Bio.SeqLoc.Position

Contents

Description

Data type for a sequence position.

Zero-based Offsetindices are used throughout, to facilitate direct use of indexing functions on SeqData.

Synopsis

Sequence positions

newtype Offset Source

Unstranded offset in a sequence

Constructors

Offset
Fields unOffset :: Int64

Instances

Enum Offset
Eq Offset
Integral Offset
Num Offset
Ord Offset
Read Offset
Real Offset
Show Offset
LocRepr Offset

data Pos Source

Stranded position in a sequence

Constructors

Pos
Fields offset :: !Offset 0-based index of the position strand :: !Strand Strand of the position

Instances

Eq Pos
Ord Pos
Read Pos
Show Pos
LocRepr Pos
Stranded Pos

Manipulating positions

slide :: Pos -> Offset -> Pos Source

Returns a position resulting from sliding the original position along the sequence by a specified offset. A positive offset will move the position away from the 5' end of the forward stand of the sequence regardless of the strand of the position itself. Thus,

 slide (revCompl pos) off == revCompl (slide pos off)

Extracting sequences

atPos :: SeqLike s => s -> Pos -> Maybe Char Source

Extract Just the item at a specific sequence position, or Nothing if the position lies outside the bounds of the sequence.