org.bdgenomics.adam.algorithms.smithwaterman

SmithWaterman

abstract class SmithWaterman extends AnyRef

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Known Subclasses
SmithWatermanConstantGapScoring, SmithWatermanGapScoringFromFn
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Instance Constructors

  1. new SmithWaterman(xSequence: String, ySequence: String)

Abstract Value Members

  1. abstract def buildScoringMatrix(): Array[Array[Double]]

  2. abstract def trackback(): (Cigar, Cigar, String, String)

    Attributes
    protected

Concrete 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. lazy val alignmentX: String

  7. lazy val alignmentY: String

  8. final def asInstanceOf[T0]: T0

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  9. lazy val cigarX: Cigar

  10. lazy val cigarY: Cigar

  11. def clone(): AnyRef

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    protected[java.lang]
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  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. var max: Double

  19. var maxX: Int

  20. var maxY: Int

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

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  22. final def notify(): Unit

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  23. final def notifyAll(): Unit

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  24. lazy val scoringMatrix: Array[Array[Double]]

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

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  26. def toString(): String

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  27. final def wait(): Unit

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    @throws( ... )

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

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

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