ADAM_2.12: Core 1.0.1 API < Back
 

# Packages

-  package root
  Definition Classes
    root
-  package org
  Definition Classes
    root
-  package bdgenomics
  Definition Classes
    org
-  package adam
  Definition Classes
    bdgenomics
-  package models
  Definition Classes
    adam
- Alphabet
- Attribute
- Coverage
- DNAAlphabet
- IUPACAlphabet
- MdTag
- MdTagEvent
- OptionalPositionOrdering
- OptionalReferenceOrdering
- OptionalRegionOrdering
- PositionOrdering
- ReadGroup
- ReadGroupDictionary
- ReferenceOrdering
- ReferencePosition
- ReferencePositionSerializer
- ReferenceRegion
- ReferenceRegionSerializer
- RegionOrdering
- SequenceDictionary
- SequenceRecord
- SnpTable
- Symbol
- TagType
- VariantContext
- VariantContextSerializer

t

org.bdgenomics.adam.models

# Alphabet 

###
Companion object Alphabet

#### trait Alphabet extends AnyRef

An alphabet of symbols and related operations

Linear Supertypes
AnyRef, Any
Known Subclasses
DNAAlphabet, IUPACAlphabet
 
Ordering

1. Alphabetic
2. By Inheritance

Inherited

1. Alphabet
2. AnyRef
3. Any

1. Hide All
2. Show All

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: Any): Boolean
   Definition Classes
     AnyRef → Any
2.  final def ##(): Int
   Definition Classes
     AnyRef → Any
3.  final def ==(arg0: Any): Boolean
   Definition Classes
     AnyRef → Any
4.  def apply(c: Char): Symbol

   c

     char to lookup as a symbol in this alphabet

   returns

     the given symbol

5.  final def asInstanceOf[T0]: T0
   Definition Classes
     Any
6.  def clone(): AnyRef
   Attributes
     protected[lang]
   Definition Classes
     AnyRef
   Annotations
     @throws( ... ) @native() @HotSpotIntrinsicCandidate()
7.  final def eq(arg0: AnyRef): Boolean
   Definition Classes
     AnyRef
8.  def equals(arg0: Any): Boolean
   Definition Classes
     AnyRef → Any
9.  final def getClass(): Class[_]
   Definition Classes
     AnyRef → Any
   Annotations
     @native() @HotSpotIntrinsicCandidate()
10.  def hashCode(): Int
    Definition Classes
      AnyRef → Any
    Annotations
      @native() @HotSpotIntrinsicCandidate()
11.  final def isInstanceOf[T0]: Boolean
    Definition Classes
      Any
12.  final def ne(arg0: AnyRef): Boolean
    Definition Classes
      AnyRef
13.  final def notify(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native() @HotSpotIntrinsicCandidate()
14.  final def notifyAll(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native() @HotSpotIntrinsicCandidate()
15.  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

16.  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

17.  def size: Int

    The number of symbols in the alphabet.

18.  lazy val symbolMap: Map[Char, Symbol]

    map of the symbol char to the symbol

19.  final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
      AnyRef
20.  def toString(): String
    Definition Classes
      AnyRef → Any
21.  final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )
22.  final def wait(arg0: Long): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... ) @native()
23.  final def wait(): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

### Deprecated Value Members

1.  def finalize(): Unit
   Attributes
     protected[lang]
   Definition Classes
     AnyRef
   Annotations
     @throws( classOf[java.lang.Throwable] ) @Deprecated
   Deprecated

### Inherited from AnyRef

### Inherited from Any

### Ungrouped