Packages

c

com.jnpersson.kmers.util

KmerTableBuilder2

final class KmerTableBuilder2 extends KmerTableBuilder

A KmerTableBuilder where each row is 2 Longs. This subclass optimizes addRow() to avoid a loop.

Linear Supertypes
KmerTableBuilder, AnyRef, Any
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  1. KmerTableBuilder2
  2. KmerTableBuilder
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Visibility
  1. Public
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Instance Constructors

  1. new KmerTableBuilder2(width: Int, tagWidth: Int, sizeEstimate: Int, k: Int)

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 addLong(x: Long): Unit

    Add a single long value.

    Add a single long value. Calling this method 'width' times adds a single k-mer to the table.

    Definition Classes
    KmerTableBuilder
  5. def addLongUnsafe(x: Long): Unit

    Add a long without checking bounds.

    Add a long without checking bounds. Users are responsible for calling beginRow() and finishRow() as needed.

    Definition Classes
    KmerTableBuilder
  6. def addLongsUnsafe(xs: Array[Long]): Unit

    Add multiple long values without checking bounds.

    Add multiple long values without checking bounds. Users are responsible for calling beginRow() and finishRow() as needed.

    Definition Classes
    KmerTableBuilder
  7. def addRow(xs: Array[Long]): Unit

    Add a complete row.

    Add a complete row. The array must have the correct number of elements matching the width of this table.

    Definition Classes
    KmerTableBuilder2 → KmerTableBuilder
  8. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  9. def beginRow(): Unit

    Start a new row in this table.

    Start a new row in this table. The row can be added to using the addLong and addLongs methods. After the row is complete, finishRow should be called. The buffers may grow when this method is called.

    Definition Classes
    KmerTableBuilder
  10. val buffers: Array[Array[Long]]

    Resizable Long buffers.

    Resizable Long buffers. These will always be of equal length.

    Attributes
    protected
    Definition Classes
    KmerTableBuilder
  11. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native() @IntrinsicCandidate()
  12. def ensureSize(reqSize: Int): Unit
    Definition Classes
    KmerTableBuilder
  13. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  14. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  15. def finishRow(): Unit

    Complete a row in this table.

    Complete a row in this table.

    Definition Classes
    KmerTableBuilder
  16. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @IntrinsicCandidate()
  17. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @IntrinsicCandidate()
  18. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  19. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  20. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @IntrinsicCandidate()
  21. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @IntrinsicCandidate()
  22. def result(sort: Boolean): KmerTable

    Construct a k-mer table that contains all the inserted k-mers.

    Construct a k-mer table that contains all the inserted k-mers. After calling this method, this builder is invalid and should be discarded.

    sort

    Whether the k-mers should be sorted.

    returns

    The resulting k-mer table

    Definition Classes
    KmerTableBuilder
  23. var size: Int

    Number of items stored in the buffers

    Number of items stored in the buffers

    Attributes
    protected
    Definition Classes
    KmerTableBuilder
  24. def skipRow(): Unit
    Definition Classes
    KmerTableBuilder
  25. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  26. def toString(): String
    Definition Classes
    AnyRef → Any
  27. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  28. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  29. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Deprecated Value Members

  1. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] ) @Deprecated
    Deprecated

Inherited from KmerTableBuilder

Inherited from AnyRef

Inherited from Any

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