AffineGapPenaltyAlignment

Value Members

1. final def !=(arg0: AnyRef): Boolean

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2. final def !=(arg0: Any): Boolean

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3. final def ##(): Int

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4. final def ==(arg0: AnyRef): Boolean

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5. final def ==(arg0: Any): Boolean

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6. def align(sequence: Seq[Byte], reference: Seq[Byte], mismatchProbability: Double = math.exp(-4), openGapProbability: Double = math.exp(-6), closeGapProbability: Double = 1 - math.exp(-1)): ReadAlignment

   Produces an alignment of an input sequence against a reference sequence

   Produces an alignment of an input sequence against a reference sequence

   sequence

   Input sequence to align

   reference

   Reference sequence to align against

   mismatchProbability

   Penalty to having a mismatch in the alignment

   openGapProbability

   Penalty to start an insertion or deletion in the alignment

   closeGapProbability

   Penalty to end in an insertion or deletion in the alignment

   returns

   An alignment path and score

7. final def asInstanceOf[T0]: T0

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8. def clone(): AnyRef

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9. final def eq(arg0: AnyRef): Boolean

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11. def finalize(): Unit

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12. final def getClass(): Class[_]

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13. def hashCode(): Int

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14. final def isInstanceOf[T0]: Boolean

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15. final def ne(arg0: AnyRef): Boolean

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16. final def notify(): Unit

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17. final def notifyAll(): Unit

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18. def scoreAlignmentPaths(sequence: Seq[Byte], reference: Seq[Byte], mismatchProbability: Double, openGapProbability: Double, closeGapProbability: Double): DenseVector[(Int, List[AlignmentState], Double)]

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

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20. def toString(): String

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21. final def wait(): Unit

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

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23. final def wait(arg0: Long): Unit

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