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# Packages

-  package root
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    root
-  package org
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    root
-  package bdgenomics
  Definition Classes
    org
-  package adam
  Definition Classes
    bdgenomics
-  package algorithms
  Definition Classes
    adam
-  package smithwaterman
  Definition Classes
    algorithms
- SmithWaterman
- SmithWatermanConstantGapScoring

c

org.bdgenomics.adam.algorithms.smithwaterman

# SmithWatermanConstantGapScoring 

###

#### case class SmithWatermanConstantGapScoring(xSequence: String, ySequence: String, wMatch: Double, wMismatch: Double, wInsert: Double, wDelete: Double) extends SmithWatermanGapScoringFromFn with Product with Serializable

Performs a pairwise alignment of two sequences using constant penalties.

xSequence

  The first sequence in the pair.

ySequence

  The second sequence in the pair.

wMatch

  The alignment gap penalty for a residue match.

wMismatch

  The alignment gap penalty for a residue mismatch.

wInsert

  The alignment gap penalty for an insertion in the first sequence.

wDelete

  The alignment gap penalty for a deletion in the first sequence.

See also

  scoreFn

Linear Supertypes
Product, Equals, SmithWatermanGapScoringFromFn, SmithWaterman, Serializable, Serializable, AnyRef, Any
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Inherited

1. SmithWatermanConstantGapScoring
2. Product
3. Equals
4. SmithWatermanGapScoringFromFn
5. SmithWaterman
6. Serializable
7. Serializable
8. AnyRef
9. Any

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Visibility

1. Public
2. All

### Instance Constructors

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

   xSequence

     The first sequence in the pair.

   ySequence

     The second sequence in the pair.

   wMatch

     The alignment gap penalty for a residue match.

   wMismatch

     The alignment gap penalty for a residue mismatch.

   wInsert

     The alignment gap penalty for an insertion in the first sequence.

   wDelete

     The alignment gap penalty for a deletion in the first sequence.

### 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 score matrix by calling scoring function for all residue pairs.

   Builds Smith-Waterman score matrix by calling scoring function for all residue pairs.

   returns

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

   Definition Classes
     SmithWatermanGapScoringFromFn → SmithWaterman
6.  lazy val cigarX: Cigar

   CIGAR strings and alignment start positions from the pairwise alignment process.

   CIGAR strings and alignment start positions from the pairwise alignment process. The alignment start position may be non-zero if two strings are the same length, but the highest scoring alignment has bases deleted in one string/inserted in the other. In this case, some bases at the start/end of one string are expected to be "trimmed".

   Definition Classes
     SmithWaterman
7.  lazy val cigarY: Cigar

   CIGAR strings and alignment start positions from the pairwise alignment process.

   CIGAR strings and alignment start positions from the pairwise alignment process. The alignment start position may be non-zero if two strings are the same length, but the highest scoring alignment has bases deleted in one string/inserted in the other. In this case, some bases at the start/end of one string are expected to be "trimmed".

   Definition Classes
     SmithWaterman
8.  def clone(): AnyRef
   Attributes
     protected[java.lang]
   Definition Classes
     AnyRef
   Annotations
     @native() @throws( ... )
9.  final def eq(arg0: AnyRef): Boolean
   Definition Classes
     AnyRef
10.  def finalize(): Unit
    Attributes
      protected[java.lang]
    Definition Classes
      AnyRef
    Annotations
      @throws( classOf[java.lang.Throwable] )
11.  final def getClass(): Class[_]
    Definition Classes
      AnyRef → Any
    Annotations
      @native()
12.  final def isInstanceOf[T0]: Boolean
    Definition Classes
      Any
13.  final def ne(arg0: AnyRef): Boolean
    Definition Classes
      AnyRef
14.  final def notify(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native()
15.  final def notifyAll(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native()
16.  def scoreFn(xPos: Int, yPos: Int, xResidue: Char, yResidue: Char): Double

    Scores residues using scoring constants.

    Scores residues using scoring constants.

    * If a deletion is observed (xResidue is a gap), then the deletion penalty is returned. * If an insertion is observed (yResidue is a gap), then the insertion penalty is returned. * Else, the residues are compared, and either the match or mismatch penalty is returned.

    The position indices are ignored, so no affine/open-continue gap model is incorporated.

    xPos

      Residue position from first sequence.

    yPos

      Residue position from second sequence.

    xResidue

      Residue from first sequence.

    yResidue

      Residue from second sequence.

    returns

      Returns the gap score for this residue pair.

    Attributes
      protected
    Definition Classes
      SmithWatermanConstantGapScoring → SmithWatermanGapScoringFromFn
17.  final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
      AnyRef
18.  val wDelete: Double
19.  val wInsert: Double
20.  val wMatch: Double
21.  val wMismatch: Double
22.  final def wait(): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )
23.  final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )
24.  final def wait(arg0: Long): Unit
    Definition Classes
      AnyRef
    Annotations
      @native() @throws( ... )
25.  val xSequence: String

    First sequence to align.

    First sequence to align.

    Definition Classes
      SmithWatermanConstantGapScoring → SmithWaterman
26.  lazy val xStart: Int

    CIGAR strings and alignment start positions from the pairwise alignment process.

    CIGAR strings and alignment start positions from the pairwise alignment process. The alignment start position may be non-zero if two strings are the same length, but the highest scoring alignment has bases deleted in one string/inserted in the other. In this case, some bases at the start/end of one string are expected to be "trimmed".

    Definition Classes
      SmithWaterman
27.  val ySequence: String

    Second sequence to align.

    Second sequence to align.

    Definition Classes
      SmithWatermanConstantGapScoring → SmithWaterman
28.  lazy val yStart: Int

    CIGAR strings and alignment start positions from the pairwise alignment process.

    CIGAR strings and alignment start positions from the pairwise alignment process. The alignment start position may be non-zero if two strings are the same length, but the highest scoring alignment has bases deleted in one string/inserted in the other. In this case, some bases at the start/end of one string are expected to be "trimmed".

    Definition Classes
      SmithWaterman

### Inherited from Product

### Inherited from Equals

### Inherited from SmithWatermanGapScoringFromFn

### Inherited from SmithWaterman

### Inherited from Serializable

### Inherited from AnyRef

### Inherited from Any

### Ungrouped