Package org.biojava.nbio.genome.io.fastq
Class FastqBuilder
- java.lang.Object
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- org.biojava.nbio.genome.io.fastq.FastqBuilder
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public final class FastqBuilder extends Object
Fluent builder API for creating FASTQ formatted sequences.- Since:
- 3.0.3
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Field Summary
Fields Modifier and Type Field Description static FastqVariant
DEFAULT_VARIANT
Default FASTQ sequence format variant,FastqVariant.FASTQ_SANGER
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Constructor Summary
Constructors Constructor Description FastqBuilder()
Create a new FASTQ formatted sequence builder.
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Method Summary
All Methods Instance Methods Concrete Methods 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.
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Field Detail
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DEFAULT_VARIANT
public static final FastqVariant DEFAULT_VARIANT
Default FASTQ sequence format variant,FastqVariant.FASTQ_SANGER
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Constructor Detail
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FastqBuilder
public FastqBuilder()
Create a new FASTQ formatted sequence builder.
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Method Detail
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getDescription
public String getDescription()
Return the description for this FASTQ formatted sequence builder.- Returns:
- the description for this FASTQ formatted sequence builder
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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
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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
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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
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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
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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
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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
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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
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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
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