class DNAAlphabet extends Alphabet
The standard DNA alphabet with A,T,C, and G
- Alphabetic
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- DNAAlphabet
- Alphabet
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- new DNAAlphabet()
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final
def
!=(arg0: Any): Boolean
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final
def
##(): Int
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final
def
==(arg0: Any): Boolean
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def
apply(c: Char): Symbol
- c
char to lookup as a symbol in this alphabet
- returns
the given symbol
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- Alphabet
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final
def
asInstanceOf[T0]: T0
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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
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- DNAAlphabet → Alphabet
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def
clone(): AnyRef
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final
def
eq(arg0: AnyRef): Boolean
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def
equals(arg0: Any): Boolean
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def
finalize(): Unit
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final
def
getClass(): Class[_]
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def
hashCode(): Int
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final
def
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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.
- Definition Classes
- Alphabet
- See also
reverseComplementExact
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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.
- Definition Classes
- Alphabet
- Exceptions thrown
IllegalArgumentException
if the string contains a symbol which is not in the alphabet- See also
reverseComplement
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def
size: Int
The number of symbols in the alphabet.
The number of symbols in the alphabet.
- Definition Classes
- Alphabet
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lazy val
symbolMap: Map[Char, Symbol]
map of the symbol char to the symbol
map of the symbol char to the symbol
- Definition Classes
- Alphabet
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val
symbols: Seq[Symbol]
the symbols in this alphabet
the symbols in this alphabet
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- DNAAlphabet → Alphabet
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final
def
synchronized[T0](arg0: ⇒ T0): T0
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def
toString(): String
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def
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