Biobase.Types.Location

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.

Documentation

data Location

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

Defined in Biobase.Types.Location

Methods

(==) :: Location -> Location -> Bool

(/=) :: Location -> Location -> Bool

Ord Location

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

Defined in Biobase.Types.Location

Methods

readsPrec :: Int -> ReadS Location

readList :: ReadS [Location]

readPrec :: ReadPrec Location

readListPrec :: ReadPrec [Location]

Show Location

Defined in Biobase.Types.Location

Methods

showsPrec :: Int -> Location -> ShowS

show :: Location -> String

showList :: [Location] -> ShowS

Generic Location

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

Defined in Biobase.Types.Location

Methods

reversing :: Location -> Location

type Rep Location

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

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)

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

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

Defined in Biobase.Types.Location

Methods

(==) :: PartialLocation -> PartialLocation -> Bool

(/=) :: PartialLocation -> PartialLocation -> Bool

Ord PartialLocation

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

Defined in Biobase.Types.Location

Methods

readsPrec :: Int -> ReadS PartialLocation

readList :: ReadS [PartialLocation]

readPrec :: ReadPrec PartialLocation

readListPrec :: ReadPrec [PartialLocation]

Show PartialLocation

Defined in Biobase.Types.Location

Methods

showsPrec :: Int -> PartialLocation -> ShowS

show :: PartialLocation -> String

showList :: [PartialLocation] -> ShowS

Generic PartialLocation

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

Reversing a reversible location means moving the start to the end.

Defined in Biobase.Types.Location

Methods

reversing :: PartialLocation -> PartialLocation

type Rep PartialLocation

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

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)