Root

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 add[Alphabet](child: NonRootNode, start: (NonRootNode) ⇒ Either[Alphabet, TerminalSymbol]): Unit

   

   Definition Classes

   Root → Node

5. def addLeaf[Alphabet](seqID: SequenceID, start: (NonRootNode) ⇒ Either[Alphabet, TerminalSymbol]): LeafNode

   

   Adds a leaf to the root given a leaf ID and the sequence ID to which the leaf is referring.

   Adds a leaf to the root given a leaf ID and the sequence ID to which the leaf is referring.

   This leaf is given number 1.

6. final def asInstanceOf[T0]: T0

   

   Definition Classes

   Any

7. def childStartingWith[Alphabet](item: Either[Alphabet, TerminalSymbol]): Option[NonRootNode]

   

   Computes the child node of this node which edge-label starts with the given item

   Computes the child node of this node which edge-label starts with the given item

   Definition Classes

   Node

8. def children: List[NonRootNode]

   

   Definition Classes

   Node

9. val childrenMap: Nodes

   

   Definition Classes

   Root → Node

10. def clone(): AnyRef

    

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

11. var dfs: Int

    

    Depth-first number

    Depth-first number

    Definition Classes

    Node

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

    

    Definition Classes

    AnyRef

13. def equals(other: Any): Boolean

    

    Definition Classes

    Root → AnyRef → Any

14. def finalize(): Unit

    

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

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

15. def findPathEndContaining[Alphabet](s: Walkable[Either[Alphabet, TerminalSymbol]], startIndex: Int, endIndex: Int)(start: (NonRootNode) ⇒ Either[Alphabet, TerminalSymbol], getEdgeLabelItem: (NonRootNode, Int) ⇒ Either[Alphabet, TerminalSymbol], labelLength: (NonRootNode) ⇒ Int): Option[(NonRootNode, Int)]

    

    Finds the path end following a sequence (given as a global sequence, the starting and end indexes of the subsequence to search) from the root node if it exists

    Finds the path end following a sequence (given as a global sequence, the starting and end indexes of the subsequence to search) from the root node if it exists

    s

    the global sequence that contains the searched subsequence

    startIndex

    the start index in the global sequence of the first character of the searched subsequence

    endIndex

    the end index in the global sequence of the last character of the searched subsequence

    start

    a function that given a NonRootNode retrieves efficiently the first item of the edge-label conducting to the given node in the tree

    getEdgeLabelItem

    a function that retrieves efficiently the ith item in the edge label to the given node

    labelLength

    a function that given a NonRootNode computes the length of the edge-label conducting to this node in the tree

    returns

    an optional pair containing the NonRootNode which path-label includes the searched subsequence along with the number of item that are in the path-label and not in the searched subsequence (i.e., the gap between the end of the search subsequence in the path-label to reach the node)

    Definition Classes

    Node

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

    

    Definition Classes

    AnyRef → Any

17. def hashCode(): Int

    

    Definition Classes

    Root → AnyRef → Any

18. final def isInstanceOf[T0]: Boolean

    

    Definition Classes

    Any

19. def leaves(): List[LeafNode]

    

    Definition Classes

    Node

20. def leavesHelper(currentNode: Node): List[LeafNode]

    

    Attributes

    protected

    Definition Classes

    Node

21. def mkString[Alphabet](label: (NonRootNode) ⇒ String): String

    

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

    

    Definition Classes

    AnyRef

23. final def notify(): Unit

    

    Definition Classes

    AnyRef

24. final def notifyAll(): Unit

    

    Definition Classes

    AnyRef

25. def parents(): List[Nothing]

    

    Definition Classes

    Root → Node

26. def pathLabel: List[NonRootNode]

    

    Computes the path label as a list of NonRootNode

    Computes the path label as a list of NonRootNode

    Beware, labels of these nodes might include special upper limits such as the END constant.

    Definition Classes

    Root → Node

27. def pathSingleLabel(getSequenceLengthBy: (SequenceID) ⇒ Int): List[Nothing]

    

    Computes the path label as a list of definitive labels given a function to get the length of a sequence from its ID

    Computes the path label as a list of definitive labels given a function to get the length of a sequence from its ID

    Definition Classes

    Root → Node

28. def remove[Alphabet](node: NonRootNode, start: (NonRootNode) ⇒ Either[Alphabet, TerminalSymbol]): Unit

    

    Definition Classes

    Root → Node

29. def size(): Int

    

    Definition Classes

    Root → Node

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

    

    Definition Classes

    AnyRef

31. def toString(): String

    

    Definition Classes

    Root → AnyRef → Any

32. final def wait(): Unit

    

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

35. def walkDown[Alphabet](s: Walkable[Either[Alphabet, TerminalSymbol]], startIndex: Int, endIndex: Int, currentEnd: Int)(start: (NonRootNode) ⇒ Either[Alphabet, TerminalSymbol], labelLength: (NonRootNode) ⇒ Int): (NonRootNode, Int)

    

    Walks down from this node following the given sequence

    Walks down from this node following the given sequence

    s

    the searched sequence

    startIndex

    the first index of search in the sequence (inclusive)

    endIndex

    the last index of search in the sequence (inclusive)

    currentEnd

    current index of the end (i in suffix S[j..i] of phase i)

    start

    computes the first item of a label

    returns

    a pair (node, length) containing the node which path label contains sequence s, and the number of items left in the path to arrive to the node (0 means a perfect match)

    Definition Classes

    Node

    Note

    walkDown is overriden by 'NonRootNode'

36. def walkDownUntilUnmatch[Alphabet](s: Walkable[Either[Alphabet, TerminalSymbol]], startIndex: Int, endIndex: Int)(start: (NonRootNode) ⇒ Either[Alphabet, TerminalSymbol], getEdgeLabelItem: (NonRootNode, Int) ⇒ Either[Alphabet, TerminalSymbol], labelLength: (NonRootNode) ⇒ Int): Option[(NonRootNode, Int, Int)]

    

    Walks down the tree following the sequence until a mismatch occurs

    Walks down the tree following the sequence until a mismatch occurs

    It dissociates the following cases:

    1. the sequence is not in the tree, even partially (returns None) 2. the sequence is partially in the tree...
       1. ... and it stops on a non-root node (returns Some(node, int > 0, 0)) b. ... and it stops in a middle of an edge (returns Some(node, int > 0, int > 0)) 3. the sequence is entirely in the tree...
       2. ... and it stops on a non-root node (returns Some(node, 0, 0)) b. ... and it stops in a middle of an edge (returns Some(node, 0, int > 0))

    s

    the searched sequence

    startIndex

    the first index of search in the sequence (inclusive)

    endIndex

    the last index of search in the sequence (inclusive)

    start

    retrieves efficiently the first item in the edge label to the given node

    getEdgeLabelItem

    retrieves efficiently the ith item in the edge label to the given node

    labelLength

    computes efficiently the length of the edge label to the given node

    returns

    None if the sequence is not partially in the tree, else a triple containing 1) the non-root node at or below the unmatch or the end of the sequence happened, 2) the number of character left in the given sequence and 3) the number of character left to reach the non-root node (0 means "perfect match")

    Definition Classes

    Root → Node