Class Fastq


  • public final class Fastq
    extends java.lang.Object
    FASTQ formatted sequence.
    Since:
    1.7.1
    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      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.
      java.lang.String getDescription()
      Return the description of this FASTQ formatted sequence.
      java.lang.String getQuality()
      Return the quality scores for this FASTQ formatted sequence.
      java.lang.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 java.lang.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 java.lang.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 java.lang.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:
        1.9.3
      • 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 specifed FASTQ formatted sequence
        Since:
        1.9.5