Enum FastqVariant

  • All Implemented Interfaces:
    java.io.Serializable, java.lang.Comparable<FastqVariant>

    public enum FastqVariant
    extends java.lang.Enum<FastqVariant>
    FASTQ sequence format variant.
    Since:
    3.0.3
    • Enum Constant Summary

      Enum Constants 
      Enum Constant Description
      FASTQ_ILLUMINA
      Illumina FASTQ sequence format variant.
      FASTQ_SANGER
      Sanger FASTQ sequence format variant.
      FASTQ_SOLEXA
      Solexa FASTQ sequence format variant.
    • Method Summary

      All Methods Static Methods Instance Methods Abstract Methods Concrete Methods 
      Modifier and Type Method Description
      protected int constrain​(double qualityScore)
      Constrain the specified quality score in double precision to the minimum and maximum quality scores in int precision.
      double errorProbability​(char c)
      Convert the specified quality in ASCII format to an error probability.
      abstract double errorProbability​(int qualityScore)
      Calculate the error probability given the specified quality score.
      java.lang.String getDescription()
      Return the description of this FASTQ sequence format variant.
      boolean isIllumina()
      Return true if this FASTQ sequence format variant is FASTQ_ILLUMINA.
      boolean isSanger()
      Return true if this FASTQ sequence format variant is FASTQ_SANGER.
      boolean isSolexa()
      Return true if this FASTQ sequence format variant is FASTQ_SOLEXA.
      java.lang.String lowercaseName()
      Return the name of this FASTQ sequence format variant in lowercase-with-dashes style.
      abstract int maximumQualityScore()
      Return the maximum quality score for this FASTQ sequence format variant.
      abstract int minimumQualityScore()
      Return the minimum quality score for this FASTQ sequence format variant.
      static FastqVariant parseFastqVariant​(java.lang.String name)
      Return the FASTQ sequence format variant with the specified name, if any.
      abstract char quality​(int qualityScore)
      Convert the specified quality score to a quality in ASCII format.
      abstract int qualityScore​(char c)
      Convert the specified quality in ASCII format to a quality score.
      abstract int qualityScore​(double errorProbability)
      Convert the specified error probability to a quality score.
      static FastqVariant valueOf​(java.lang.String name)
      Returns the enum constant of this type with the specified name.
      static FastqVariant[] values()
      Returns an array containing the constants of this enum type, in the order they are declared.
      • Methods inherited from class java.lang.Enum

        clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
      • Methods inherited from class java.lang.Object

        getClass, notify, notifyAll, wait, wait, wait
    • Enum Constant Detail

      • FASTQ_SANGER

        public static final FastqVariant FASTQ_SANGER
        Sanger FASTQ sequence format variant.
      • FASTQ_SOLEXA

        public static final FastqVariant FASTQ_SOLEXA
        Solexa FASTQ sequence format variant.
      • FASTQ_ILLUMINA

        public static final FastqVariant FASTQ_ILLUMINA
        Illumina FASTQ sequence format variant.
    • Method Detail

      • values

        public static FastqVariant[] values()
        Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:
        for (FastqVariant c : FastqVariant.values())
            System.out.println(c);
        
        Returns:
        an array containing the constants of this enum type, in the order they are declared
      • valueOf

        public static FastqVariant valueOf​(java.lang.String name)
        Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)
        Parameters:
        name - the name of the enum constant to be returned.
        Returns:
        the enum constant with the specified name
        Throws:
        java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
        java.lang.NullPointerException - if the argument is null
      • getDescription

        public java.lang.String getDescription()
        Return the description of this FASTQ sequence format variant. The description will not be null.
        Returns:
        the description of this FASTQ sequence format variant
      • isSanger

        public boolean isSanger()
        Return true if this FASTQ sequence format variant is FASTQ_SANGER.
        Returns:
        true if this FASTQ sequence format variant is FASTQ_SANGER
      • isSolexa

        public boolean isSolexa()
        Return true if this FASTQ sequence format variant is FASTQ_SOLEXA.
        Returns:
        true if this FASTQ sequence format variant is FASTQ_SOLEXA
      • isIllumina

        public boolean isIllumina()
        Return true if this FASTQ sequence format variant is FASTQ_ILLUMINA.
        Returns:
        true if this FASTQ sequence format variant is FASTQ_ILLUMINA
      • minimumQualityScore

        public abstract int minimumQualityScore()
        Return the minimum quality score for this FASTQ sequence format variant.
        Returns:
        the minimum quality score for this FASTQ sequence format variant.
      • maximumQualityScore

        public abstract int maximumQualityScore()
        Return the maximum quality score for this FASTQ sequence format variant.
        Returns:
        the maximum quality score for this FASTQ sequence format variant.
      • qualityScore

        public abstract int qualityScore​(char c)
        Convert the specified quality in ASCII format to a quality score.
        Parameters:
        c - quality in ASCII format
        Returns:
        the specified quality in ASCII format converted to a quality score
      • qualityScore

        public abstract int qualityScore​(double errorProbability)
        Convert the specified error probability to a quality score.
        Parameters:
        errorProbability - error probability
        Returns:
        the specified error probability converted to a quality score
        Since:
        4.2
      • quality

        public abstract char quality​(int qualityScore)
        Convert the specified quality score to a quality in ASCII format.
        Parameters:
        qualityScore - quality score, must be >= minimumQualityScore() and <= maximumQualityScore()
        Returns:
        the quality in ASCII format converted from the specified quality score
        Since:
        3.0.6
      • errorProbability

        public double errorProbability​(char c)
        Convert the specified quality in ASCII format to an error probability.
        Parameters:
        c - quality in ASCII format
        Returns:
        the specified quality in ASCII format converted to an error probability
      • errorProbability

        public abstract double errorProbability​(int qualityScore)
        Calculate the error probability given the specified quality score.
        Parameters:
        qualityScore - quality score
        Returns:
        the error probability given the specified quality score
      • lowercaseName

        public java.lang.String lowercaseName()
        Return the name of this FASTQ sequence format variant in lowercase-with-dashes style.
        Returns:
        the name of this FASTQ sequence format variant in lowercase-with-dashes style
      • constrain

        protected int constrain​(double qualityScore)
        Constrain the specified quality score in double precision to the minimum and maximum quality scores in int precision.
        Parameters:
        qualityScore - quality score in double precision
        Returns:
        the specified quality score in double precision constrained to the minimum and maximum quality scores in int precision
        Since:
        4.2
      • parseFastqVariant

        public static FastqVariant parseFastqVariant​(java.lang.String name)
        Return the FASTQ sequence format variant with the specified name, if any. The name may be specified in either UPPERCASE_WITH_UNDERSCORES or lowercase-with-dashes style.
        Parameters:
        name - name
        Returns:
        the FASTQ sequence format variant with the specified name, or null if no such FASTQ sequence format variant exists