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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
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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[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native() @HotSpotIntrinsicCandidate()
  9. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  10. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  11. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  12. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  13. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  14. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  15. 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
  16. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  17. val wDelete: Double
  18. val wInsert: Double
  19. val wMatch: Double
  20. val wMismatch: Double
  21. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  22. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  23. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  24. val xSequence: String

    First sequence to align.

    First sequence to align.

    Definition Classes
    SmithWatermanConstantGapScoringSmithWaterman
  25. 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
  26. val ySequence: String

    Second sequence to align.

    Second sequence to align.

    Definition Classes
    SmithWatermanConstantGapScoringSmithWaterman
  27. 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

Deprecated Value Members

  1. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] ) @Deprecated @deprecated
    Deprecated

    (Since version ) see corresponding Javadoc for more information.

Inherited from Product

Inherited from Equals

Inherited from SmithWatermanGapScoringFromFn

Inherited from SmithWaterman

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

Ungrouped