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.  final def asInstanceOf[T0]: T0

   Definition Classes

   Any

5.  def clone(): AnyRef

   Attributes

   protected[lang]

   Definition Classes

   AnyRef

   Annotations

   @throws( ... ) @native()

6.  final def eq(arg0: AnyRef): Boolean

   Definition Classes

   AnyRef

7.  def finalize(): Unit

   Attributes

   protected[lang]

   Definition Classes

   AnyRef

   Annotations

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

8.  val forwardOnly: Boolean

   Whether to include only canonical (forward oriented) k-mers when reducing

   Whether to include only canonical (forward oriented) k-mers when reducing

   Definition Classes

   MaxReducer → Reducer

9.  final def getClass(): Class[_]

   Definition Classes

   AnyRef → Any

   Annotations

   @native()

10.  def hasNonZeroTag(tags: Array[Tag]): Boolean

    Definition Classes

    Reducer

11.  val intersect: Boolean

    Definition Classes

    MaxReducer → CountReducer

12.  final def isInstanceOf[T0]: Boolean

    Definition Classes

    Any

13.  val k: Int

    Definition Classes

    MaxReducer → Reducer

14.  final def ne(arg0: AnyRef): Boolean

    Definition Classes

    AnyRef

15.  final def notify(): Unit

    Definition Classes

    AnyRef

    Annotations

    @native()

16.  final def notifyAll(): Unit

    Definition Classes

    AnyRef

    Annotations

    @native()

17.  def preprocessFirst(bucket: ReducibleBucket): ReducibleBucket

    Preprocess bucket A prior to op(A,B)

    Preprocess bucket A prior to op(A,B)

    Definition Classes

    Reducer

18.  def preprocessSecond(bucket: ReducibleBucket): ReducibleBucket

    Preprocess bucket B prior to op(A,B)

    Preprocess bucket B prior to op(A,B)

    Definition Classes

    Reducer

19.  def reduceCounts(count1: Tag, count2: Tag): Tag

    Definition Classes

    MaxReducer → CountReducer

20.  def reduceEqualKmers(table: KmerTable, into: Int, from: Int): Unit

    Apply a binary operation op(into, from) on the tags of the k-mers at these positions, writing the result in the tags of "into", writing the zero value into the tags of "from".

    Apply a binary operation op(into, from) on the tags of the k-mers at these positions, writing the result in the tags of "into", writing the zero value into the tags of "from". This method will only be called on equal k-mers.

    table

    The table containing k-mers

    into

    Target k-mer index in the table (k-mer A in op(A,B))

    from

    Source k-mer index in the table (k-mer B in op(A,B))

    Definition Classes

    CountReducer → Reducer

21.  def shouldKeep(table: KmerTable, kmer: Int): Boolean

    Whether to keep the k-mer (together with tag data) after reduction.

    Whether to keep the k-mer (together with tag data) after reduction.

    table

    The table containing k-mers

    kmer

    Index of k-mer to be tested

    Definition Classes

    CountReducer → Reducer

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

    Definition Classes

    AnyRef

23.  val tagOffset: Int

    Definition Classes

    CountReducer → Reducer

24.  final def wait(): Unit

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

26.  final def wait(arg0: Long): Unit

    Definition Classes

    AnyRef

    Annotations

    @throws( ... ) @native()

27.  val zeroValue: Tag

    A special value that is used to indicate non-existent/redundant k-mers.

    A special value that is used to indicate non-existent/redundant k-mers. Should also have the property that op(A, zero) == op(zero, A) for all A

    Definition Classes

    Reducer