Value Members

1.  final def !=(arg0: Any): Boolean

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2.  final def ##(): Int

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3.  final def ==(arg0: Any): Boolean

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4.  val CommonNonAutosomalContigNames: Seq[String]

   Common contig/chrom names for non-autosomal sequences in mammals.

5.  final def asInstanceOf[T0]: T0

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6.  def clone(): AnyRef

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   protected[java.lang]

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   @native() @throws( ... )

7.  final def compatible(base1: Byte, base2: Byte): Boolean

   Returns true if two bases are compatible.

   Returns true if two bases are compatible. Compatibility is defined as having any overlap in the set of acceptable bases. E.g.:

   • compatible('T', 't') == true
   • compatible('T', 'U') == true
   • compatible('A', 'R') == true
   • compatible('M', 'S') == true
   • compatible('A', 'C') == false
   • compatible('M', 'K') == false

   base1

   the first base to be compared

   base2

   the second base to be compared

   returns

   true if the bases share at least one concrete base in common, false otherwise

8.  final def complement(b: Byte): Byte

   Complements a single base.

   Complements a single base. U and u are always complemented to A and a respectively. IUPAC ambiguity codes are handled appropriately - they are complemented to the IUPAC code that represents the set of bases that can pair with the input IUPAC code.

   Any byte that is not a valid upper- or lower-case DNA base, RNA base or IUPAC code will cause an exception to be thrown.

   b

   the base to be complemented

   returns

   the complement of that base

   Annotations

   @inline()

9.  def complement(bs: Array[Byte]): Unit

   Complements the bases in the array in place.

   Complements the bases in the array in place. See complement() for how complementing is performed.

   bs

   an array of bases as bytes to be complemented in place

10.  def complement(s: String): String

    Returns the sequence that is the complement of the provided sequence.

11.  def countMismatches(s1: String, s2: String): Int

    Counts the number of mismatches between two sequences of the same length.

12.  final def eq(arg0: AnyRef): Boolean

    Definition Classes

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13.  def equals(arg0: Any): Boolean

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14.  def finalize(): Unit

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    protected[java.lang]

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    @throws( classOf[java.lang.Throwable] )

15.  def gcContent(s: String): Double

    Calculates GC content for a DNA sequence as a fraction (between 0 and 1).

    Calculates GC content for a DNA sequence as a fraction (between 0 and 1).

    s

    a DNA sequence

    returns

    the fraction GC content for the given sequence, zero if the sequence is empty

16.  final def getClass(): Class[_]

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    @native()

17.  def hashCode(): Int

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    @native()

18.  def homopolymers(s: String, minLength: Int): Int

    Returns the number of homopolymers of a given minimum length within the sequence.

    Returns the number of homopolymers of a given minimum length within the sequence.

    s

    a DNA or RNA sequence

    minLength

    the minimum length of homopolymer to count (must be greater than 0)

    returns

    the number of homopolymers of length >= minLength in the sequence

19.  final def isInstanceOf[T0]: Boolean

    Definition Classes

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20.  def iupacCode(bases: Iterable[Byte]): Byte

    Returns the IUPAC code for the set of bases given.

21.  def longestDinuc(s: String): OffsetAndLength

    Returns the offset (0-based) and length of the longest dinucleotide run in the sequence.

    Returns the offset (0-based) and length of the longest dinucleotide run in the sequence. In the case that there are multiple dinucleotide runs of the same length, the earliest one is returned.

    s

    a DNA or RNA sequence

    returns

    the offset and length of the longest dinucleotide sequence

22.  def longestHomopolymer(s: String): OffsetAndLength

    Returns the offset (0-based) and length of the longest homopolymer in the sequence.

    Returns the offset (0-based) and length of the longest homopolymer in the sequence. In the case that there are multiple homopolymers of the same length, the earliest one is returned.

    s

    a DNA or RNA sequence

    returns

    the offset and length of the longest homopolymer

23.  final def ne(arg0: AnyRef): Boolean

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24.  final def notify(): Unit

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    @native()

25.  final def notifyAll(): Unit

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    @native()

26.  def revcomp(bs: Array[Byte]): Unit

    Reverse complements an array of bases in place.

    Reverse complements an array of bases in place. See complement() for how bases are complemented.

27.  def revcomp(s: String): String

    Reverse complements a string of bases.

28.  final def synchronized[T0](arg0: ⇒ T0): T0

    Definition Classes

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29.  def toString(): String

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30.  final def wait(): Unit

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    @throws( ... )

31.  final def wait(arg0: Long, arg1: Int): Unit

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    @throws( ... )

32.  final def wait(arg0: Long): Unit

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    @native() @throws( ... )