org.bdgenomics.adam.algorithms.smithwaterman

SmithWatermanConstantGapScoring

class SmithWatermanConstantGapScoring extends SmithWatermanGapScoringFromFn

Linear Supertypes
SmithWatermanGapScoringFromFn, SmithWaterman, Serializable, Serializable, AnyRef, Any
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Inherited
  1. SmithWatermanConstantGapScoring
  2. SmithWatermanGapScoringFromFn
  3. SmithWaterman
  4. Serializable
  5. Serializable
  6. AnyRef
  7. Any
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Instance Constructors

  1. new SmithWatermanConstantGapScoring(xSequence: String, ySequence: String, wMatch: Double, wMismatch: Double, wInsert: Double, wDelete: Double)

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. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  7. def buildScoringMatrix(): (Array[Array[Double]], Array[Array[Char]])

    Builds Smith-Waterman scoring matrix.

    Builds Smith-Waterman scoring matrix.

    returns

    2D array of doubles, along with move direction at each point.

    Definition Classes
    SmithWatermanGapScoringFromFn → SmithWaterman
    Note

    To work with the move function, expected move directions are:

    * I: move in I coordinate * J: move in J coordinate * B: move in both I and J * T: terminate move

    See also

    move

  8. lazy val cigarX: Cigar

    Definition Classes
    SmithWaterman

  9. lazy val cigarY: Cigar

    Definition Classes
    SmithWaterman

  10. def clone(): AnyRef

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

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

    Definition Classes
    AnyRef

  12. def equals(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any

  13. def finalize(): Unit

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

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

    Definition Classes
    AnyRef → Any

  15. def hashCode(): Int

    Definition Classes
    AnyRef → Any

  16. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  17. lazy val moveMatrix: Array[Array[Char]]

    Definition Classes
    SmithWaterman

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

    Definition Classes
    AnyRef

  19. final def notify(): Unit

    Definition Classes
    AnyRef

  20. final def notifyAll(): Unit

    Definition Classes
    AnyRef

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

    Definition Classes
    SmithWaterman

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

    Definition Classes
    AnyRef

  23. def toString(): String

    Definition Classes
    AnyRef → Any

  24. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  27. lazy val xStart: Int

    Definition Classes
    SmithWaterman

  28. lazy val yStart: Int

    Definition Classes
    SmithWaterman

Inherited from SmithWatermanGapScoringFromFn

Inherited from SmithWaterman

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

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