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c

com.jnpersson.kmers.util

KmerTableBuilder

class KmerTableBuilder extends AnyRef

Builder for k-mer tables. K-mers are built by gradually adding longs in order. The builder is not reusable.

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KmerTableBuilder1, KmerTableBuilder2, KmerTableBuilder3
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Instance Constructors

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

    width

    Total width of k-mers (in longs, e.g. ceil(k/32)), including tag data. This is the total number of columns in the final table.

    tagWidth

    With of extra longs used to annotate k-mers with additional information (part of width)

    sizeEstimate

    Estimated number of k-mers that will be inserted. This is the number of rows in the final table.

    k

    k

Value Members

  1. final def !=(arg0: Any): Boolean
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  2. final def ##(): Int
    Definition Classes
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  3. final def ==(arg0: Any): Boolean
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  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.

  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.

  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.

  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.

  8. final def asInstanceOf[T0]: T0
    Definition Classes
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  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.

  10. val buffers: Array[Array[Long]]

    Resizable Long buffers.

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

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

    Complete a row in this table.

  16. final def getClass(): Class[_]
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  17. def hashCode(): Int
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  18. final def isInstanceOf[T0]: Boolean
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  19. final def ne(arg0: AnyRef): Boolean
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  20. final def notify(): Unit
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  21. final def notifyAll(): Unit
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  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

  23. var size: Int

    Number of items stored in the buffers

    Number of items stored in the buffers

    Attributes
    protected
  24. def skipRow(): Unit
  25. final def synchronized[T0](arg0: ⇒ T0): T0
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  26. def toString(): String
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  27. final def wait(arg0: Long, arg1: Int): Unit
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  28. final def wait(arg0: Long): Unit
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  29. final def wait(): Unit
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Deprecated Value Members

  1. def finalize(): Unit
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    @throws( classOf[java.lang.Throwable] ) @Deprecated
    Deprecated

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