org.hammerlab.guacamole.util

Bases

object Bases

We represent a nucleotide base as a Byte, whose value is equal to the ASCII value of the character representing the base (for example: A, C, T, G). We represent a nucleotide sequence as a Seq[Byte].

This is an optimization over java Chars and Strings which use two bytes per character.

Note

If b is a base (say "A") then b.toString does NOT give you want (in this case it would give you "65"). Use the baseToString() function defined here.

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  1. final def !=(arg0: AnyRef): Boolean

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  2. final def !=(arg0: Any): Boolean

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  3. final def ##(): Int

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  4. final def ==(arg0: AnyRef): Boolean

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  5. final def ==(arg0: Any): Boolean

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  6. val A: Byte

    Standard bases.

    Standard bases. Note that other bases are sometimes used as well (e.g. "N").

  7. val ALT: Seq[Byte]

  8. object BasesOrdering extends Ordering[Seq[Byte]]

  9. val C: Byte

  10. val G: Byte

  11. val N: Byte

  12. val T: Byte

  13. def allStandardBases(bases: Seq[Byte]): Boolean

    Are all the given bases standard?

  14. final def asInstanceOf[T0]: T0

    Definition Classes
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  15. def assertAllStandardBases(bases: Seq[Byte]): Unit

    Throw an error if any of the given bases are not standard.

  16. def assertStandardBase(base: Byte): Unit

    Throw an error if the given base is not one of the canonical DNA bases.

  17. def baseToString(base: Byte): String

    Convert a base to a 1-character string.

  18. def basesToString(bases: Iterable[Byte]): String

    Convert a base sequence to a String.

  19. def clone(): AnyRef

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    @throws( ... )

  20. def complement(bases: Seq[Byte]): Seq[Byte]

    Watson-Crick complement of a sequence of bases.

  21. def complement(base: Byte): Byte

    Watson-Crick complement of a base.

  22. final def eq(arg0: AnyRef): Boolean

    Definition Classes
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  23. def equals(arg0: Any): Boolean

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  24. def finalize(): Unit

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  25. final def getClass(): Class[_]

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  26. def hashCode(): Int

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  27. final def isInstanceOf[T0]: Boolean

    Definition Classes
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  28. def isStandardBase(base: Byte): Boolean

    Is the given base one of the 4 canonical DNA bases?

  29. final def ne(arg0: AnyRef): Boolean

    Definition Classes
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  30. final def notify(): Unit

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  31. final def notifyAll(): Unit

    Definition Classes
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  32. def reverseComplement(bases: Seq[Byte]): Seq[Byte]

    Watson-Crick complement of a sequence of bases, with the sequence reversed.

  33. def stringToBases(string: String): IndexedSeq[Byte]

    Convert a string (e.

    Convert a string (e.g. "AAAGGC") to a byte array.

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

    Definition Classes
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  35. def toString(): String

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  36. def unmaskBases(bases: Array[Byte]): Unit

    Convert a mixed sequence of bases (lower and upper-case) to upper case Lower-case bases typically represent masked bases

    Convert a mixed sequence of bases (lower and upper-case) to upper case Lower-case bases typically represent masked bases

    Works in place.

    bases

    Byte array of bases

    returns

    Unmasked (upper-case) byte array of bases

  37. final def wait(): Unit

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

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  39. final def wait(arg0: Long): Unit

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