Safe Haskell	None
Language	Haskell2010

DP.Backtraced.Codon

Description

The Backtraced column structure is for codon-based alignments, including special cases.

Synopsis

data BtCodon c aa
- = Match {
  - _codon :: !(Codon c)
  - _aa :: !aa
  }
- | Frameshift {
  - _frameshift :: !(Vector c)
  - _aa :: !aa
  }
- | Insert {
  - _codon :: !(Codon c)
  - _aa :: !aa
  }
- | Shifted {
  - _frameshift :: !(Vector c)
  - _aa :: !aa
  }
- | Region {
  - _region :: !(Vector c)
  - _annotation :: !ByteString
  }
- | Delete {
  }

Documentation

data BtCodon c aa Source #

A single Backtraced column. Since such a column will be part of a Backtraced (Z:.BtCodon c aa:. ...) structure, it is always possible to extend even further, by having more entries.

Constructors

Match	A canonical match. A codon and the translated amino acid need to be set.
Fields _codon :: !(Codon c) _aa :: !aa
Frameshift	A frameshifting match. The vector of frameshifted nucleotides will have a number of characters `c`, that encode for a single amino acid.
Fields _frameshift :: !(Vector c) _aa :: !aa
Insert
Fields _codon :: !(Codon c) _aa :: !aa
Shifted
Fields _frameshift :: !(Vector c) _aa :: !aa
Region
Fields _region :: !(Vector c) _annotation :: !ByteString
Delete