Biobase.Types.Taxonomy

Biological classification of species.

Documentation

data Classification

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

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

Defined in Biobase.Types.Taxonomy

Methods

(==) :: Classification -> Classification -> Bool

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

Ord Classification

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

Defined in Biobase.Types.Taxonomy

Methods

readsPrec :: Int -> ReadS Classification

readList :: ReadS [Classification]

readPrec :: ReadPrec Classification

readListPrec :: ReadPrec [Classification]

Show Classification

Defined in Biobase.Types.Taxonomy

Methods

showsPrec :: Int -> Classification -> ShowS

show :: Classification -> String

showList :: [Classification] -> ShowS

Generic Classification

Defined in Biobase.Types.Taxonomy

Associated Types

type Rep Classification :: Type -> Type

Methods

from :: Classification -> Rep Classification x

to :: Rep Classification x -> Classification

Hashable Classification

Defined in Biobase.Types.Taxonomy

Methods

hashWithSalt :: Int -> Classification -> Int

hash :: Classification -> Int

ToJSON Classification

Defined in Biobase.Types.Taxonomy

Methods

toJSON :: Classification -> Value

toEncoding :: Classification -> Encoding

toJSONList :: [Classification] -> Value

toEncodingList :: [Classification] -> Encoding

FromJSON Classification

Defined in Biobase.Types.Taxonomy

Methods

parseJSON :: Value -> Parser Classification

parseJSONList :: Value -> Parser [Classification]

Binary Classification

Defined in Biobase.Types.Taxonomy

Methods

put :: Classification -> Put

get :: Get Classification

putList :: [Classification] -> Put

Serialize Classification

Defined in Biobase.Types.Taxonomy

Methods

put :: Putter Classification

get :: Get Classification

NFData Classification

Defined in Biobase.Types.Taxonomy

Methods

rnf :: Classification -> ()

Unbox Classification

Defined in Biobase.Types.Taxonomy

Vector Vector Classification

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

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

Defined in Biobase.Types.Taxonomy

type Rep Classification = D1 ('MetaData "Classification" "Biobase.Types.Taxonomy" "BiobaseTypes-0.2.1.0-KNWEaQoA0aY419BnftjfF1" '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

Defined in Biobase.Types.Taxonomy

newtype Vector Classification = V_Classification (Vector Int)

newtype MVector s Classification

Defined in Biobase.Types.Taxonomy

newtype MVector s Classification = MV_Classification (MVector s Int)

data Taxon

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

Defined in Biobase.Types.Taxonomy

Methods

(==) :: Taxon -> Taxon -> Bool

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

Read Taxon

Defined in Biobase.Types.Taxonomy

Methods

readsPrec :: Int -> ReadS Taxon

readList :: ReadS [Taxon]

readPrec :: ReadPrec Taxon

readListPrec :: ReadPrec [Taxon]

Show Taxon

Defined in Biobase.Types.Taxonomy

Methods

showsPrec :: Int -> Taxon -> ShowS

show :: Taxon -> String

showList :: [Taxon] -> ShowS

Generic Taxon

Defined in Biobase.Types.Taxonomy

Associated Types

type Rep Taxon :: Type -> Type

Methods

from :: Taxon -> Rep Taxon x

to :: Rep Taxon x -> Taxon

Hashable Taxon

Defined in Biobase.Types.Taxonomy

Methods

hashWithSalt :: Int -> Taxon -> Int

hash :: Taxon -> Int

ToJSON Taxon

Defined in Biobase.Types.Taxonomy

Methods

toJSON :: Taxon -> Value

toEncoding :: Taxon -> Encoding

toJSONList :: [Taxon] -> Value

toEncodingList :: [Taxon] -> Encoding

FromJSON Taxon

Defined in Biobase.Types.Taxonomy

Methods

parseJSON :: Value -> Parser Taxon

parseJSONList :: Value -> Parser [Taxon]

Binary Taxon

Defined in Biobase.Types.Taxonomy

Methods

put :: Taxon -> Put

get :: Get Taxon

putList :: [Taxon] -> Put

Serialize Taxon

Defined in Biobase.Types.Taxonomy

Methods

put :: Putter Taxon

get :: Get Taxon

NFData Taxon

Defined in Biobase.Types.Taxonomy

Methods

rnf :: Taxon -> ()

type Rep Taxon

Defined in Biobase.Types.Taxonomy

type Rep Taxon = D1 ('MetaData "Taxon" "Biobase.Types.Taxonomy" "BiobaseTypes-0.2.1.0-KNWEaQoA0aY419BnftjfF1" '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))))))