org.bdgenomics.adam.algorithms.smithwaterman

# SmithWaterman

#### abstract class SmithWaterman extends Serializable

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

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

### Value Members

1. #### final def !=(arg0: Any): Boolean

   Definition Classes
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2. #### final def ##(): Int

   Definition Classes
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3. #### final def ==(arg0: Any): Boolean

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4. #### final def asInstanceOf[T0]: T0

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5. #### lazy val cigarX: Cigar

6. #### lazy val cigarY: Cigar

7. #### def clone(): AnyRef

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     protected[java.lang]
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     @throws( ... )

8. #### final def eq(arg0: AnyRef): Boolean

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9. #### def equals(arg0: Any): Boolean

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10. #### def finalize(): Unit

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      protected[java.lang]
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      @throws( classOf[java.lang.Throwable] )

11. #### final def getClass(): Class[_]

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12. #### def hashCode(): Int

    Definition Classes
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13. #### final def isInstanceOf[T0]: Boolean

    Definition Classes
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14. #### lazy val moveMatrix: Array[Array[Char]]

15. #### final def ne(arg0: AnyRef): Boolean

    Definition Classes
      AnyRef

16. #### final def notify(): Unit

    Definition Classes
      AnyRef

17. #### final def notifyAll(): Unit

    Definition Classes
      AnyRef

18. #### lazy val scoringMatrix: Array[Array[Double]]

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

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20. #### def toString(): String

    Definition Classes
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21. #### final def wait(): Unit

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      @throws( ... )

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

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23. #### final def wait(arg0: Long): Unit

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24. #### lazy val xStart: Int

25. #### lazy val yStart: Int

### Inherited from Serializable

### Inherited from AnyRef

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