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

Enum Class FastqVariant

java.lang.Object
java.lang.Enum<FastqVariant>
org.biojava.nbio.sequencing.io.fastq.FastqVariant
All Implemented Interfaces:
Serializable, Comparable<FastqVariant>, Constable
public enum FastqVariant extends Enum<FastqVariant>
FASTQ sequence format variant.
Since:
3.0.3

  • Enum Constant Details

    • 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 Details

    • values

      public static FastqVariant[] values()
      Returns an array containing the constants of this enum class, in the order they are declared.
      Returns:
      an array containing the constants of this enum class, in the order they are declared

    • valueOf

      public static FastqVariant valueOf(String name)
      Returns the enum constant of this class with the specified name. The string must match exactly an identifier used to declare an enum constant in this class. (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 class 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

    • 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 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