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com.jnpersson.kmers.minimizer

MinimizerPriorities

trait MinimizerPriorities extends Serializable

Defines a bidirectional mapping between encoded minimizers and their priorities. Priorities and minimizers are both represented as NTBitArray objects. If the bit array is a priority, the first 2*width bits should be interpreted as an unsigned integer, where a smaller value indicates a higher priority minimizer. If the bit array is a minimizer, then it can be interpreted as a 2-bit encoded string of nucleotides in the usual way.

The unsigned integer space representing priorities is no larger than the number of m-mers, so e.g. for nucleotides, for width m there is up to 4m possible minimizers and no more than 4m priorities.

The forward mapping (priorityOf) may be many-to-one, and not necessarily reversible. In this case, the reverse mapping (motifFor) returns a representative minimizer.

Linear Supertypes
Serializable, Serializable, AnyRef, Any
Known Subclasses
CanonicalPriorities, ExtendedTable, MinTable, RandomXOR, SpacedSeed
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  1. MinimizerPriorities
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Abstract Value Members

  1. abstract def motifFor(priority: NTBitArray): NTBitArray

    Get the minimizer for a given priority.

    Get the minimizer for a given priority. Inverse of the function above. Only defined for values originally computed by the priorityOf function.

  2. abstract def priorityOf(motif: NTBitArray): NTBitArray

    Get the priority of the given minimizer.

    Get the priority of the given minimizer. If not every m-mer is a minimizer, then util.NTBitArray.empty indicates an invalid minimizer.

  3. abstract def width: Int

    Minimizer width (m)

Concrete Value Members

  1. final def !=(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  2. final def ##(): Int
    Definition Classes
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  3. final def ==(arg0: Any): Boolean
    Definition Classes
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  4. final def asInstanceOf[T0]: T0
    Definition Classes
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  5. def clone(): AnyRef
    Attributes
    protected[lang]
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    Annotations
    @throws( ... ) @native() @IntrinsicCandidate()
  6. lazy val decoder: ThreadLocal[NTBitDecoder]
    Attributes
    protected
    Annotations
    @transient()
  7. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  8. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  9. final def getClass(): Class[_]
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    @native() @IntrinsicCandidate()
  10. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @IntrinsicCandidate()
  11. def humanReadable(priority: NTBitArray): NTSeq

    Human-readable string corresponding to a given minimizer.

    Human-readable string corresponding to a given minimizer. Not optimized for frequent use.

  12. def humanReadable(priority: Long): NTSeq
  13. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  14. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  15. final def notify(): Unit
    Definition Classes
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    @native() @IntrinsicCandidate()
  16. final def notifyAll(): Unit
    Definition Classes
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    @native() @IntrinsicCandidate()
  17. def numLargeBuckets: Long

    Number of buckets (minimizers) expected to be very large (frequent), if any

  18. def numMinimizers: Option[Long]

    Total number of distinct minimizers in this ordering, if available.

    Total number of distinct minimizers in this ordering, if available. This may be an upper bound. The largest value returned by priorityOf will be smaller than this value.

  19. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  20. def toString(): String
    Definition Classes
    AnyRef → Any
  21. final def wait(arg0: Long, arg1: Int): Unit
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    @throws( ... )
  22. final def wait(arg0: Long): Unit
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    @throws( ... ) @native()
  23. final def wait(): Unit
    Definition Classes
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    @throws( ... )
  24. def writePriorityOf(motif: NTBitArray, buffer: NTBitArray): NTBitArray

    Write the priority of the given minimizer to the provided buffer.

    Write the priority of the given minimizer to the provided buffer. If not every m-mer is a minimizer, then util.NTBitArray.empty indicates an invalid minimizer.

    motif

    The motif to get the priority of

    buffer

    The buffer to write the priority to

    returns

    The buffer for chaining

Deprecated Value Members

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

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