Class FastqBuilder


  • public final class FastqBuilder
    extends Object
    Fluent builder API for creating FASTQ formatted sequences.
    Since:
    3.0.3
    • Field Detail

    • 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:
        6.0.0
    • 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