Safe Haskell	None
Language	Haskell2010

Bio.Sequence.Range

Synopsis

data Range
- = Point {
  - _location :: Int
  }
- | Span {
  - _lower :: RangeBorder
  - _upper :: RangeBorder
  }
- | Between {
  - _before :: Int
  - _after :: Int
  }
- | Join {
  - _ranges :: [Range]
  }
- | Complement {
  - _range :: Range
  }
data Border
- = Precise
- | Exceeded
data RangeBorder = RangeBorder {
- _borderType :: Border
- _borderLocation :: Int
}
borderType :: Lens' RangeBorder Border
borderLocation :: Lens' RangeBorder Int
location :: Traversal' Range Int
lower :: Traversal' Range RangeBorder
upper :: Traversal' Range RangeBorder
before :: Traversal' Range Int
after :: Traversal' Range Int
ranges :: Traversal' Range [Range]
range :: Traversal' Range Range
checkRange :: Int -> Range -> Bool
shiftRange :: Int -> Range -> Range
mapRange :: (Int -> Int) -> Range -> Range
swapRange :: Range -> Range
point :: Int -> Range
preciseSpan :: (Int, Int) -> Range
between :: (Int, Int) -> Range
extendRight :: Int -> Range -> Range
extendLeft :: Int -> Range -> Range
overlap :: Range -> Range -> Bool
rangeMargins :: Range -> (Int, Int)

Documentation

data Range Source #

Constructors

Point	The exact location of a single base feature Example in GB: conf 258
Fields _location :: Int
Span	A region consisting of a simple span of bases. The symbols `<`and `>` are used to indicate that the beginning or end of the feature is beyond the range of the presented sequence. Examples in GB: tRNA 1..87 tRNA <1..87 tRNA 1..>87
Fields _lower :: RangeBorder _upper :: RangeBorder
Between	The feature is between bases. Example in GB: misc_recomb 105^106
Fields _before :: Int _after :: Int
Join	The feature consists of the union of several ranges. Example in GB: origin join(1, 23..50, 77..>100)
Fields _ranges :: [Range]
Complement	Indicates that the range is complementary. Example in GB: rep complement(69..420)
Fields _range :: Range

Instances

Instances details

Eq Range Source #
Instance details Defined in Bio.Sequence.Range Methods (==) :: Range -> Range -> Bool # (/=) :: Range -> Range -> Bool #
Show Range Source #
Instance details Defined in Bio.Sequence.Range Methods showsPrec :: Int -> Range -> ShowS # show :: Range -> String # showList :: [Range] -> ShowS #
Generic Range Source #
Instance details Defined in Bio.Sequence.Range Associated Types type Rep Range :: Type -> Type # Methods from :: Range -> Rep Range x # to :: Rep Range x -> Range #
NFData Range Source #
Instance details Defined in Bio.Sequence.Range Methods rnf :: Range -> () #
type Rep Range Source #
Instance details Defined in Bio.Sequence.Range type Rep Range = D1 ('MetaData "Range" "Bio.Sequence.Range" "cobot-io-0.1.4.3-FtR1iZLExqtGkRGhoXEUKM" 'False) ((C1 ('MetaCons "Point" 'PrefixI 'True) (S1 ('MetaSel ('Just "_location") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Int)) :+: C1 ('MetaCons "Span" 'PrefixI 'True) (S1 ('MetaSel ('Just "_lower") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 RangeBorder) :: S1 ('MetaSel ('Just "_upper") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 RangeBorder))) :+: (C1 ('MetaCons "Between" 'PrefixI 'True) (S1 ('MetaSel ('Just "_before") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Int) :: S1 ('MetaSel ('Just "_after") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Int)) :+: (C1 ('MetaCons "Join" 'PrefixI 'True) (S1 ('MetaSel ('Just "_ranges") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 [Range])) :+: C1 ('MetaCons "Complement" 'PrefixI 'True) (S1 ('MetaSel ('Just "_range") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Range)))))

data Border Source #

The type of range border. A border is Exceeded when its end point is beyond the specified base number, otherwise it is Precise. In GenBank, for example, Exceeded borders are marked with and.

Constructors

Precise
Exceeded

Instances

Instances details

Eq Border Source #
Instance details Defined in Bio.Sequence.Range Methods (==) :: Border -> Border -> Bool # (/=) :: Border -> Border -> Bool #
Show Border Source #
Instance details Defined in Bio.Sequence.Range Methods showsPrec :: Int -> Border -> ShowS # show :: Border -> String # showList :: [Border] -> ShowS #
Generic Border Source #
Instance details Defined in Bio.Sequence.Range Associated Types type Rep Border :: Type -> Type # Methods from :: Border -> Rep Border x # to :: Rep Border x -> Border #
NFData Border Source #
Instance details Defined in Bio.Sequence.Range Methods rnf :: Border -> () #
type Rep Border Source #
Instance details Defined in Bio.Sequence.Range type Rep Border = D1 ('MetaData "Border" "Bio.Sequence.Range" "cobot-io-0.1.4.3-FtR1iZLExqtGkRGhoXEUKM" 'False) (C1 ('MetaCons "Precise" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Exceeded" 'PrefixI 'False) (U1 :: Type -> Type))

data RangeBorder Source #

The end point of a range with indication whether it is Precise of Exceeded (see Border).

Constructors

RangeBorder
Fields _borderType :: Border _borderLocation :: Int

Instances

Instances details

Eq RangeBorder Source #
Instance details Defined in Bio.Sequence.Range Methods (==) :: RangeBorder -> RangeBorder -> Bool # (/=) :: RangeBorder -> RangeBorder -> Bool #
Show RangeBorder Source #
Instance details Defined in Bio.Sequence.Range Methods showsPrec :: Int -> RangeBorder -> ShowS # show :: RangeBorder -> String # showList :: [RangeBorder] -> ShowS #
Generic RangeBorder Source #
Instance details Defined in Bio.Sequence.Range Associated Types type Rep RangeBorder :: Type -> Type # Methods from :: RangeBorder -> Rep RangeBorder x # to :: Rep RangeBorder x -> RangeBorder #
NFData RangeBorder Source #
Instance details Defined in Bio.Sequence.Range Methods rnf :: RangeBorder -> () #
type Rep RangeBorder Source #
Instance details Defined in Bio.Sequence.Range type Rep RangeBorder = D1 ('MetaData "RangeBorder" "Bio.Sequence.Range" "cobot-io-0.1.4.3-FtR1iZLExqtGkRGhoXEUKM" 'False) (C1 ('MetaCons "RangeBorder" 'PrefixI 'True) (S1 ('MetaSel ('Just "_borderType") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Border) :*: S1 ('MetaSel ('Just "_borderLocation") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Int)))