Class

bio.RNA

IUPACSequence

Related Doc: package RNA

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class IUPACSequence extends bio.Sequence[NTSymbol]

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Inherited
  1. IUPACSequence
  2. Sequence
  3. AttributeAccess
  4. AbstractSequence
  5. AnyRef
  6. Any
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Instance Constructors

  1. new IUPACSequence(sequence: Sequence)

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  2. new IUPACSequence(id: String, descr: String, str: String)

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  3. new IUPACSequence(id: String, str: String)

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  4. new IUPACSequence(str: String)

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  5. new IUPACSequence(list: List[NTSymbol])

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  6. new IUPACSequence(seqlist: List[NTSymbol], attributelist: List[Attribute])

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Type Members

  1. type SequenceType = IUPACSequence

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    Definition Classes
    IUPACSequenceSequence

Value Members

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

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    Definition Classes
    AnyRef → Any
  2. final def ##(): Int

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    Definition Classes
    AnyRef → Any
  3. final def ==(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any
  4. def apply(n: Int): NTSymbol

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    returns

    the n-th element of this Sequence. The first element is at position 0.

    Definition Classes
    Sequence
  5. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any
  6. def attrAdd(attributelist: List[Attribute]): SequenceType

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    Add a list of attributes to Sequence and return a new Sequence object

    Add a list of attributes to Sequence and return a new Sequence object

    Definition Classes
    Sequence
  7. def attrAdd(attribute: Attribute): SequenceType

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    Add an attribute to Sequence and return a new Sequence object

    Add an attribute to Sequence and return a new Sequence object

    Definition Classes
    Sequence
  8. def attribFirst(message: Message, attributes: List[Attribute]): Option[Any]

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    returns

    the first attribute value matching message

    Definition Classes
    AttributeAccess
  9. def attribList(message: Message, attributes: List[Attribute]): List[Attribute]

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    returns

    list of attributes matching message

    Definition Classes
    AttributeAccess
  10. def attribValues(message: Message, attributes: List[Attribute]): List[Any]

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    returns

    the values of messages as a list

    Definition Classes
    AttributeAccess
  11. lazy val attributes: List[Attribute]

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    Definition Classes
    Sequence
  12. def clone(): AnyRef

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  13. def create(seqlist: List[NTSymbol], attributelist: List[Attribute]): IUPACSequence

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    Every derived class should have a factory, so methods like 'delete', defined in the abstract class, work in a type safe way.

    Every derived class should have a factory, so methods like 'delete', defined in the abstract class, work in a type safe way.

    Definition Classes
    IUPACSequenceSequence
  14. def delete(pos: Int, num: Int): SequenceType

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    Delete part of the sequence

    Delete part of the sequence

    Definition Classes
    Sequence
  15. def description: String

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    returns

    first (primary) Description in attribute list

    Definition Classes
    SequenceAbstractSequence
  16. def descriptionList: List[Attribute]

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    Definition Classes
    Sequence
  17. final def eq(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef
  18. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any
  19. def finalize(): Unit

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  20. final def getClass(): Class[_]

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    Definition Classes
    AnyRef → Any
  21. def hasDescription: Boolean

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    Definition Classes
    SequenceAbstractSequence
  22. def hashCode(): Int

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    Definition Classes
    AnyRef → Any
  23. def id: String

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    Definition Classes
    SequenceAbstractSequence
  24. def idList: List[Attribute]

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    Definition Classes
    Sequence
  25. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any
  26. def length: Integer

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    Definition Classes
    SequenceAbstractSequence
  27. final def ne(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef
  28. final def notify(): Unit

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    Definition Classes
    AnyRef
  29. final def notifyAll(): Unit

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    Definition Classes
    AnyRef
  30. lazy val seq: List[NTSymbol]

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    Definition Classes
    Sequence
  31. final def synchronized[T0](arg0: ⇒ T0): T0

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    Definition Classes
    AnyRef
  32. def toList: List[NTSymbol]

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    returns

    Nucleotide List

    Definition Classes
    SequenceAbstractSequence
  33. def toString(): String

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    returns

    Nucleotide List as a String

    Definition Classes
    Sequence → AnyRef → Any
  34. def transcribe: IUPACSequence

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    returns

    transcribed DNA.Sequence as RNA.Sequence

  35. def translate(): List[AASymbol]

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  36. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  37. final def wait(arg0: Long, arg1: Int): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  38. final def wait(arg0: Long): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from bio.Sequence[NTSymbol]

Inherited from AttributeAccess

Inherited from AbstractSequence

Inherited from AnyRef

Inherited from Any

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