Package org.biojava.nbio.genome.io.fastq

Class Fastq

java.lang.Object

org.biojava.nbio.genome.io.fastq.Fastq

public final class Fastq
extends Object

FASTQ formatted sequence.

Since:

3.0.3

Method Summary

Modifier and Type	Method	Description
static FastqBuilder	builder()	Create and return a new FastqBuilder.
static FastqBuilder	builder(Fastq fastq)	Create and return a new FastqBuilder configured from the specified FASTQ formatted sequence.
Fastq	convertTo(FastqVariant variant)	Create and return a new FASTQ formatted sequence from this converted to the specified FASTQ sequence format variant.
String	getDescription()	Return the description of this FASTQ formatted sequence.
String	getQuality()	Return the quality scores for this FASTQ formatted sequence.
String	getSequence()	Return the sequence for this FASTQ formatted sequence.
FastqVariant	getVariant()	Return the FASTQ sequence format variant for this FASTQ formatted sequence.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

getDescription

public String getDescription()

Return the description of this FASTQ formatted sequence. The description will not be null.

Returns:

the description of this FASTQ formatted sequence

getSequence

public String getSequence()

Return the sequence for this FASTQ formatted sequence. The sequence will not be null.

Returns:

the sequence for this FASTQ formatted sequence

getQuality

public String getQuality()

Return the quality scores for this FASTQ formatted sequence. The quality scores will not be null.

Returns:

the quality scores for this FASTQ formatted sequence

getVariant

public FastqVariant getVariant()

Return the FASTQ sequence format variant for this FASTQ formatted sequence. The FASTQ sequence format variant will not be null.

Returns:

the FASTQ sequence format variant for this FASTQ formatted sequence

convertTo

public Fastq convertTo(FastqVariant variant)

Create and return a new FASTQ formatted sequence from this converted to the specified FASTQ sequence format variant.

Parameters:

variant - FASTQ sequence format variant, must not be null

Returns:

a new FASTQ formatted sequence from this converted to the specified FASTQ sequence format variant

Since:

4.2

builder

public static final FastqBuilder builder()

Create and return a new FastqBuilder. The FastqBuilder will not be null.

Returns:

a new FastqBuilder

builder

public static final FastqBuilder builder(Fastq fastq)

Create and return a new FastqBuilder configured from the specified FASTQ formatted sequence. The FastqBuilder will not be null.

Parameters:

fastq - FASTQ formatted sequence, must not be null

Returns:

a new FastqBuilder configured from the specified FASTQ formatted sequence

Since:

6.0.0