org.bdgenomics.adam.models

Alphabet

trait Alphabet extends AnyRef

An alphabet of symbols and related operations

Linear Supertypes
AnyRef, Any
Known Subclasses
DNAAlphabet
Ordering
  1. Alphabetic
  2. By inheritance
Inherited
  1. Alphabet
  2. AnyRef
  3. Any
  1. Hide All
  2. Show all
Learn more about member selection
Visibility
  1. Public
  2. All

Abstract Value Members

  1. abstract val caseSensitive: Boolean

    flag if symbols are case-sensitive.

    flag if symbols are case-sensitive. if true, this alphabet will treat symbols representing upper and lower case symbols as distinct if false, this alphabet will treat upper or lower case chars as the same for its symbols

  2. abstract val symbols: Seq[Symbol]

    the symbols in this alphabet

Concrete Value Members

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

    Definition Classes
    AnyRef

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

    Definition Classes
    Any

  3. final def ##(): Int

    Definition Classes
    AnyRef → Any

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

    Definition Classes
    AnyRef

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

    Definition Classes
    Any

  6. def apply(c: Char): Symbol

    c

    char to lookup as a symbol in this alphabet

    returns

    the given symbol

  7. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  8. def clone(): AnyRef

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef

  10. def equals(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any

  11. def finalize(): Unit

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )

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

    Definition Classes
    AnyRef → Any

  13. def hashCode(): Int

    Definition Classes
    AnyRef → Any

  14. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

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

    Definition Classes
    AnyRef

  16. final def notify(): Unit

    Definition Classes
    AnyRef

  17. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  18. def reverseComplement(s: String, notFound: (Char) ⇒ Symbol = (c: Char) => Symbol(c, c)): String

    Reverses the string and compliments each residue.

    Reverses the string and compliments each residue.

    If a residue has no known complement, that residue is replaced with a placeholder "not-found" value.

    s

    Each char in this string represents a symbol on the alphabet.

    notFound

    If the char is not in the alphabet then this function is called. default behavior is to return a new Symbol representing the unknown character, so that the unknown char is treated as the complement

    returns

    the reversed complement of the given string.

    See also

    reverseComplementExact

  19. def reverseComplementExact(s: String): String

    Reverses the string and compliments each residue.

    Reverses the string and compliments each residue.

    Fails if a residue has no complement.

    s

    Each char in this string represents a symbol on the alphabet. If the char is not in the alphabet then a NoSuchElementException is thrown

    returns

    the reversed complement of the given string.

    Exceptions thrown
    IllegalArgumentException

    if the string contains a symbol which is not in the alphabet

    See also

    reverseComplement

  20. def size: Int

    The number of symbols in the alphabet.

  21. lazy val symbolMap: Map[Char, Symbol]

    map of the symbol char to the symbol

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

    Definition Classes
    AnyRef

  23. def toString(): String

    Definition Classes
    AnyRef → Any

  24. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from AnyRef

Inherited from Any

Ungrouped