SmithWaterman

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 _optimalAlignment(i: Int, j: Int, A: String, B: String, mismatchPenalty: Int, H: matrix.JblasMatrixModule.Matrix[Int]): Stream[(Char, Char)]

7. def alignStep(i: Int, j: Int, A: String, B: String, H: matrix.JblasMatrixModule.Matrix[Int], mismatchPenalty: Int): (Char, Char, Int, Int)

8. final def asInstanceOf[T0]: T0

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9. def clone(): AnyRef

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10. def computeH(A: String, B: String, mismatchPenalty: Int): matrix.JblasMatrixModule.Matrix[Int]

    Computes the "H" matrix for two DNA sequences, A and B

    Computes the "H" matrix for two DNA sequences, A and B

    Same as Needleman-Wunsch's F matrix, except that all entries in the matrix are non-negative.

11. val defaultMismatchPenalty: Int

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. val gap: Char

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

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17. def hashCode(): Int

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18. final def isInstanceOf[T0]: Boolean

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19. def metricSpace(mismatchPenalty: Int = defaultMismatchPenalty): MetricSpace[String, Int]

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

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21. final def notify(): Unit

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22. final def notifyAll(): Unit

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23. def optimalAlignment(A: String, B: String, mismatchPenalty: Int = defaultMismatchPenalty): (String, String)

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

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25. def toString(): String

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26. def w(x: Char, y: Char, mismatchPenalty: Int): Int

27. final def wait(): Unit

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

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

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