Safe Haskell	None
Language	Haskell2010

Biobase.Types.Position

Description

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.

Synopsis

data FwdPosition = FwdPosition {
- _fwdStrand :: !Strand
- _fwdStart :: !(Index 0)
}
fwdStrand :: Lens' FwdPosition Strand
fwdStart :: Lens' FwdPosition (Index 0)
_FwdPosition :: Iso' FwdPosition (Strand, Index 0)

Documentation

data FwdPosition 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. 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

Instances details

Eq FwdPosition Source #
Instance details Defined in Biobase.Types.Position Methods (==) :: FwdPosition -> FwdPosition -> Bool # (/=) :: FwdPosition -> FwdPosition -> Bool #
Data FwdPosition Source #
Instance details 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 Source #
Instance details 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 Source #
Instance details Defined in Biobase.Types.Position Methods readsPrec :: Int -> ReadS FwdPosition # readList :: ReadS [FwdPosition] # readPrec :: ReadPrec FwdPosition # readListPrec :: ReadPrec [FwdPosition] #
Show FwdPosition Source #
Instance details Defined in Biobase.Types.Position Methods showsPrec :: Int -> FwdPosition -> ShowS # show :: FwdPosition -> String # showList :: [FwdPosition] -> ShowS #
Generic FwdPosition Source #
Instance details 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 Source #
Instance details Defined in Biobase.Types.Position Methods info :: FwdPosition -> String #
NFData FwdPosition Source #
Instance details Defined in Biobase.Types.Position Methods rnf :: FwdPosition -> () #
Reversing FwdPosition Source #	Reversing a reversible location means moving the start to the end.
Instance details Defined in Biobase.Types.Position Methods reversing :: FwdPosition -> FwdPosition #
ModifyLocation FwdPosition Int Source #
Instance details Defined in Biobase.Types.Location Methods locAppendLeft :: forall k (i :: k). Int -> Location i FwdPosition Int -> Location i FwdPosition Int Source # locAppendRight :: forall k (i :: k). Int -> Location i FwdPosition Int -> Location i FwdPosition Int Source # locSplitAt :: forall k (i :: k). Int -> Location i FwdPosition Int -> (Location i FwdPosition Int, Location i FwdPosition Int) Source # locLength :: forall k (i :: k). Location i FwdPosition Int -> Int Source #
ModifyLocation FwdPosition (BioSequence w) Source #
Instance details Defined in Biobase.Types.Location Methods locAppendLeft :: forall k (i :: k). BioSequence w -> Location i FwdPosition (BioSequence w) -> Location i FwdPosition (BioSequence w) Source # locAppendRight :: forall k (i :: k). BioSequence w -> Location i FwdPosition (BioSequence w) -> Location i FwdPosition (BioSequence w) Source # locSplitAt :: forall k (i :: k). Int -> Location i FwdPosition (BioSequence w) -> (Location i FwdPosition (BioSequence w), Location i FwdPosition (BioSequence w)) Source # locLength :: forall k (i :: k). Location i FwdPosition (BioSequence w) -> Int Source #
Info (BioSequence w) => Info (Location i FwdPosition (BioSequence w)) Source #
Instance details Defined in Biobase.Types.Location Methods info :: Location i FwdPosition (BioSequence w) -> String #
Reversing (Location i FwdPosition (BioSequence w)) Source #
Instance details 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)) Source #
Instance details 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)) Source #
Instance details Defined in Biobase.Types.Location Methods complement :: Iso' (Location i FwdPosition (BioSequence w)) (Location i FwdPosition (BioSequence w)) Source #
Complement (BioSequence w) => Complement (PIS i FwdPosition (BioSequence w)) Source #
Instance details Defined in Biobase.Types.Location Methods complement :: Iso' (PIS i FwdPosition (BioSequence w)) (PIS i FwdPosition (BioSequence w)) Source #
type Rep FwdPosition Source #
Instance details 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 Source #

fwdStart :: Lens' FwdPosition (Index 0) Source #

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