Type Members

1.  class Aligner extends AnyRef

   Implementation of an aligner with generic scoring function and affine gap penalty support.

   Implementation of an aligner with generic scoring function and affine gap penalty support. Supports multiple alignment Modes for global, semi-global and local alignment.

   A scoring function (scoringFunction) is taken to score pair-wise aligned bases. A default implementation is supplied via the companion Aligner object which uses a fixed match score and mismatch penalty.

   When generating CIGARs for alignments the aligner uses the isMatch() method to determine whether to treat an aligned pair of bases as a match or mismatch. The default implementation of this method treats U bases as T bases to allow DNA/RNA alignments. It also will identify as matches any pair of bases (including IUPAC ambiguity codes) that share at least one base in common. This behaviour can be modified by overriding the isMatch() method.

2.  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

3.  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

4.  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).

5.  class LinearMatrix[A] extends Matrix[A]

   Implements a matrix using a single linear array.

6.  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 coordinates, the first of which is the row offset starting at 0, and the second of which is the column offset, starting at 0.

7.  sealed trait Mode extends EnumEntry

   Trait that entries in Mode will extend.

8.  final class SimpleIntMatrix extends Matrix[Int]

   Specialized matrix for storing integers that is markedly faster than using LinearMatrix[Int].

   Specialized matrix for storing integers that is markedly faster than using LinearMatrix[Int]. The performance increase comes from two factors:

   1. Using an array of arrays turns out to be faster than a single large array (in some cases) 2. Specializing to Int and not using ClassTag

   Using this matrix provides a ~30-50% speedup in Aligner when aligning short sequences.

9.  type NeedlemanWunschAligner = Aligner

   Annotations

   @deprecated

   Deprecated

   (Since version 0.5.2) Use Aligner instead.