Packages

t

com.jnpersson.kmers

AdvancedMinimizerConfiguration

trait AdvancedMinimizerConfiguration extends MinimizerCLIConf

Extra configuration options relating to advanced minimizer orderings

Self Type
AdvancedMinimizerConfiguration with ScallopConf
Linear Supertypes
MinimizerCLIConf, AnyRef, Any
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Inherited
  1. AdvancedMinimizerConfiguration
  2. MinimizerCLIConf
  3. AnyRef
  4. Any
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Visibility
  1. Public
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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. val allMinimizers: ScallopOption[Boolean]
  5. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  6. val canonicalMinimizers: ScallopOption[Boolean]
    Definition Classes
    MinimizerCLIConf
  7. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native() @IntrinsicCandidate()
  8. def defaultAllMinimizers: Boolean
  9. def defaultCanonicalMinimizers: Boolean

    For some minimizer orderings, whether to use canonical orientation

    For some minimizer orderings, whether to use canonical orientation

    Attributes
    protected
    Definition Classes
    MinimizerCLIConf
  10. def defaultK: Int
    Attributes
    protected
    Definition Classes
    MinimizerCLIConf
  11. def defaultMinimizerSpaces: Int
    Definition Classes
    MinimizerCLIConf
  12. def defaultMinimizerWidth: Int
    Attributes
    protected
    Definition Classes
    MinimizerCLIConf
  13. def defaultOrdering: String
    Attributes
    protected
    Definition Classes
    MinimizerCLIConf
  14. def defaultXORMask: Long

    For the XOR ordering, which mask to use

    For the XOR ordering, which mask to use

    Attributes
    protected
    Definition Classes
    MinimizerCLIConf
  15. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  16. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  17. val extendMinimizers: ScallopOption[Int]
  18. def extendMinimizersIfConfigured(inner: MinimizerSource): MinimizerSource
    Attributes
    protected
  19. def extendedWithSuffix: Boolean
    Attributes
    protected
  20. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @IntrinsicCandidate()
  21. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @IntrinsicCandidate()
  22. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  23. val k: ScallopOption[Int]
    Definition Classes
    MinimizerCLIConf
  24. val minimizerSpaces: ScallopOption[Int]
    Definition Classes
    MinimizerCLIConf
  25. val minimizerWidth: ScallopOption[Int]
    Definition Classes
    MinimizerCLIConf
  26. val minimizers: ScallopOption[String]
  27. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  28. val normalize: ScallopOption[Boolean]
  29. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @IntrinsicCandidate()
  30. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @IntrinsicCandidate()
  31. val ordering: ScallopOption[MinimizerOrdering]
    Definition Classes
    MinimizerCLIConf
  32. def orderingChoices: Seq[String]
    Attributes
    protected
    Definition Classes
    AdvancedMinimizerConfiguration → MinimizerCLIConf
  33. def orderingHidden: Boolean
    Attributes
    protected
    Definition Classes
    AdvancedMinimizerConfiguration → MinimizerCLIConf
  34. def parseMinimizerSource: MinimizerSource
    Definition Classes
    AdvancedMinimizerConfiguration → MinimizerCLIConf
  35. def parseOrdering(x: String): MinimizerOrdering
    Attributes
    protected
    Definition Classes
    AdvancedMinimizerConfiguration → MinimizerCLIConf
  36. def parseOrderingNonCanonical(x: String): MinimizerOrdering
    Attributes
    protected
    Definition Classes
    AdvancedMinimizerConfiguration → MinimizerCLIConf
  37. def requireSuppliedK(): Unit
    Definition Classes
    MinimizerCLIConf
  38. val sample: ScallopOption[Double]
  39. def seedMask(inner: MinimizerPriorities): MinimizerPriorities

    Apply a spaced seed mask to minimizer priorities

    Apply a spaced seed mask to minimizer priorities

    Definition Classes
    MinimizerCLIConf
  40. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  41. def toString(): String
    Definition Classes
    AnyRef → Any
  42. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  43. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  44. 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 MinimizerCLIConf

Inherited from AnyRef

Inherited from Any

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