org.bdgenomics.adam.algorithms.smithwaterman

# SmithWatermanConstantGapScoring

#### class SmithWatermanConstantGapScoring extends SmithWatermanGapScoringFromFn

Linear Supertypes
SmithWatermanGapScoringFromFn, SmithWaterman, Serializable, Serializable, AnyRef, Any
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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: Any): Boolean

   Definition Classes
     AnyRef → Any

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

   Definition Classes
     AnyRef → Any

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

   Definition Classes
     AnyRef → Any

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

   Definition Classes
     Any

5. #### 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

6. #### lazy val cigarX: Cigar

   Definition Classes
     SmithWaterman

7. #### lazy val cigarY: Cigar

   Definition Classes
     SmithWaterman

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

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

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

   Definition Classes
     AnyRef

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

    Definition Classes
      AnyRef → Any

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

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

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

    Definition Classes
      AnyRef → Any

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

    Definition Classes
      AnyRef → Any

14. #### final def isInstanceOf[T0]: Boolean

    Definition Classes
      Any

15. #### lazy val moveMatrix: Array[Array[Char]]

    Definition Classes
      SmithWaterman

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

    Definition Classes
      AnyRef

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

    Definition Classes
      AnyRef

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

    Definition Classes
      AnyRef

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

    Definition Classes
      SmithWaterman

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

    Definition Classes
      AnyRef

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

    Definition Classes
      AnyRef → Any

22. #### final def wait(): Unit

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

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

    Definition Classes
      AnyRef
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      @throws( ... )

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

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

25. #### lazy val xStart: Int

    Definition Classes
      SmithWaterman

26. #### lazy val yStart: Int

    Definition Classes
      SmithWaterman

### Inherited from SmithWatermanGapScoringFromFn

### Inherited from SmithWaterman

### Inherited from Serializable

### Inherited from AnyRef

### Inherited from Any

### Ungrouped