object Sequences

Utility methods for working with DNA or RNA sequences

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  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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  7. def countMismatches(s1: String, s2: String): Int

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

  8. final def eq(arg0: AnyRef): Boolean
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  9. def equals(arg0: Any): Boolean
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  10. def finalize(): Unit
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  11. final def getClass(): Class[_]
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  12. def hashCode(): Int
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  13. final def isInstanceOf[T0]: Boolean
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  14. def longestHomopolymer(s: String): (Int, Int)

    Returns the 0-based index of, and the length of, the longest homopolymer in a non-empty string.

    Returns the 0-based index of, and the length of, the longest homopolymer in a non-empty string. If there are multiple homopolymers of the same length the _first_ one is returned.

    s

    a sequence

    returns

    a tuple of (0-based index, length) of the longest homopolymer in the string

  15. final def ne(arg0: AnyRef): Boolean
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  16. final def notify(): Unit
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  17. final def notifyAll(): Unit
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  18. final def synchronized[T0](arg0: ⇒ T0): T0
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  19. def toString(): String
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  20. final def wait(): Unit
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  21. final def wait(arg0: Long, arg1: Int): Unit
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  22. final def wait(arg0: Long): Unit
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