Package org.biojava.nbio.sequencing.io.fastq

Class FastqBuilder

java.lang.Object
org.biojava.nbio.sequencing.io.fastq.FastqBuilder
public final class FastqBuilder extends Object
Fluent builder API for creating FASTQ formatted sequences.
Since:
3.0.3

  • Field Details

    • DEFAULT_VARIANT

      public static final FastqVariant DEFAULT_VARIANT
      Default FASTQ sequence format variant, FastqVariant.FASTQ_SANGER.

  • Constructor Details

    • FastqBuilder

      public FastqBuilder()
      Create a new FASTQ formatted sequence builder.

  • Method Details

    • 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