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1.  final def !=(arg0: Any): Boolean

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2.  final def ##(): Int

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3.  final def ==(arg0: Any): Boolean

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4.  final def asInstanceOf[T0]: T0

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5.  def clone(): AnyRef

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6.  final def eq(arg0: AnyRef): Boolean

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7.  def equals(arg0: Any): Boolean

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8.  def finalize(): Unit

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9.  final def getClass(): Class[_]

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10.  def hashCode(): Int

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11.  final def isInstanceOf[T0]: Boolean

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12.  def minimizerSignatureTable(template: MinTable): MinTable

    Create a MinTable that de-prioritizes motifs where either the motif or its reverse complement: 1.

    Create a MinTable that de-prioritizes motifs where either the motif or its reverse complement: 1. Starts with AAA or ACA, or 2. Contains AA anywhere except the beginning

    The signature ordering is applied on top of an existing ordering in a template table. The existing ordering in that table will then be partially reordered based on the signature priority of each motif.

13.  final def ne(arg0: AnyRef): Boolean

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14.  final def notify(): Unit

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15.  final def notifyAll(): Unit

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16.  def randomOrdering(template: MinTable): MinTable

    Based on a template space, create a MinTable with a random motif ordering.

    Based on a template space, create a MinTable with a random motif ordering.

    template

    The template ordering to scramble

17.  def signatureHighPriority(motif: String): Boolean

    Is the given motif a high priority motif in the minimizer signature ordering?

    Is the given motif a high priority motif in the minimizer signature ordering?

    motif

    The motif to test

18.  final def synchronized[T0](arg0: ⇒ T0): T0

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19.  def toString(): String

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20.  final def wait(): Unit

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21.  final def wait(arg0: Long, arg1: Int): Unit

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22.  final def wait(arg0: Long): Unit

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