Biobase.Types.Position

Annotate the genomic position of features or elements. A position has strand information, and different ways to encode where a feature is located. The position points to the first element (e.g. nucleotide).

Together with the Location module, it becomes possible to annotate substrings.

Documentation

data FwdPosition

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. In that case, FwdPosition allows expressing the hit in the coordinate system of the plus strand. Tools like blast do something similar, and express locations on the minus as y-x with y>x.

0123456789
 >-->
     <--<
9876543210

Constructors

FwdPosition

Plus-based location.

Fields

• _fwdStrand :: !Strand

  Strand we are on

• _fwdStart :: !(Index 0)

  Start of the hit on the plus strand

Instances

Eq FwdPosition

Defined in Biobase.Types.Position

Methods

(==) :: FwdPosition -> FwdPosition -> Bool

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

Data FwdPosition

Defined in Biobase.Types.Position

Methods

gfoldl :: (forall d b. Data d => c (d -> b) -> d -> c b) -> (forall g. g -> c g) -> FwdPosition -> c FwdPosition

gunfold :: (forall b r. Data b => c (b -> r) -> c r) -> (forall r. r -> c r) -> Constr -> c FwdPosition

toConstr :: FwdPosition -> Constr

dataTypeOf :: FwdPosition -> DataType

dataCast1 :: Typeable t => (forall d. Data d => c (t d)) -> Maybe (c FwdPosition)

dataCast2 :: Typeable t => (forall d e. (Data d, Data e) => c (t d e)) -> Maybe (c FwdPosition)

gmapT :: (forall b. Data b => b -> b) -> FwdPosition -> FwdPosition

gmapQl :: (r -> r' -> r) -> r -> (forall d. Data d => d -> r') -> FwdPosition -> r

gmapQr :: forall r r'. (r' -> r -> r) -> r -> (forall d. Data d => d -> r') -> FwdPosition -> r

gmapQ :: (forall d. Data d => d -> u) -> FwdPosition -> [u]

gmapQi :: Int -> (forall d. Data d => d -> u) -> FwdPosition -> u

gmapM :: Monad m => (forall d. Data d => d -> m d) -> FwdPosition -> m FwdPosition

gmapMp :: MonadPlus m => (forall d. Data d => d -> m d) -> FwdPosition -> m FwdPosition

gmapMo :: MonadPlus m => (forall d. Data d => d -> m d) -> FwdPosition -> m FwdPosition

Ord FwdPosition

Defined in Biobase.Types.Position

Methods

compare :: FwdPosition -> FwdPosition -> Ordering

(<) :: FwdPosition -> FwdPosition -> Bool

(<=) :: FwdPosition -> FwdPosition -> Bool

(>) :: FwdPosition -> FwdPosition -> Bool

(>=) :: FwdPosition -> FwdPosition -> Bool

max :: FwdPosition -> FwdPosition -> FwdPosition

min :: FwdPosition -> FwdPosition -> FwdPosition

Read FwdPosition

Defined in Biobase.Types.Position

Methods

readsPrec :: Int -> ReadS FwdPosition

readList :: ReadS [FwdPosition]

readPrec :: ReadPrec FwdPosition

readListPrec :: ReadPrec [FwdPosition]

Show FwdPosition

Defined in Biobase.Types.Position

Methods

showsPrec :: Int -> FwdPosition -> ShowS

show :: FwdPosition -> String

showList :: [FwdPosition] -> ShowS

Generic FwdPosition

Defined in Biobase.Types.Position

Associated Types

type Rep FwdPosition :: Type -> Type

Methods

from :: FwdPosition -> Rep FwdPosition x

to :: Rep FwdPosition x -> FwdPosition

Info FwdPosition

Defined in Biobase.Types.Position

Methods

info :: FwdPosition -> String

NFData FwdPosition

Defined in Biobase.Types.Position

Methods

rnf :: FwdPosition -> ()

Reversing FwdPosition

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

Defined in Biobase.Types.Position

Methods

reversing :: FwdPosition -> FwdPosition

ModifyLocation FwdPosition Int

Defined in Biobase.Types.Location

Methods

locAppendLeft :: forall k (i :: k). Int -> Location i FwdPosition Int -> Location i FwdPosition Int

locAppendRight :: forall k (i :: k). Int -> Location i FwdPosition Int -> Location i FwdPosition Int

locSplitAt :: forall k (i :: k). Int -> Location i FwdPosition Int -> (Location i FwdPosition Int, Location i FwdPosition Int)

locLength :: forall k (i :: k). Location i FwdPosition Int -> Int

ModifyLocation FwdPosition (BioSequence w)

Defined in Biobase.Types.Location

Methods

locAppendLeft :: forall k (i :: k). BioSequence w -> Location i FwdPosition (BioSequence w) -> Location i FwdPosition (BioSequence w)

locAppendRight :: forall k (i :: k). BioSequence w -> Location i FwdPosition (BioSequence w) -> Location i FwdPosition (BioSequence w)

locSplitAt :: forall k (i :: k). Int -> Location i FwdPosition (BioSequence w) -> (Location i FwdPosition (BioSequence w), Location i FwdPosition (BioSequence w))

locLength :: forall k (i :: k). Location i FwdPosition (BioSequence w) -> Int

Info (BioSequence w) => Info (Location i FwdPosition (BioSequence w))

Defined in Biobase.Types.Location

Methods

info :: Location i FwdPosition (BioSequence w) -> String

Reversing (Location i FwdPosition (BioSequence w))

Defined in Biobase.Types.Location

Methods

reversing :: Location i FwdPosition (BioSequence w) -> Location i FwdPosition (BioSequence w)

Reversing (Location i FwdPosition (BioSequence w)) => Reversing (PIS i FwdPosition (BioSequence w))

Defined in Biobase.Types.Location

Methods

reversing :: PIS i FwdPosition (BioSequence w) -> PIS i FwdPosition (BioSequence w)

Complement (BioSequence w) => Complement (Location i FwdPosition (BioSequence w))

Defined in Biobase.Types.Location

Methods

complement :: Iso' (Location i FwdPosition (BioSequence w)) (Location i FwdPosition (BioSequence w))

Complement (BioSequence w) => Complement (PIS i FwdPosition (BioSequence w))

Defined in Biobase.Types.Location

Methods

complement :: Iso' (PIS i FwdPosition (BioSequence w)) (PIS i FwdPosition (BioSequence w))

type Rep FwdPosition

Defined in Biobase.Types.Position

type Rep FwdPosition = D1 ('MetaData "FwdPosition" "Biobase.Types.Position" "BiobaseTypes-0.2.1.0-KNWEaQoA0aY419BnftjfF1" 'False) (C1 ('MetaCons "FwdPosition" 'PrefixI 'True) (S1 ('MetaSel ('Just "_fwdStrand") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Strand) :*: S1 ('MetaSel ('Just "_fwdStart") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 (Index 0))))

fwdStrand :: Lens' FwdPosition Strand

fwdStart :: Lens' FwdPosition (Index 0)

_FwdPosition :: Iso' FwdPosition (Strand, Index 0)