Safe Haskell	None
Language	Haskell2010

Biobase.Types.Location

Description

Annotate the genomic Location of features or elements. A Location is always contiguous, using strand, 0-based position, and length. Transformation to different systems of annotation is made possible.

Synopsis

data Location = Location {
- _lStrand :: !Strand
- _lStart :: !(Index 0)
- _lLength :: !Int
- _lTotalLength :: !Int
}
lTotalLength :: Lens' Location Int
lStrand :: Lens' Location Strand
lStart :: Lens' Location (Index 0)
lLength :: Lens' Location Int
_Location :: Iso' Location (Strand, Index 0, Int, Int)
startEndInclusive :: KnownNat k => Iso' Location (Strand, (Index k, Index k), Int)
data PartialLocation
- = PartialLocation {
  - _plStrand :: !Strand
  - _plStart :: !(Index 0)
  - _plLength :: !Int
  }
- | ReversedPartialLocation {
  - _plStrand :: !Strand
  - _plEnd :: !(Index 0)
  - _plLength :: !Int
  }
plStrand :: Lens' PartialLocation Strand
plStart :: Traversal' PartialLocation (Index 0)
plLength :: Lens' PartialLocation Int
plEnd :: Traversal' PartialLocation (Index 0)
_ReversedPartialLocation :: Prism' PartialLocation (Strand, Index 0, Int)
_PartialLocation :: Prism' PartialLocation (Strand, Index 0, Int)
locationPartial :: Iso' Location (PartialLocation, Int)

Documentation

data Location Source #

Location information.

Constructors

Location
Fields _lStrand :: !Strand On which strand are we _lStart :: !(Index 0) Start, 0-based _lLength :: !Int number of characters in this location _lTotalLength :: !Int the total length of the "contig" (or whatever) this location is positioned in.

Instances

Eq Location Source #
Instance details Defined in Biobase.Types.Location Methods (==) :: Location -> Location -> Bool # (/=) :: Location -> Location -> Bool #
Ord Location Source #
Instance details Defined in Biobase.Types.Location Methods compare :: Location -> Location -> Ordering # (<) :: Location -> Location -> Bool # (<=) :: Location -> Location -> Bool # (>) :: Location -> Location -> Bool # (>=) :: Location -> Location -> Bool # max :: Location -> Location -> Location # min :: Location -> Location -> Location #
Read Location Source #
Instance details Defined in Biobase.Types.Location Methods readsPrec :: Int -> ReadS Location # readList :: ReadS [Location] # readPrec :: ReadPrec Location # readListPrec :: ReadPrec [Location] #
Show Location Source #
Instance details Defined in Biobase.Types.Location Methods showsPrec :: Int -> Location -> ShowS # show :: Location -> String # showList :: [Location] -> ShowS #
Generic Location Source #
Instance details Defined in Biobase.Types.Location Associated Types type Rep Location :: Type -> Type # Methods from :: Location -> Rep Location x # to :: Rep Location x -> Location #
Reversing Location Source #
Instance details Defined in Biobase.Types.Location Methods reversing :: Location -> Location #
type Rep Location Source #
Instance details Defined in Biobase.Types.Location type Rep Location = D1 (MetaData "Location" "Biobase.Types.Location" "BiobaseTypes-0.2.0.1-B9coIbijR6NEFcCxvqIOZp" False) (C1 (MetaCons "Location" PrefixI True) ((S1 (MetaSel (Just "_lStrand") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 Strand) :: S1 (MetaSel (Just "_lStart") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 (Index 0))) :: (S1 (MetaSel (Just "_lLength") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 Int) :*: S1 (MetaSel (Just "_lTotalLength") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 Int))))

lTotalLength :: Lens' Location Int Source #

lStrand :: Lens' Location Strand Source #

lStart :: Lens' Location (Index 0) Source #

lLength :: Lens' Location Int Source #

_Location :: Iso' Location (Strand, Index 0, Int, Int) Source #

startEndInclusive :: KnownNat k => Iso' Location (Strand, (Index k, Index k), Int) Source #

An isomorphism between locations, and triples of Strand,Start,End, where end is inclusive. For length==0 locations, this will mean start<end on the plus strand.

This should hold for all k, in Index k.

data PartialLocation Source #

During streaming construction, it is possible that we know a feature is on the - strand, but the length of the contig is not known yet.

0         1         2
012345678901234567890
  >---                    +        2 4    Location +  2 4
     <---                 Reversed 5 4    Location - 12 4
098765432109876543210
2         1         0

Constructors

PartialLocation	Location, when it is not yet known how long the contig will be.
Fields _plStrand :: !Strand _plStart :: !(Index 0) _plLength :: !Int
ReversedPartialLocation	The reversed strand. However, we have an `plEnd`, not a `plStart` now!
Fields _plStrand :: !Strand _plEnd :: !(Index 0) _plLength :: !Int

Instances

Eq PartialLocation Source #
Instance details Defined in Biobase.Types.Location Methods (==) :: PartialLocation -> PartialLocation -> Bool # (/=) :: PartialLocation -> PartialLocation -> Bool #
Ord PartialLocation Source #
Instance details Defined in Biobase.Types.Location Methods compare :: PartialLocation -> PartialLocation -> Ordering # (<) :: PartialLocation -> PartialLocation -> Bool # (<=) :: PartialLocation -> PartialLocation -> Bool # (>) :: PartialLocation -> PartialLocation -> Bool # (>=) :: PartialLocation -> PartialLocation -> Bool # max :: PartialLocation -> PartialLocation -> PartialLocation # min :: PartialLocation -> PartialLocation -> PartialLocation #
Read PartialLocation Source #
Instance details Defined in Biobase.Types.Location Methods readsPrec :: Int -> ReadS PartialLocation # readList :: ReadS [PartialLocation] # readPrec :: ReadPrec PartialLocation # readListPrec :: ReadPrec [PartialLocation] #
Show PartialLocation Source #
Instance details Defined in Biobase.Types.Location Methods showsPrec :: Int -> PartialLocation -> ShowS # show :: PartialLocation -> String # showList :: [PartialLocation] -> ShowS #
Generic PartialLocation Source #
Instance details Defined in Biobase.Types.Location Associated Types type Rep PartialLocation :: Type -> Type # Methods from :: PartialLocation -> Rep PartialLocation x # to :: Rep PartialLocation x -> PartialLocation #
Reversing PartialLocation Source #	Reversing a reversible location means moving the start to the end.
Instance details Defined in Biobase.Types.Location Methods reversing :: PartialLocation -> PartialLocation #
type Rep PartialLocation Source #
Instance details Defined in Biobase.Types.Location type Rep PartialLocation = D1 (MetaData "PartialLocation" "Biobase.Types.Location" "BiobaseTypes-0.2.0.1-B9coIbijR6NEFcCxvqIOZp" False) (C1 (MetaCons "PartialLocation" PrefixI True) (S1 (MetaSel (Just "_plStrand") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 Strand) :: (S1 (MetaSel (Just "_plStart") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 (Index 0)) :: S1 (MetaSel (Just "_plLength") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 Int))) :+: C1 (MetaCons "ReversedPartialLocation" PrefixI True) (S1 (MetaSel (Just "_plStrand") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 Strand) :: (S1 (MetaSel (Just "_plEnd") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 (Index 0)) :: S1 (MetaSel (Just "_plLength") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 Int))))

plStrand :: Lens' PartialLocation Strand Source #

plStart :: Traversal' PartialLocation (Index 0) Source #

plLength :: Lens' PartialLocation Int Source #

plEnd :: Traversal' PartialLocation (Index 0) Source #

_ReversedPartialLocation :: Prism' PartialLocation (Strand, Index 0, Int) Source #

_PartialLocation :: Prism' PartialLocation (Strand, Index 0, Int) Source #

locationPartial :: Iso' Location (PartialLocation, Int) Source #