GappedCodonSequence

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(n: Int): CodonSymbol

   
   returns

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

   Definition Classes

   Sequence

5. final def asInstanceOf[T0]: T0

   

   Definition Classes

   Any

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

   

   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

   

   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]

   
   returns

   the first attribute value matching message

   Definition Classes

   AttributeAccess

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

   
   returns

   list of attributes matching message

   Definition Classes

   AttributeAccess

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

    
    returns

    the values of messages as a list

    Definition Classes

    AttributeAccess

11. lazy val attributes: List[Attribute]

    

    Definition Classes

    Sequence

12. def clone(): AnyRef

    

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

13. def create(seqlist: List[CodonSymbol], attributelist: List[Attribute]): GappedCodonSequence

    

    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

    GappedCodonSequence → Sequence

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

    

    Delete part of the sequence

    Delete part of the sequence

    Definition Classes

    Sequence

15. def description: String

    
    returns

    first (primary) Description in attribute list

    Definition Classes

    Sequence → AbstractSequence

16. def descriptionList: List[Attribute]

    

    Definition Classes

    Sequence

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

    

    Definition Classes

    AnyRef

18. def equals(arg0: Any): Boolean

    

    Definition Classes

    AnyRef → Any

19. def finalize(): Unit

    

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

    @throws( classOf[java.lang.Throwable] )

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

    

    Definition Classes

    AnyRef → Any

21. def getCodon(n: Int): List[NTSymbol]

    

22. def hasDescription: Boolean

    

    Definition Classes

    Sequence → AbstractSequence

23. def hashCode(): Int

    

    Definition Classes

    AnyRef → Any

24. def id: String

    

    Definition Classes

    Sequence → AbstractSequence

25. def idList: List[Attribute]

    

    Definition Classes

    Sequence

26. final def isInstanceOf[T0]: Boolean

    

    Definition Classes

    Any

27. def length: Integer

    

    Definition Classes

    Sequence → AbstractSequence

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

    

    Definition Classes

    AnyRef

29. final def notify(): Unit

    

    Definition Classes

    AnyRef

30. final def notifyAll(): Unit

    

    Definition Classes

    AnyRef

31. lazy val seq: List[CodonSymbol]

    

    Definition Classes

    Sequence

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

    

    Definition Classes

    AnyRef

33. def toAminoAcid: List[AASymbol]

    

34. def toDNA: List[NTSymbol]

    

35. def toList: List[CodonSymbol]

    
    returns

    Nucleotide List

    Definition Classes

    Sequence → AbstractSequence

36. def toRNA: List[NTSymbol]

    

37. def toString(): String

    
    returns

    Nucleotide List as a String

    Definition Classes

    GappedCodonSequence → Sequence → AnyRef → Any

38. final def wait(): Unit

    

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )