Package org.biojava.nbio.genome.io.fastq

Enum FastqVariant

    • 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​(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:
        IllegalArgumentException - if this enum type has no constant with the specified name
        NullPointerException - if the argument is null

      • getDescription

        public 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

      • 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 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​(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