Package org.biojava.bio.program.fastq

Class FastqBuilder

java.lang.Object

org.biojava.bio.program.fastq.FastqBuilder

public final class FastqBuilder
extends Object

Fluent builder API for creating FASTQ formatted sequences.

Since:

1.7.1

Field Summary

Fields

Modifier and Type	Field	Description
static FastqVariant	DEFAULT_VARIANT	Default FASTQ sequence format variant, FastqVariant.FASTQ_SANGER.

Constructor Summary

Constructors

Constructor	Description
FastqBuilder()	Create a new FASTQ formatted sequence builder.
FastqBuilder(Fastq fastq)	Create a new FASTQ formatted sequence builder configured from the specified FASTQ formatted sequence.

Method Summary

Modifier and Type	Method	Description
FastqBuilder	appendQuality(String quality)	Return this FASTQ formatted sequence builder configured with the specified quality scores appended to its current quality scores.
FastqBuilder	appendSequence(String sequence)	Return this FASTQ formatted sequence builder configured with the specified sequence appended to its current sequence.
Fastq	build()	Build and return a new FASTQ formatted sequence configured from the properties of this builder.
String	getDescription()	Return the description for this FASTQ formatted sequence builder.
boolean	sequenceAndQualityLengthsMatch()	Return true if the sequence and quality scores for this FASTQ formatted sequence builder are equal in length.
FastqBuilder	withDescription(String description)	Return this FASTQ formatted sequence builder configured with the specified description.
FastqBuilder	withQuality(String quality)	Return this FASTQ formatted sequence builder configured with the specified quality scores.
FastqBuilder	withSequence(String sequence)	Return this FASTQ formatted sequence builder configured with the specified sequence.
FastqBuilder	withVariant(FastqVariant variant)	Return this FASTQ formatted sequence builder configured with the specified FASTQ sequence format variant.

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_VARIANT

public static final FastqVariant DEFAULT_VARIANT

Default FASTQ sequence format variant, FastqVariant.FASTQ_SANGER.

Constructor Detail

FastqBuilder

public FastqBuilder()

Create a new FASTQ formatted sequence builder.

FastqBuilder

public FastqBuilder(Fastq fastq)

Create a new FASTQ formatted sequence builder configured from the specified FASTQ formatted sequence.

Parameters:

fastq - FASTQ formatted sequence, must not be null

Since:

1.9.5

Method Detail

getDescription

public String getDescription()

Return the description for this FASTQ formatted sequence builder.

Returns:

the description for this FASTQ formatted sequence builder

withDescription

public FastqBuilder withDescription(String description)

Return this FASTQ formatted sequence builder configured with the specified description.

Parameters:

description - description for this FASTQ formatted sequence builder, must not be null

Returns:

this FASTQ formatted sequence builder configured with the specified description

withSequence

public FastqBuilder withSequence(String sequence)

Return this FASTQ formatted sequence builder configured with the specified sequence.

Parameters:

sequence - sequence for this FASTQ formatted sequence builder, must not be null

Returns:

this FASTQ formatted sequence builder configured with the specified sequence

appendSequence

public FastqBuilder appendSequence(String sequence)

Return this FASTQ formatted sequence builder configured with the specified sequence appended to its current sequence.

Parameters:

sequence - sequence to append to the sequence for this FASTQ formatted sequence builder, must not be null

Returns:

this FASTQ formatted sequence builder configured with the specified sequence appended to its current sequence

withQuality

public FastqBuilder withQuality(String quality)

Return this FASTQ formatted sequence builder configured with the specified quality scores.

Parameters:

quality - quality scores for this FASTQ formatted sequence builder, must not be null

Returns:

this FASTQ formatted sequence builder configured with the specified quality scores

appendQuality

public FastqBuilder appendQuality(String quality)

Return this FASTQ formatted sequence builder configured with the specified quality scores appended to its current quality scores.

Parameters:

quality - quality scores to append to the quality scores for this FASTQ formatted sequence builder, must not be null

Returns:

this FASTQ formatted sequence builder configured with the specified quality scores appended to its current quality scores

sequenceAndQualityLengthsMatch

public boolean sequenceAndQualityLengthsMatch()

Return true if the sequence and quality scores for this FASTQ formatted sequence builder are equal in length.

Returns:

true if the sequence and quality scores for this FASTQ formatted sequence builder are equal in length

withVariant

public FastqBuilder withVariant(FastqVariant variant)

Return this FASTQ formatted sequence builder configured with the specified FASTQ sequence format variant.

Parameters:

variant - FASTQ sequence format variant for this FASTQ formatted sequence builder, must not be null

Returns:

this FASTQ formatted sequence builder configured with the specified FASTQ sequence format variant

build

public Fastq build()

Build and return a new FASTQ formatted sequence configured from the properties of this builder.

Returns:

a new FASTQ formatted sequence configured from the properties of this builder

Throws:

IllegalStateException - if the configuration of this builder results in an illegal state