NeedlemanWunsch

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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. object Default

   

5. def _optimalAlignment[S, N, M, I, V](i: I, j: I, A: S, B: S, similarity: (N, N) ⇒ V, gap: N, gapPenalty: V, F: M)(implicit arg0: Eq[N], arg1: Ring[I], arg2: Order[I], arg3: AdditiveMonoid[V], arg4: Eq[V], la: LinearAlgebra[M, I, I, V], indexed: Indexed[S, I, N]): Stream[(N, N)]

   

6. def alignStep[S, N, M, I, V](i: I, j: I, A: S, B: S, F: M, similarity: (N, N) ⇒ V, gap: N, gapPenalty: V)(implicit arg0: Eq[N], arg1: Ring[I], arg2: Order[I], arg3: AdditiveMonoid[V], arg4: Eq[V], la: LinearAlgebra[M, I, I, V], indexed: Indexed[S, I, N]): (N, N, I, I)

   

7. def alignmentScore[S, N, I, M, V, SS, G](A: S, B: S, gap: N, similarity: (N, N) ⇒ V, gapPenalty: V)(implicit arg0: Eq[N], arg1: Ring[I], arg2: Eq[I], arg3: AdditiveMonoid[V], arg4: Eq[V], indexed: Indexed[S, I, N], finite: Finite[S, I], zipper: Zipper[S, N, S, N, SS], functor: Functor[SS, (N, N), V, G], agg: Aggregatable[G, V, V]): V

   

   Computes the alignment score

   Computes the alignment score

   Arguments A and B must be of the same length

   alignmentScore("AGACTAGTTAC", "CGA---GACGT")

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8. def alignmentScoreK1[C[_], N, I, M, V](a: C[N], b: C[N], gap: N, similarity: (N, N) ⇒ V, gapPenalty: V)(implicit arg0: Eq[N], arg1: Ring[I], arg2: Eq[I], arg3: AdditiveMonoid[V], arg4: Eq[V], indexed: IndexedK1[C, I, N], finite: FiniteK1[C, N, I], zipper: ZipperK1[C, N, N], functor: FunctorK1[C, (N, N), V], agg: AggregatableK1[C, V, V]): V

   

9. final def asInstanceOf[T0]: T0

   

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10. def clone(): AnyRef

    

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11. def computeF[I, S, N, M, V](A: S, B: S, similarity: (N, N) ⇒ V, gapPenalty: V)(implicit arg0: Ring[I], arg1: AdditiveMonoid[V], arg2: Order[V], la: LinearAlgebra[M, I, I, V], indexed: Indexed[S, I, N], finite: Finite[S, I], module: Module[V, I]): M

    

    Computes the "F" matrix for two nucleotide sequences, A and B

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

    

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13. def equals(arg0: Any): Boolean

    

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14. def finalize(): Unit

    

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

    

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16. def hashCode(): Int

    

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17. final def isInstanceOf[T0]: Boolean

    

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

    

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19. final def notify(): Unit

    

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20. final def notifyAll(): Unit

    

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21. def optimalAlignment[S, N, M, I, V](A: S, B: S, similarity: (N, N) ⇒ V, gap: N, gapPenalty: V)(implicit arg0: Eq[N], arg1: Ring[I], arg2: Order[I], arg3: AdditiveMonoid[V], arg4: Order[V], arg5: Eq[V], la: LinearAlgebra[M, I, I, V], indexed: Indexed[S, I, N], finite: Finite[S, I], fs: FromStream[S, N], module: Module[V, I]): (S, S)

    

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

    

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23. def toString(): String

    

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24. final def wait(): Unit

    

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

    

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

    

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