encodes this sequence

symbolAt

public char symbolAt(int position)

Returns a character representation of element at specified position.

Parameters:

position - position in this sequence

Returns:

character representation of element at specified position

toMotif

public Motif<S> toMotif()

Converts sequnce to motif data structure efficient for exact and fuzzy wildcard-aware matching and searching of sequences.

Returns:

motif

containWildcards

public boolean containWildcards()

getSequence

public S getSequence()

Specified by:

getSequence in interface HasSequence<S extends Sequence<S>>

getBuilder

public SequenceBuilder<S> getBuilder()

Description copied from interface: Seq

Returns a builder for corresponding seq type.

Specified by:

getBuilder in interface Seq<S extends Sequence<S>>

Returns:

builder for corresponding seq type

equals

public boolean equals(Object obj)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

toString

public String toString()

Overrides:

toString in class Object

compareTo

public int compareTo(S o)

Specified by:

compareTo in interface Comparable<S extends Sequence<S>>

indexOf

public int indexOf(S subSequence)

Tests whether this sequence contains subSequence and returns position of the first matched letter in this sequence or -1 if it does not contain subSequence.

Parameters:

subSequence - subsequence

Returns:

position of the first matched letter in this sequence or -1 if it does not contain subSequence