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t

com.jnpersson.kmers

MinimizerCLIConf

trait MinimizerCLIConf extends AnyRef

Command-line configuration for minimizer schemes

Self Type
MinimizerCLIConf with ScallopConf
Linear Supertypes
AnyRef, Any
Known Subclasses
AdvancedMinimizerConfiguration
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  1. MinimizerCLIConf
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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
    Definition Classes
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  4. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  5. val canonicalMinimizers: ScallopOption[Boolean]
  6. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
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    Annotations
    @throws( ... ) @native() @IntrinsicCandidate()
  7. def defaultCanonicalMinimizers: Boolean

    For some minimizer orderings, whether to use canonical orientation

    For some minimizer orderings, whether to use canonical orientation

    Attributes
    protected
  8. def defaultK: Int
    Attributes
    protected
  9. def defaultMinimizerSpaces: Int
  10. def defaultMinimizerWidth: Int
    Attributes
    protected
  11. def defaultOrdering: String
    Attributes
    protected
  12. def defaultXORMask: Long

    For the XOR ordering, which mask to use

    For the XOR ordering, which mask to use

    Attributes
    protected
  13. final def eq(arg0: AnyRef): Boolean
    Definition Classes
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  14. def equals(arg0: Any): Boolean
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  15. final def getClass(): Class[_]
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    @native() @IntrinsicCandidate()
  16. def hashCode(): Int
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    @native() @IntrinsicCandidate()
  17. final def isInstanceOf[T0]: Boolean
    Definition Classes
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  18. val k: ScallopOption[Int]
  19. val minimizerSpaces: ScallopOption[Int]
  20. val minimizerWidth: ScallopOption[Int]
  21. final def ne(arg0: AnyRef): Boolean
    Definition Classes
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  22. final def notify(): Unit
    Definition Classes
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    @native() @IntrinsicCandidate()
  23. final def notifyAll(): Unit
    Definition Classes
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    @native() @IntrinsicCandidate()
  24. val ordering: ScallopOption[MinimizerOrdering]
  25. def orderingChoices: Seq[String]
    Attributes
    protected
  26. def orderingHidden: Boolean
    Attributes
    protected
  27. def parseMinimizerSource: MinimizerSource
  28. def parseOrdering(x: String): MinimizerOrdering
    Attributes
    protected
  29. def parseOrderingNonCanonical(x: String): MinimizerOrdering
    Attributes
    protected
  30. def requireSuppliedK(): Unit
  31. def seedMask(inner: MinimizerPriorities): MinimizerPriorities

    Apply a spaced seed mask to minimizer priorities

  32. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
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  33. def toString(): String
    Definition Classes
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  34. final def wait(arg0: Long, arg1: Int): Unit
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    @throws( ... )
  35. final def wait(arg0: Long): Unit
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  36. final def wait(): Unit
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    @throws( ... )

Deprecated Value Members

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

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