com.milaboratory.core.sequence

Class NucleotideSequence

java.lang.Object

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

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

com.milaboratory.core.sequence.NucleotideSequence

All Implemented Interfaces:

HasSequence<NucleotideSequence>, NSeq<NucleotideSequence>, Seq<NucleotideSequence>, Serializable, Comparable<NucleotideSequence>

public final class NucleotideSequence
extends Sequence<S>
implements NSeq<NucleotideSequence>, Serializable

Representation of nucleotide sequence.

Author:

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

See Also:

Sequence, NucleotideAlphabet, Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static NucleotideAlphabet	ALPHABET Nucleotide alphabet
protected byte[]	data
static NucleotideSequence	EMPTY Empty instance

Constructor Summary

Constructors

Constructor and Description
NucleotideSequence(byte[] data) Creates nucleotide sequence from specified Bit2Array (will be copied in constructor).
NucleotideSequence(char[] sequence) Creates nucleotide sequence from char array of nucleotides (e.g.
NucleotideSequence(String sequence) Creates nucleotide sequence from its string representation (e.g.

Method Summary

Methods

Modifier and Type	Method and Description
byte[]	asArray() Returns an array of bytes that encodes this sequence.
byte	codeAt(int position) Returns letter code at specified position.
boolean	containsWildcards() Returns true if sequence contains wildcards.
boolean	containsWildcards(int from, int to) Returns true if sequence contains wildcards in specified region.
protected static byte[]	dataFromChars(Alphabet alphabet, char[] chars)
boolean	equals(Object o)
static NucleotideSequence	fromSequence(byte[] sequence, int offset, int length) Creates nucleotide sequence from specified byte array.
NucleotideAlphabet	getAlphabet() Returns the alphabet corresponding to this type of sequence.
S	getRange(int from, int to) Returns a subsequence of this starting at from (inclusive) and ending at to (exclusive).
NucleotideSequence	getRange(Range range) Returns a subsequence of this bounded by specified range.
NucleotideSequence	getReverseComplement() Returns reverse complement of this sequence.
int	hashCode()
int	size() Returns size of this sequence

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

compareTo, containWildcards, getBuilder, getSequence, indexOf, symbolAt, toMotif, toString

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

concatenate

Methods inherited from class java.lang.Object

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

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

concatenate, getBuilder, getRange, size

Field Detail

ALPHABET

public static final NucleotideAlphabet ALPHABET

Nucleotide alphabet

EMPTY

public static final NucleotideSequence EMPTY

Empty instance

data

protected final byte[] data

Constructor Detail

NucleotideSequence

public NucleotideSequence(String sequence)

Creates nucleotide sequence from its string representation (e.g. "ATCGG" or "atcgg").

Parameters:

sequence - string representation of sequence (case insensitive)

Throws:

IllegalArgumentException - if sequence contains unknown nucleotide symbol

NucleotideSequence

public NucleotideSequence(char[] sequence)

Creates nucleotide sequence from char array of nucleotides (e.g. ['A','T','C','G','G']).

Parameters:

sequence - char array of nucleotides

Throws:

IllegalArgumentException - if sequence contains unknown nucleotide symbol

NucleotideSequence

public NucleotideSequence(byte[] data)

Creates nucleotide sequence from specified Bit2Array (will be copied in constructor).

Parameters:

data - Bit2Array

Method Detail

getRange

public NucleotideSequence getRange(Range range)

Description copied from interface: Seq

Returns a subsequence of this bounded by specified range.

Specified by:

getRange in interface Seq<NucleotideSequence>

Overrides:

getRange in class AbstractSeq<NucleotideSequence>

Parameters:

range - a range that defines starting (inclusive) and ending (exclusive) points of subsequence

Returns:

subsequence of this bounded by specified range.

getReverseComplement

public NucleotideSequence getReverseComplement()

Returns reverse complement of this sequence.

Specified by:

getReverseComplement in interface NSeq<NucleotideSequence>

Returns:

reverse complement sequence

containsWildcards

public boolean containsWildcards(int from,
                        int to)

Returns true if sequence contains wildcards in specified region.

Returns:

true if sequence contains wildcards in specified region

containsWildcards

public boolean containsWildcards()

Returns true if sequence contains wildcards.

Returns:

true if sequence contains wildcards

getAlphabet

public NucleotideAlphabet getAlphabet()

Description copied from class: Sequence

Returns the alphabet corresponding to this type of sequence.

Returns:

alphabet corresponding to this type of sequence

fromSequence

public static NucleotideSequence fromSequence(byte[] sequence,
                              int offset,
                              int length)

Creates nucleotide sequence from specified byte array.

Parameters:

sequence - byte array

offset - offset in sequence

length - length of resulting sequence

Returns:

nucleotide sequence

codeAt

public byte codeAt(int position)

Description copied from class: Sequence

Returns letter code at specified position.

Specified by:

codeAt in class Sequence<S extends com.milaboratory.core.sequence.AbstractArraySequence<S>>

Parameters:

position - position in sequence

Returns:

element at specified position

size

public int size()

Description copied from interface: Seq

Returns size of this sequence

Specified by:

size in interface Seq<S extends com.milaboratory.core.sequence.AbstractArraySequence<S>>

Returns:

size of this sequence

asArray

public byte[] asArray()

Description copied from class: Sequence

Returns an array of bytes that encodes this sequence.

Overrides:

asArray in class Sequence<S extends com.milaboratory.core.sequence.AbstractArraySequence<S>>

Returns:

array of bytes that encodes this sequence

getRange

public S getRange(int from,
         int to)

Description copied from interface: Seq

Returns a subsequence of this starting at from (inclusive) and ending at to (exclusive).

Specified by:

getRange in interface Seq<S extends com.milaboratory.core.sequence.AbstractArraySequence<S>>

Parameters:

from - starting point of subsequence (inclusive)

to - ending point of subsequence (exclusive)

Returns:

subsequence of this starting at from (inclusive) and ending at to (exclusive)

equals

public final boolean equals(Object o)

Overrides:

equals in class Sequence<S extends com.milaboratory.core.sequence.AbstractArraySequence<S>>

hashCode

public final int hashCode()

Overrides:

hashCode in class Sequence<S extends com.milaboratory.core.sequence.AbstractArraySequence<S>>

dataFromChars

protected static byte[] dataFromChars(Alphabet alphabet,
                   char[] chars)