com.milaboratory.core.sequence

Class NSequenceWithQuality

java.lang.Object

com.milaboratory.core.sequence.SequenceWithQuality<NucleotideSequence>

com.milaboratory.core.sequence.NSequenceWithQuality

All Implemented Interfaces:

MultiNSequenceWithQuality, NSeq<NSequenceWithQuality>, Seq<NSequenceWithQuality>, Serializable

public final class NSequenceWithQuality
extends SequenceWithQuality<NucleotideSequence>
implements NSeq<NSequenceWithQuality>, MultiNSequenceWithQuality

Container of nucleotide sequence with its quality.

Author:

Dmitry Bolotin, Stanislav Poslavsky

See Also:

SequenceWithQuality, Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static NSequenceWithQuality	EMPTY

Constructor Summary

Constructors

Constructor and Description
NSequenceWithQuality(NucleotideSequence sequence)
NSequenceWithQuality(NucleotideSequence sequence, byte quality)
NSequenceWithQuality(NucleotideSequence sequence, SequenceQuality quality) Creates nucleotide sequence with its quality
NSequenceWithQuality(String sequence)
NSequenceWithQuality(String sequence, String quality)

Method Summary

Methods

Modifier and Type	Method and Description
NSequenceWithQuality	concatenate(NSequenceWithQuality other) Returns a concatenation of this and other sequence (so this will be followed by other in the result).
NSequenceWithQuality	get(int id)
NSequenceWithQualityBuilder	getBuilder() Returns a builder for corresponding seq type.
NSequenceWithQuality	getRange(int from, int to) Returns a subsequence of this starting at from (inclusive) and ending at to (exclusive).
NSequenceWithQuality	getRange(Range range) Returns a subsequence of this bounded by specified range.
NSequenceWithQuality	getReverseComplement() Returns reverse complement sequence with reversed quality.
int	numberOfSequences()

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

equals, getQuality, getSequence, getSubSequence, getSubSequence, hashCode, size, toPrettyString, toString

Methods inherited from class java.lang.Object

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

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

size

Field Detail

EMPTY

public static final NSequenceWithQuality EMPTY

Constructor Detail

NSequenceWithQuality

public NSequenceWithQuality(NucleotideSequence sequence,
                    SequenceQuality quality)

Creates nucleotide sequence with its quality

Parameters:

sequence - nucleotide sequence

quality - quality

Throws:

IllegalArgumentException - if sequence.size() != quality.size()

NSequenceWithQuality

public NSequenceWithQuality(String sequence,
                    String quality)

NSequenceWithQuality

public NSequenceWithQuality(String sequence)

NSequenceWithQuality

public NSequenceWithQuality(NucleotideSequence sequence,
                    byte quality)

NSequenceWithQuality

public NSequenceWithQuality(NucleotideSequence sequence)

Method Detail

getReverseComplement

public NSequenceWithQuality getReverseComplement()

Returns reverse complement sequence with reversed quality.

Specified by:

getReverseComplement in interface NSeq<NSequenceWithQuality>

Returns:

reverse complement sequence with reversed quality

numberOfSequences

public int numberOfSequences()

Specified by:

numberOfSequences in interface MultiNSequenceWithQuality

get

public NSequenceWithQuality get(int id)

Specified by:

get in interface MultiNSequenceWithQuality

getRange

public NSequenceWithQuality 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<NSequenceWithQuality>

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)

getRange

public NSequenceWithQuality getRange(Range range)

Description copied from interface: Seq

Returns a subsequence of this bounded by specified range.

Specified by:

getRange in interface Seq<NSequenceWithQuality>

Parameters:

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

Returns:

subsequence of this bounded by specified range.

getBuilder

public NSequenceWithQualityBuilder getBuilder()

Description copied from interface: Seq

Returns a builder for corresponding seq type.

Specified by:

getBuilder in interface Seq<NSequenceWithQuality>

Returns:

builder for corresponding seq type

concatenate

public NSequenceWithQuality concatenate(NSequenceWithQuality other)

Description copied from interface: Seq

Returns a concatenation of this and other sequence (so this will be followed by other in the result).

Specified by:

concatenate in interface Seq<NSequenceWithQuality>

Parameters:

other - other sequence

Returns:

concatenation of this and other sequences