DeBruijnGraph

Value Members

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

   Definition Classes

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

   Definition Classes

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3. final def ##(): Int

   Definition Classes

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4. final def ==(arg0: AnyRef): Boolean

   Definition Classes

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5. final def ==(arg0: Any): Boolean

   Definition Classes

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6. final def asInstanceOf[T0]: T0

   Definition Classes

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7. def children(node: Kmer): List[Kmer]

   Find all children of a given node

   Find all children of a given node

   node

   Kmer to find parents of

   returns

   List of Kmers where their prefix matches this node's suffix

8. def clone(): AnyRef

   Attributes

   protected[java.lang]

   Definition Classes

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   Annotations

   @throws( ... )

9. def depthFirstSearch(source: Kmer, sink: Kmer, minPathLength: Int = 1, maxPathLength: Int = Int.MaxValue, maxPaths: Int = 10, avoidLoops: Boolean = true, debugPrint: Boolean = false): List[Path]

   Find a path from source to sink in the graph

   Find a path from source to sink in the graph

   source

   Kmer node to begin search

   sink

   Kmer to search for

   minPathLength

   Minimum number of kmers to traverse before finding the sink

   maxPathLength

   Maximum number of kmers to traverse before finding the sink

   maxPaths

   Maximum number of paths to find from source to sink

   avoidLoops

   If avoiding loops, skip nodes that have already been visited

   returns

   Set

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

    Definition Classes

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11. def equals(arg0: Any): Boolean

    Definition Classes

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12. def finalize(): Unit

    Attributes

    protected[java.lang]

    Definition Classes

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    Annotations

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

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

    Definition Classes

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14. def hashCode(): Int

    Definition Classes

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15. final def isInstanceOf[T0]: Boolean

    Definition Classes

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16. val kmerCounts: Map[Seq[Byte], Int]

17. val kmerSize: Int

18. val mergeIndex: Map[Kmer, (Sequence, Int)]

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

    Definition Classes

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20. final def notify(): Unit

    Definition Classes

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21. final def notifyAll(): Unit

    Definition Classes

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22. def parents(node: Kmer): List[Kmer]

    Find all parents of a given node

    Find all parents of a given node

    node

    Kmer to find parents of

    returns

    List of Kmers where their suffix matches this nodes prefix

23. val prefixTable: Map[SubKmer, List[Kmer]]

24. def sinks: Iterable[Kmer]

    Find all nodes that have out-degree = 0

25. def sources: Iterable[Kmer]

    Find all nodes that have in-degree = 0

26. val suffixTable: Map[SubKmer, List[Kmer]]

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

    Definition Classes

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28. def toString(): String

    Definition Classes

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29. final def wait(): Unit

    Definition Classes

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    Annotations

    @throws( ... )

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

    Definition Classes

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    Annotations

    @throws( ... )

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

    Definition Classes

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    Annotations

    @throws( ... )