seqloc-0.2.1: Handle sequence locations for bioinformatics

Bio.SeqLoc.OnSeq

Contents

Description

Data types for sequence locations and sequence positions associated with specific, named sequences.

Synopsis

Documentation

newtype SeqName Source

Constructors

SeqName 

Fields

unSeqName :: ByteString
 

Instances

data OnSeq s Source

Constructors

OnSeq 

Fields

onSeqName :: !SeqName
 
unOnSeq :: !s
 

Instances

Eq s => Eq (OnSeq s) 
Ord s => Ord (OnSeq s) 
Read s => Read (OnSeq s) 
Show s => Show (OnSeq s) 
LocRepr s => LocRepr (OnSeq s) 
Stranded s => Stranded (OnSeq s) 

Positions on named sequences

type SeqOffset = OnSeq OffsetSource

type SeqPos = OnSeq PosSource

A position on a named sequence

Contiguous location spans on named sequences

type ContigSeqLoc = OnSeq ContigLocSource

A location consisting of a contiguous span of positions on a named sequence.

Arbitrary location spans on named sequences

type SpliceSeqLoc = OnSeq SpliceLocSource

A general location, consisting of spans of sequence positions on a specific, named sequence.

andSameSeq :: (a -> b -> Bool) -> OnSeq a -> OnSeq b -> BoolSource