ADAM_2.12: Core 0.33.0 API < Back
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# Packages

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

p

org.bdgenomics.adam.algorithms

# smithwaterman 

#### package smithwaterman

### Type Members

1.  trait SmithWaterman extends Serializable

   Abstract class for implementing a Smith-Waterman pairwise alignment.

   Abstract class for implementing a Smith-Waterman pairwise alignment.

   Contains shell code for everything except for building the pairwise alignment score matrix. This way, a new scoring method (e.g., affine gap, residue specific scores) can be implemented without needing to implement core functionality like trackback, etc.

2.  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.

   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

### Ungrouped