org.bdgenomics.adam.algorithms.smithwaterman

SmithWatermanGapScoringFromFn

abstract class SmithWatermanGapScoringFromFn extends SmithWaterman

Linear Supertypes
SmithWaterman, AnyRef, Any
Known Subclasses
SmithWatermanConstantGapScoring
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  1. SmithWatermanGapScoringFromFn
  2. SmithWaterman
  3. AnyRef
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Instance Constructors

  1. new SmithWatermanGapScoringFromFn(xSequence: String, ySequence: String, scoreFn: (Int, Int, Char, Char) ⇒ Double)

Abstract Value Members

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

    Attributes
    protected
    Definition Classes
    SmithWaterman

Concrete Value Members

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

    Definition Classes
    AnyRef

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

    Definition Classes
    Any

  3. final def ##(): Int

    Definition Classes
    AnyRef → Any

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

    Definition Classes
    AnyRef

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

    Definition Classes
    Any

  6. lazy val alignmentX: String

    Definition Classes
    SmithWaterman

  7. lazy val alignmentY: String

    Definition Classes
    SmithWaterman

  8. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  9. def buildScoringMatrix(): Array[Array[Double]]

    Definition Classes
    SmithWatermanGapScoringFromFn → SmithWaterman

  10. lazy val cigarX: Cigar

    Definition Classes
    SmithWaterman

  11. lazy val cigarY: Cigar

    Definition Classes
    SmithWaterman

  12. def clone(): AnyRef

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef

  14. def equals(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any

  15. def finalize(): Unit

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )

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

    Definition Classes
    AnyRef → Any

  17. def hashCode(): Int

    Definition Classes
    AnyRef → Any

  18. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  19. var max: Double

    Definition Classes
    SmithWaterman

  20. var maxX: Int

    Definition Classes
    SmithWaterman

  21. var maxY: Int

    Definition Classes
    SmithWaterman

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

    Definition Classes
    AnyRef

  23. final def notify(): Unit

    Definition Classes
    AnyRef

  24. final def notifyAll(): Unit

    Definition Classes
    AnyRef

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

    Definition Classes
    SmithWaterman

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

    Definition Classes
    AnyRef

  27. def toString(): String

    Definition Classes
    AnyRef → Any

  28. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from SmithWaterman

Inherited from AnyRef

Inherited from Any

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