Packages

package alignment

Ordering
  1. Alphabetic
Visibility
  1. Public
  2. All

Type Members

  1. case class Alignment (query: Array[Byte], target: Array[Byte], queryStart: Int, targetStart: Int, cigar: Cigar, score: Int) extends Product with Serializable

    A general class to describe the alignment between two sequences or partial ranges thereof

    A general class to describe the alignment between two sequences or partial ranges thereof

    query

    the query sequence

    target

    the target sequence

    queryStart

    the 1-based position in the query sequence where the alignment begins

    targetStart

    the 1-based position in the target sequence where the alignment begins

    cigar

    a Cigar object describing the alignment of the two sequences

    score

    the alignment score

  2. case class Cigar (elems: IndexedSeq[CigarElem]) extends Iterable[CigarElem] with Product with Serializable

    Object representation of a Cigar string representing an alignment between two sequences.

    Object representation of a Cigar string representing an alignment between two sequences.

    elems

    the ordered sequence of elements in the Cigar

  3. case class CigarElem (operator: CigarOperator, length: Int) extends Product with Serializable

    Represents an element in a Cigar.

    Represents an element in a Cigar.

    operator

    the type of element (e.g. match, insertion, etc.)

    length

    the length of the element in bases (must be greater than 0).

  4. class LinearMatrix [A] extends Matrix[A]

    Implements a matrix using a single linear array.

  5. trait Matrix [A] extends AnyRef

    Defines methods applicable to a 2D matrix.

    Defines methods applicable to a 2D matrix. Matrix cells are accessed with a pair of coordiantes, the first of which is the row offset starting at 0, and the second of which is the column offset, starting at 0.

  6. class NeedlemanWunschAligner extends AnyRef

    Implementation of the Needleman-Wunsch algorithm for global alignment of two sequences with support for an affine gap penalty.

Value Members

  1. object Alignment extends Serializable

    Companion object for Alignment.

  2. object Cigar extends Serializable

    Companion object for Cigar that offers alternative constructors.

  3. object Matrix

    Factory method(s) for Matrices.

  4. object NeedlemanWunschAligner

Ungrouped