Safe Haskell	None
Language	Haskell2010

Biobase.Types.Taxonomy

Description

Biological classification of species.

Synopsis

data Classification
- = Kingdom
- | Phylum
- | Class
- | Order
- | SubOrder
- | Family
- | Genus
- | Species
- | Unknown
data Taxon = Taxon {
- species :: !SpeciesName
- accession :: !(Accession Species)
- classification :: !(Vector (TaxonomicRank, Classification))
}

Documentation

data Classification Source #

Taxonomic classification. Enum together with a final Unknown is somewhat fishy.

TODO What should the order be? Kingdom > Species or Kingdom < Species?

Constructors

Kingdom
Phylum
Class
Order
SubOrder
Family
Genus
Species
Unknown

Instances

Enum Classification Source #
Instance details Defined in Biobase.Types.Taxonomy Methods succ :: Classification -> Classification # pred :: Classification -> Classification # toEnum :: Int -> Classification # fromEnum :: Classification -> Int # enumFrom :: Classification -> [Classification] # enumFromThen :: Classification -> Classification -> [Classification] # enumFromTo :: Classification -> Classification -> [Classification] # enumFromThenTo :: Classification -> Classification -> Classification -> [Classification] #
Eq Classification Source #
Instance details Defined in Biobase.Types.Taxonomy Methods (==) :: Classification -> Classification -> Bool # (/=) :: Classification -> Classification -> Bool #
Ord Classification Source #
Instance details Defined in Biobase.Types.Taxonomy Methods compare :: Classification -> Classification -> Ordering # (<) :: Classification -> Classification -> Bool # (<=) :: Classification -> Classification -> Bool # (>) :: Classification -> Classification -> Bool # (>=) :: Classification -> Classification -> Bool # max :: Classification -> Classification -> Classification # min :: Classification -> Classification -> Classification #
Read Classification Source #
Instance details Defined in Biobase.Types.Taxonomy Methods readsPrec :: Int -> ReadS Classification # readList :: ReadS [Classification] # readPrec :: ReadPrec Classification # readListPrec :: ReadPrec [Classification] #
Show Classification Source #
Instance details Defined in Biobase.Types.Taxonomy Methods showsPrec :: Int -> Classification -> ShowS # show :: Classification -> String # showList :: [Classification] -> ShowS #
Generic Classification Source #
Instance details Defined in Biobase.Types.Taxonomy Associated Types type Rep Classification :: Type -> Type # Methods from :: Classification -> Rep Classification x # to :: Rep Classification x -> Classification #
NFData Classification Source #
Instance details Defined in Biobase.Types.Taxonomy Methods rnf :: Classification -> () #
Hashable Classification Source #
Instance details Defined in Biobase.Types.Taxonomy Methods hashWithSalt :: Int -> Classification -> Int # hash :: Classification -> Int #
ToJSON Classification Source #
Instance details Defined in Biobase.Types.Taxonomy Methods toJSON :: Classification -> Value # toEncoding :: Classification -> Encoding # toJSONList :: [Classification] -> Value # toEncodingList :: [Classification] -> Encoding #
FromJSON Classification Source #
Instance details Defined in Biobase.Types.Taxonomy Methods parseJSON :: Value -> Parser Classification # parseJSONList :: Value -> Parser [Classification] #
Binary Classification Source #
Instance details Defined in Biobase.Types.Taxonomy Methods put :: Classification -> Put # get :: Get Classification # putList :: [Classification] -> Put #
Serialize Classification Source #
Instance details Defined in Biobase.Types.Taxonomy Methods put :: Putter Classification # get :: Get Classification #
Unbox Classification Source #
Instance details Defined in Biobase.Types.Taxonomy
Vector Vector Classification Source #
Instance details Defined in Biobase.Types.Taxonomy Methods basicUnsafeFreeze :: PrimMonad m => Mutable Vector (PrimState m) Classification -> m (Vector Classification) # basicUnsafeThaw :: PrimMonad m => Vector Classification -> m (Mutable Vector (PrimState m) Classification) # basicLength :: Vector Classification -> Int # basicUnsafeSlice :: Int -> Int -> Vector Classification -> Vector Classification # basicUnsafeIndexM :: Monad m => Vector Classification -> Int -> m Classification # basicUnsafeCopy :: PrimMonad m => Mutable Vector (PrimState m) Classification -> Vector Classification -> m () # elemseq :: Vector Classification -> Classification -> b -> b #
MVector MVector Classification Source #
Instance details Defined in Biobase.Types.Taxonomy Methods basicLength :: MVector s Classification -> Int # basicUnsafeSlice :: Int -> Int -> MVector s Classification -> MVector s Classification # basicOverlaps :: MVector s Classification -> MVector s Classification -> Bool # basicUnsafeNew :: PrimMonad m => Int -> m (MVector (PrimState m) Classification) # basicInitialize :: PrimMonad m => MVector (PrimState m) Classification -> m () # basicUnsafeReplicate :: PrimMonad m => Int -> Classification -> m (MVector (PrimState m) Classification) # basicUnsafeRead :: PrimMonad m => MVector (PrimState m) Classification -> Int -> m Classification # basicUnsafeWrite :: PrimMonad m => MVector (PrimState m) Classification -> Int -> Classification -> m () # basicClear :: PrimMonad m => MVector (PrimState m) Classification -> m () # basicSet :: PrimMonad m => MVector (PrimState m) Classification -> Classification -> m () # basicUnsafeCopy :: PrimMonad m => MVector (PrimState m) Classification -> MVector (PrimState m) Classification -> m () # basicUnsafeMove :: PrimMonad m => MVector (PrimState m) Classification -> MVector (PrimState m) Classification -> m () # basicUnsafeGrow :: PrimMonad m => MVector (PrimState m) Classification -> Int -> m (MVector (PrimState m) Classification) #
type Rep Classification Source #
Instance details Defined in Biobase.Types.Taxonomy type Rep Classification = D1 (MetaData "Classification" "Biobase.Types.Taxonomy" "BiobaseTypes-0.2.0.1-B9coIbijR6NEFcCxvqIOZp" False) (((C1 (MetaCons "Kingdom" PrefixI False) (U1 :: Type -> Type) :+: C1 (MetaCons "Phylum" PrefixI False) (U1 :: Type -> Type)) :+: (C1 (MetaCons "Class" PrefixI False) (U1 :: Type -> Type) :+: C1 (MetaCons "Order" PrefixI False) (U1 :: Type -> Type))) :+: ((C1 (MetaCons "SubOrder" PrefixI False) (U1 :: Type -> Type) :+: C1 (MetaCons "Family" PrefixI False) (U1 :: Type -> Type)) :+: (C1 (MetaCons "Genus" PrefixI False) (U1 :: Type -> Type) :+: (C1 (MetaCons "Species" PrefixI False) (U1 :: Type -> Type) :+: C1 (MetaCons "Unknown" PrefixI False) (U1 :: Type -> Type)))))
newtype Vector Classification Source #
Instance details Defined in Biobase.Types.Taxonomy newtype Vector Classification = V_Classification (Vector Int)
newtype MVector s Classification Source #
Instance details Defined in Biobase.Types.Taxonomy newtype MVector s Classification = MV_Classification (MVector s Int)

data Taxon Source #

A somewhat generic representation of a species within a taxonomic context.

Constructors

Taxon
Fields species :: !SpeciesName the full, formal name of a species accession :: !(Accession Species) the accession for the species (or `""` if unknown) classification :: !(Vector (TaxonomicRank, Classification)) vector with classification information

Instances

Eq Taxon Source #
Instance details Defined in Biobase.Types.Taxonomy Methods (==) :: Taxon -> Taxon -> Bool # (/=) :: Taxon -> Taxon -> Bool #
Read Taxon Source #
Instance details Defined in Biobase.Types.Taxonomy Methods readsPrec :: Int -> ReadS Taxon # readList :: ReadS [Taxon] # readPrec :: ReadPrec Taxon # readListPrec :: ReadPrec [Taxon] #
Show Taxon Source #
Instance details Defined in Biobase.Types.Taxonomy Methods showsPrec :: Int -> Taxon -> ShowS # show :: Taxon -> String # showList :: [Taxon] -> ShowS #
Generic Taxon Source #
Instance details Defined in Biobase.Types.Taxonomy Associated Types type Rep Taxon :: Type -> Type # Methods from :: Taxon -> Rep Taxon x # to :: Rep Taxon x -> Taxon #
NFData Taxon Source #
Instance details Defined in Biobase.Types.Taxonomy Methods rnf :: Taxon -> () #
Hashable Taxon Source #
Instance details Defined in Biobase.Types.Taxonomy Methods hashWithSalt :: Int -> Taxon -> Int # hash :: Taxon -> Int #
ToJSON Taxon Source #
Instance details Defined in Biobase.Types.Taxonomy Methods toJSON :: Taxon -> Value # toEncoding :: Taxon -> Encoding # toJSONList :: [Taxon] -> Value # toEncodingList :: [Taxon] -> Encoding #
FromJSON Taxon Source #
Instance details Defined in Biobase.Types.Taxonomy Methods parseJSON :: Value -> Parser Taxon # parseJSONList :: Value -> Parser [Taxon] #
Binary Taxon Source #
Instance details Defined in Biobase.Types.Taxonomy Methods put :: Taxon -> Put # get :: Get Taxon # putList :: [Taxon] -> Put #
Serialize Taxon Source #
Instance details Defined in Biobase.Types.Taxonomy Methods put :: Putter Taxon # get :: Get Taxon #
type Rep Taxon Source #
Instance details Defined in Biobase.Types.Taxonomy type Rep Taxon = D1 (MetaData "Taxon" "Biobase.Types.Taxonomy" "BiobaseTypes-0.2.0.1-B9coIbijR6NEFcCxvqIOZp" False) (C1 (MetaCons "Taxon" PrefixI True) (S1 (MetaSel (Just "species") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 SpeciesName) :: (S1 (MetaSel (Just "accession") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 (Accession Species)) :: S1 (MetaSel (Just "classification") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 (Vector (TaxonomicRank, Classification))))))