Safe Haskell	Safe-Inferred
Language	Haskell2010

Poseidon.Janno

Synopsis

data JannoRow = JannoRow {
- jPoseidonID :: String
- jGeneticSex :: JannoSex
- jGroupName :: JannoStringList
- jAlternativeIDs :: Maybe JannoStringList
- jRelationTo :: Maybe JannoStringList
- jRelationDegree :: Maybe JannoRelationDegreeList
- jRelationType :: Maybe JannoStringList
- jRelationNote :: Maybe String
- jCollectionID :: Maybe String
- jCountry :: Maybe String
- jCountryISO :: Maybe JannoCountry
- jLocation :: Maybe String
- jSite :: Maybe String
- jLatitude :: Maybe Latitude
- jLongitude :: Maybe Longitude
- jDateType :: Maybe JannoDateType
- jDateC14Labnr :: Maybe JannoStringList
- jDateC14UncalBP :: Maybe JannoIntList
- jDateC14UncalBPErr :: Maybe JannoIntList
- jDateBCADStart :: Maybe BCADAge
- jDateBCADMedian :: Maybe BCADAge
- jDateBCADStop :: Maybe BCADAge
- jDateNote :: Maybe String
- jMTHaplogroup :: Maybe String
- jYHaplogroup :: Maybe String
- jSourceTissue :: Maybe JannoStringList
- jNrLibraries :: Maybe Int
- jLibraryNames :: Maybe JannoStringList
- jCaptureType :: Maybe (JannoList JannoCaptureType)
- jUDG :: Maybe JannoUDG
- jLibraryBuilt :: Maybe JannoLibraryBuilt
- jGenotypePloidy :: Maybe JannoGenotypePloidy
- jDataPreparationPipelineURL :: Maybe JURI
- jEndogenous :: Maybe Percent
- jNrSNPs :: Maybe Int
- jCoverageOnTargets :: Maybe Double
- jDamage :: Maybe Percent
- jContamination :: Maybe JannoStringList
- jContaminationErr :: Maybe JannoStringList
- jContaminationMeas :: Maybe JannoStringList
- jContaminationNote :: Maybe String
- jGeneticSourceAccessionIDs :: Maybe (JannoList AccessionID)
- jPrimaryContact :: Maybe String
- jPublication :: Maybe JannoStringList
- jComments :: Maybe String
- jKeywords :: Maybe JannoStringList
- jAdditionalColumns :: CsvNamedRecord
}
newtype JannoSex = JannoSex {
- sfSex :: Sex
}
newtype JannoList a = JannoList {
- getJannoList :: [a]
}
data Sex
- = Male
- | Female
- | Unknown
newtype BCADAge = BCADAge Int
newtype JannoCountry = JannoCountry Country
makeJannoCountryUnsafe :: String -> JannoCountry
newtype Latitude = Latitude Double
newtype Longitude = Longitude Double
data JannoDateType
- = C14
- | Contextual
- | Modern
data JannoCaptureType
- = Shotgun
- | A1240K
- | ArborComplete
- | ArborPrimePlus
- | ArborAncestralPlus
- | TwistAncientDNA
- | OtherCapture
- | ReferenceGenome
data JannoGenotypePloidy
- = Diploid
- | Haploid
newtype Percent = Percent Double
data JannoUDG
- = Minus
- | Half
- | Plus
- | Mixed
newtype JURI = JURI String
data RelationDegree
- = Identical
- | First
- | Second
- | ThirdToFifth
- | SixthToTenth
- | Unrelated
- | OtherDegree
data JannoLibraryBuilt
- = DS
- | SS
- | MixedSSDS
- | Other
data AccessionID
- = INSDCProject String
- | INSDCStudy String
- | INSDCBioSample String
- | INSDCSample String
- | INSDCExperiment String
- | INSDCRun String
- | INSDCAnalysis String
- | OtherID String
makeAccessionID :: MonadFail m => String -> m AccessionID
makeLatitude :: MonadFail m => Double -> m Latitude
makeLongitude :: MonadFail m => Double -> m Longitude
writeJannoFile :: FilePath -> JannoRows -> IO ()
readJannoFile :: FilePath -> PoseidonIO JannoRows
createMinimalJanno :: [EigenstratIndEntry] -> JannoRows
createMinimalSample :: EigenstratIndEntry -> JannoRow
jannoHeaderString :: [String]
newtype CsvNamedRecord = CsvNamedRecord NamedRecord
newtype JannoRows = JannoRows [JannoRow]
type JannoStringList = JannoList String
filterLookup :: FromField a => NamedRecord -> ByteString -> Parser a
filterLookupOptional :: FromField a => NamedRecord -> ByteString -> Parser (Maybe a)
getCsvNR :: CsvNamedRecord -> NamedRecord
encodingOptions :: EncodeOptions
decodingOptions :: DecodeOptions
explicitNA :: ByteString -> ByteString
removeUselessSuffix :: String -> String
parseCsvParseError :: Parser CsvParseError
renderCsvParseError :: CsvParseError -> String
getMaybeJannoList :: Maybe (JannoList a) -> [a]

Documentation

data JannoRow Source #

A data type to represent a sample/janno file row See https://github.com/poseidon-framework/poseidon2-schema/blob/master/janno_columns.tsv for more details

Constructors

JannoRow

Fields

jPoseidonID :: String
jGeneticSex :: JannoSex
jGroupName :: JannoStringList
jAlternativeIDs :: Maybe JannoStringList
jRelationTo :: Maybe JannoStringList
jRelationDegree :: Maybe JannoRelationDegreeList
jRelationType :: Maybe JannoStringList
jRelationNote :: Maybe String
jCollectionID :: Maybe String
jCountry :: Maybe String
jCountryISO :: Maybe JannoCountry
jLocation :: Maybe String
jSite :: Maybe String
jLatitude :: Maybe Latitude
jLongitude :: Maybe Longitude
jDateType :: Maybe JannoDateType
jDateC14Labnr :: Maybe JannoStringList
jDateC14UncalBP :: Maybe JannoIntList
jDateC14UncalBPErr :: Maybe JannoIntList
jDateBCADStart :: Maybe BCADAge
jDateBCADMedian :: Maybe BCADAge
jDateBCADStop :: Maybe BCADAge
jDateNote :: Maybe String
jMTHaplogroup :: Maybe String
jYHaplogroup :: Maybe String
jSourceTissue :: Maybe JannoStringList
jNrLibraries :: Maybe Int
jLibraryNames :: Maybe JannoStringList
jCaptureType :: Maybe (JannoList JannoCaptureType)
jUDG :: Maybe JannoUDG
jLibraryBuilt :: Maybe JannoLibraryBuilt
jGenotypePloidy :: Maybe JannoGenotypePloidy
jDataPreparationPipelineURL :: Maybe JURI
jEndogenous :: Maybe Percent
jNrSNPs :: Maybe Int
jCoverageOnTargets :: Maybe Double
jDamage :: Maybe Percent
jContamination :: Maybe JannoStringList
jContaminationErr :: Maybe JannoStringList
jContaminationMeas :: Maybe JannoStringList
jContaminationNote :: Maybe String
jGeneticSourceAccessionIDs :: Maybe (JannoList AccessionID)
jPrimaryContact :: Maybe String
jPublication :: Maybe JannoStringList
jComments :: Maybe String
jKeywords :: Maybe JannoStringList
jAdditionalColumns :: CsvNamedRecord

Instances

Instances details

FromJSON JannoRow Source #
Instance details Defined in Poseidon.Janno Methods parseJSON :: Value -> Parser JannoRow parseJSONList :: Value -> Parser [JannoRow]
ToJSON JannoRow Source #
Instance details Defined in Poseidon.Janno Methods toJSON :: JannoRow -> Value toEncoding :: JannoRow -> Encoding toJSONList :: [JannoRow] -> Value toEncodingList :: [JannoRow] -> Encoding
Generic JannoRow Source #
Instance details Defined in Poseidon.Janno Associated Types type Rep JannoRow :: Type -> Type # Methods from :: JannoRow -> Rep JannoRow x # to :: Rep JannoRow x -> JannoRow #
Show JannoRow Source #
Instance details Defined in Poseidon.Janno Methods showsPrec :: Int -> JannoRow -> ShowS # show :: JannoRow -> String # showList :: [JannoRow] -> ShowS #
DefaultOrdered JannoRow Source #
Instance details Defined in Poseidon.Janno Methods headerOrder :: JannoRow -> Header
FromNamedRecord JannoRow Source #
Instance details Defined in Poseidon.Janno Methods parseNamedRecord :: NamedRecord -> Parser JannoRow
ToNamedRecord JannoRow Source #
Instance details Defined in Poseidon.Janno Methods toNamedRecord :: JannoRow -> NamedRecord
Generic JannoRow Source #
Instance details Defined in Poseidon.Janno Associated Types type Code JannoRow :: [[Type]] Methods from :: JannoRow -> Rep JannoRow to :: Rep JannoRow -> JannoRow
HasDatatypeInfo JannoRow Source #
Instance details Defined in Poseidon.Janno Associated Types type DatatypeInfoOf JannoRow :: DatatypeInfo Methods datatypeInfo :: proxy JannoRow -> DatatypeInfo (Code JannoRow)
Eq JannoRow Source #
Instance details Defined in Poseidon.Janno Methods (==) :: JannoRow -> JannoRow -> Bool # (/=) :: JannoRow -> JannoRow -> Bool #
type Rep JannoRow Source #
Instance details Defined in Poseidon.Janno type Rep JannoRow
type Code JannoRow Source #
Instance details Defined in Poseidon.Janno type Code JannoRow
type DatatypeInfoOf JannoRow Source #
Instance details Defined in Poseidon.Janno type DatatypeInfoOf JannoRow = 'ADT "Poseidon.Janno" "JannoRow" '['Record "JannoRow" '['FieldInfo "jPoseidonID", 'FieldInfo "jGeneticSex", 'FieldInfo "jGroupName", 'FieldInfo "jAlternativeIDs", 'FieldInfo "jRelationTo", 'FieldInfo "jRelationDegree", 'FieldInfo "jRelationType", 'FieldInfo "jRelationNote", 'FieldInfo "jCollectionID", 'FieldInfo "jCountry", 'FieldInfo "jCountryISO", 'FieldInfo "jLocation", 'FieldInfo "jSite", 'FieldInfo "jLatitude", 'FieldInfo "jLongitude", 'FieldInfo "jDateType", 'FieldInfo "jDateC14Labnr", 'FieldInfo "jDateC14UncalBP", 'FieldInfo "jDateC14UncalBPErr", 'FieldInfo "jDateBCADStart", 'FieldInfo "jDateBCADMedian", 'FieldInfo "jDateBCADStop", 'FieldInfo "jDateNote", 'FieldInfo "jMTHaplogroup", 'FieldInfo "jYHaplogroup", 'FieldInfo "jSourceTissue", 'FieldInfo "jNrLibraries", 'FieldInfo "jLibraryNames", 'FieldInfo "jCaptureType", 'FieldInfo "jUDG", 'FieldInfo "jLibraryBuilt", 'FieldInfo "jGenotypePloidy", 'FieldInfo "jDataPreparationPipelineURL", 'FieldInfo "jEndogenous", 'FieldInfo "jNrSNPs", 'FieldInfo "jCoverageOnTargets", 'FieldInfo "jDamage", 'FieldInfo "jContamination", 'FieldInfo "jContaminationErr", 'FieldInfo "jContaminationMeas", 'FieldInfo "jContaminationNote", 'FieldInfo "jGeneticSourceAccessionIDs", 'FieldInfo "jPrimaryContact", 'FieldInfo "jPublication", 'FieldInfo "jComments", 'FieldInfo "jKeywords", 'FieldInfo "jAdditionalColumns"]] '['['StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy]]

newtype JannoSex Source #

A datatype for genetic sex

Constructors

JannoSex
Fields sfSex :: Sex

Instances

Instances details

FromJSON JannoSex Source #
Instance details Defined in Poseidon.Janno Methods parseJSON :: Value -> Parser JannoSex parseJSONList :: Value -> Parser [JannoSex]
ToJSON JannoSex Source #
Instance details Defined in Poseidon.Janno Methods toJSON :: JannoSex -> Value toEncoding :: JannoSex -> Encoding toJSONList :: [JannoSex] -> Value toEncodingList :: [JannoSex] -> Encoding
Show JannoSex Source #
Instance details Defined in Poseidon.Janno Methods showsPrec :: Int -> JannoSex -> ShowS # show :: JannoSex -> String # showList :: [JannoSex] -> ShowS #
FromField JannoSex Source #
Instance details Defined in Poseidon.Janno Methods parseField :: Field -> Parser JannoSex
ToField JannoSex Source #
Instance details Defined in Poseidon.Janno Methods toField :: JannoSex -> Field
Eq JannoSex Source #
Instance details Defined in Poseidon.Janno Methods (==) :: JannoSex -> JannoSex -> Bool # (/=) :: JannoSex -> JannoSex -> Bool #
Ord JannoSex Source #
Instance details Defined in Poseidon.Janno Methods compare :: JannoSex -> JannoSex -> Ordering # (<) :: JannoSex -> JannoSex -> Bool # (<=) :: JannoSex -> JannoSex -> Bool # (>) :: JannoSex -> JannoSex -> Bool # (>=) :: JannoSex -> JannoSex -> Bool # max :: JannoSex -> JannoSex -> JannoSex # min :: JannoSex -> JannoSex -> JannoSex #
PresenceCountable JannoSex Source #
Instance details Defined in Poseidon.CLI.Survey Methods countPresence :: JannoSex -> Int Source #

newtype JannoList a Source #

A general datatype for janno list columns

Constructors

JannoList
Fields getJannoList :: [a]

Instances

Instances details

PresenceCountable JannoStringList Source #
Instance details Defined in Poseidon.CLI.Survey Methods countPresence :: JannoStringList -> Int Source #
FromJSON a => FromJSON (JannoList a) Source #
Instance details Defined in Poseidon.Janno Methods parseJSON :: Value -> Parser (JannoList a) parseJSONList :: Value -> Parser [JannoList a]
ToJSON a => ToJSON (JannoList a) Source #
Instance details Defined in Poseidon.Janno Methods toJSON :: JannoList a -> Value toEncoding :: JannoList a -> Encoding toJSONList :: [JannoList a] -> Value toEncodingList :: [JannoList a] -> Encoding
Generic (JannoList a) Source #
Instance details Defined in Poseidon.Janno Associated Types type Rep (JannoList a) :: Type -> Type # Methods from :: JannoList a -> Rep (JannoList a) x # to :: Rep (JannoList a) x -> JannoList a #
Show a => Show (JannoList a) Source #
Instance details Defined in Poseidon.Janno Methods showsPrec :: Int -> JannoList a -> ShowS # show :: JannoList a -> String # showList :: [JannoList a] -> ShowS #
FromField a => FromField (JannoList a) Source #
Instance details Defined in Poseidon.Janno Methods parseField :: Field -> Parser (JannoList a)
(ToField a, Show a) => ToField (JannoList a) Source #
Instance details Defined in Poseidon.Janno Methods toField :: JannoList a -> Field
Eq a => Eq (JannoList a) Source #
Instance details Defined in Poseidon.Janno Methods (==) :: JannoList a -> JannoList a -> Bool # (/=) :: JannoList a -> JannoList a -> Bool #
Ord a => Ord (JannoList a) Source #
Instance details Defined in Poseidon.Janno Methods compare :: JannoList a -> JannoList a -> Ordering # (<) :: JannoList a -> JannoList a -> Bool # (<=) :: JannoList a -> JannoList a -> Bool # (>) :: JannoList a -> JannoList a -> Bool # (>=) :: JannoList a -> JannoList a -> Bool # max :: JannoList a -> JannoList a -> JannoList a # min :: JannoList a -> JannoList a -> JannoList a #
type Rep (JannoList a) Source #
Instance details Defined in Poseidon.Janno type Rep (JannoList a) = D1 ('MetaData "JannoList" "Poseidon.Janno" "poseidon-hs-1.5.5.0-64IxIR1JUiELWCZhD8ICmR" 'True) (C1 ('MetaCons "JannoList" 'PrefixI 'True) (S1 ('MetaSel ('Just "getJannoList") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 [a])))

data Sex #

Constructors

Male
Female
Unknown

Instances

Instances details

Show Sex
Instance details Defined in SequenceFormats.Eigenstrat Methods showsPrec :: Int -> Sex -> ShowS # show :: Sex -> String # showList :: [Sex] -> ShowS #
Eq Sex
Instance details Defined in SequenceFormats.Eigenstrat Methods (==) :: Sex -> Sex -> Bool # (/=) :: Sex -> Sex -> Bool #

newtype BCADAge Source #

A datatype for BC-AD ages

Constructors

BCADAge Int

Instances

Instances details

FromJSON BCADAge Source #
Instance details Defined in Poseidon.Janno Methods parseJSON :: Value -> Parser BCADAge parseJSONList :: Value -> Parser [BCADAge]
ToJSON BCADAge Source #
Instance details Defined in Poseidon.Janno Methods toJSON :: BCADAge -> Value toEncoding :: BCADAge -> Encoding toJSONList :: [BCADAge] -> Value toEncodingList :: [BCADAge] -> Encoding
Generic BCADAge Source #
Instance details Defined in Poseidon.Janno Associated Types type Rep BCADAge :: Type -> Type # Methods from :: BCADAge -> Rep BCADAge x # to :: Rep BCADAge x -> BCADAge #
Show BCADAge Source #
Instance details Defined in Poseidon.Janno Methods showsPrec :: Int -> BCADAge -> ShowS # show :: BCADAge -> String # showList :: [BCADAge] -> ShowS #
FromField BCADAge Source #
Instance details Defined in Poseidon.Janno Methods parseField :: Field -> Parser BCADAge
ToField BCADAge Source #
Instance details Defined in Poseidon.Janno Methods toField :: BCADAge -> Field
Eq BCADAge Source #
Instance details Defined in Poseidon.Janno Methods (==) :: BCADAge -> BCADAge -> Bool # (/=) :: BCADAge -> BCADAge -> Bool #
Ord BCADAge Source #
Instance details Defined in Poseidon.Janno Methods compare :: BCADAge -> BCADAge -> Ordering # (<) :: BCADAge -> BCADAge -> Bool # (<=) :: BCADAge -> BCADAge -> Bool # (>) :: BCADAge -> BCADAge -> Bool # (>=) :: BCADAge -> BCADAge -> Bool # max :: BCADAge -> BCADAge -> BCADAge # min :: BCADAge -> BCADAge -> BCADAge #
type Rep BCADAge Source #
Instance details Defined in Poseidon.Janno type Rep BCADAge = D1 ('MetaData "BCADAge" "Poseidon.Janno" "poseidon-hs-1.5.5.0-64IxIR1JUiELWCZhD8ICmR" 'True) (C1 ('MetaCons "BCADAge" 'PrefixI 'False) (S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Int)))

newtype JannoCountry Source #

A datatype for countries in ISO-alpha2 code format

Constructors

JannoCountry Country

Instances

Instances details

FromJSON JannoCountry Source #
Instance details Defined in Poseidon.Janno Methods parseJSON :: Value -> Parser JannoCountry parseJSONList :: Value -> Parser [JannoCountry]
ToJSON JannoCountry Source #
Instance details Defined in Poseidon.Janno Methods toJSON :: JannoCountry -> Value toEncoding :: JannoCountry -> Encoding toJSONList :: [JannoCountry] -> Value toEncodingList :: [JannoCountry] -> Encoding
Show JannoCountry Source #
Instance details Defined in Poseidon.Janno Methods showsPrec :: Int -> JannoCountry -> ShowS # show :: JannoCountry -> String # showList :: [JannoCountry] -> ShowS #
FromField JannoCountry Source #
Instance details Defined in Poseidon.Janno Methods parseField :: Field -> Parser JannoCountry
ToField JannoCountry Source #
Instance details Defined in Poseidon.Janno Methods toField :: JannoCountry -> Field
Eq JannoCountry Source #
Instance details Defined in Poseidon.Janno Methods (==) :: JannoCountry -> JannoCountry -> Bool # (/=) :: JannoCountry -> JannoCountry -> Bool #
Ord JannoCountry Source #
Instance details Defined in Poseidon.Janno Methods compare :: JannoCountry -> JannoCountry -> Ordering # (<) :: JannoCountry -> JannoCountry -> Bool # (<=) :: JannoCountry -> JannoCountry -> Bool # (>) :: JannoCountry -> JannoCountry -> Bool # (>=) :: JannoCountry -> JannoCountry -> Bool # max :: JannoCountry -> JannoCountry -> JannoCountry # min :: JannoCountry -> JannoCountry -> JannoCountry #

makeJannoCountryUnsafe :: String -> JannoCountry Source #

newtype Latitude Source #

A datatype for Latitudes

Constructors

Latitude Double

Instances

Instances details

FromJSON Latitude Source #
Instance details Defined in Poseidon.Janno Methods parseJSON :: Value -> Parser Latitude parseJSONList :: Value -> Parser [Latitude]
ToJSON Latitude Source #
Instance details Defined in Poseidon.Janno Methods toJSON :: Latitude -> Value toEncoding :: Latitude -> Encoding toJSONList :: [Latitude] -> Value toEncodingList :: [Latitude] -> Encoding
Generic Latitude Source #
Instance details Defined in Poseidon.Janno Associated Types type Rep Latitude :: Type -> Type # Methods from :: Latitude -> Rep Latitude x # to :: Rep Latitude x -> Latitude #
Show Latitude Source #
Instance details Defined in Poseidon.Janno Methods showsPrec :: Int -> Latitude -> ShowS # show :: Latitude -> String # showList :: [Latitude] -> ShowS #
FromField Latitude Source #
Instance details Defined in Poseidon.Janno Methods parseField :: Field -> Parser Latitude
ToField Latitude Source #
Instance details Defined in Poseidon.Janno Methods toField :: Latitude -> Field
Eq Latitude Source #
Instance details Defined in Poseidon.Janno Methods (==) :: Latitude -> Latitude -> Bool # (/=) :: Latitude -> Latitude -> Bool #
Ord Latitude Source #
Instance details Defined in Poseidon.Janno Methods compare :: Latitude -> Latitude -> Ordering # (<) :: Latitude -> Latitude -> Bool # (<=) :: Latitude -> Latitude -> Bool # (>) :: Latitude -> Latitude -> Bool # (>=) :: Latitude -> Latitude -> Bool # max :: Latitude -> Latitude -> Latitude # min :: Latitude -> Latitude -> Latitude #
type Rep Latitude Source #
Instance details Defined in Poseidon.Janno type Rep Latitude = D1 ('MetaData "Latitude" "Poseidon.Janno" "poseidon-hs-1.5.5.0-64IxIR1JUiELWCZhD8ICmR" 'True) (C1 ('MetaCons "Latitude" 'PrefixI 'False) (S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Double)))

newtype Longitude Source #

A datatype for Longitudes

Constructors

Longitude Double

Instances

Instances details

FromJSON Longitude Source #
Instance details Defined in Poseidon.Janno Methods parseJSON :: Value -> Parser Longitude parseJSONList :: Value -> Parser [Longitude]
ToJSON Longitude Source #
Instance details Defined in Poseidon.Janno Methods toJSON :: Longitude -> Value toEncoding :: Longitude -> Encoding toJSONList :: [Longitude] -> Value toEncodingList :: [Longitude] -> Encoding
Generic Longitude Source #
Instance details Defined in Poseidon.Janno Associated Types type Rep Longitude :: Type -> Type # Methods from :: Longitude -> Rep Longitude x # to :: Rep Longitude x -> Longitude #
Show Longitude Source #
Instance details Defined in Poseidon.Janno Methods showsPrec :: Int -> Longitude -> ShowS # show :: Longitude -> String # showList :: [Longitude] -> ShowS #
FromField Longitude Source #
Instance details Defined in Poseidon.Janno Methods parseField :: Field -> Parser Longitude
ToField Longitude Source #
Instance details Defined in Poseidon.Janno Methods toField :: Longitude -> Field
Eq Longitude Source #
Instance details Defined in Poseidon.Janno Methods (==) :: Longitude -> Longitude -> Bool # (/=) :: Longitude -> Longitude -> Bool #
Ord Longitude Source #
Instance details Defined in Poseidon.Janno Methods compare :: Longitude -> Longitude -> Ordering # (<) :: Longitude -> Longitude -> Bool # (<=) :: Longitude -> Longitude -> Bool # (>) :: Longitude -> Longitude -> Bool # (>=) :: Longitude -> Longitude -> Bool # max :: Longitude -> Longitude -> Longitude # min :: Longitude -> Longitude -> Longitude #
type Rep Longitude Source #
Instance details Defined in Poseidon.Janno type Rep Longitude = D1 ('MetaData "Longitude" "Poseidon.Janno" "poseidon-hs-1.5.5.0-64IxIR1JUiELWCZhD8ICmR" 'True) (C1 ('MetaCons "Longitude" 'PrefixI 'False) (S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Double)))

data JannoDateType Source #

A datatype to represent Date_Type in a janno file

Constructors

C14
Contextual
Modern

Instances

Instances details

FromJSON JannoDateType Source #
Instance details Defined in Poseidon.Janno Methods parseJSON :: Value -> Parser JannoDateType parseJSONList :: Value -> Parser [JannoDateType]
ToJSON JannoDateType Source #
Instance details Defined in Poseidon.Janno Methods toJSON :: JannoDateType -> Value toEncoding :: JannoDateType -> Encoding toJSONList :: [JannoDateType] -> Value toEncodingList :: [JannoDateType] -> Encoding
Bounded JannoDateType Source #
Instance details Defined in Poseidon.Janno Methods minBound :: JannoDateType # maxBound :: JannoDateType #
Enum JannoDateType Source #
Instance details Defined in Poseidon.Janno Methods succ :: JannoDateType -> JannoDateType # pred :: JannoDateType -> JannoDateType # toEnum :: Int -> JannoDateType # fromEnum :: JannoDateType -> Int # enumFrom :: JannoDateType -> [JannoDateType] # enumFromThen :: JannoDateType -> JannoDateType -> [JannoDateType] # enumFromTo :: JannoDateType -> JannoDateType -> [JannoDateType] # enumFromThenTo :: JannoDateType -> JannoDateType -> JannoDateType -> [JannoDateType] #
Generic JannoDateType Source #
Instance details Defined in Poseidon.Janno Associated Types type Rep JannoDateType :: Type -> Type # Methods from :: JannoDateType -> Rep JannoDateType x # to :: Rep JannoDateType x -> JannoDateType #
Show JannoDateType Source #
Instance details Defined in Poseidon.Janno Methods showsPrec :: Int -> JannoDateType -> ShowS # show :: JannoDateType -> String # showList :: [JannoDateType] -> ShowS #
FromField JannoDateType Source #
Instance details Defined in Poseidon.Janno Methods parseField :: Field -> Parser JannoDateType
ToField JannoDateType Source #
Instance details Defined in Poseidon.Janno Methods toField :: JannoDateType -> Field
Eq JannoDateType Source #
Instance details Defined in Poseidon.Janno Methods (==) :: JannoDateType -> JannoDateType -> Bool # (/=) :: JannoDateType -> JannoDateType -> Bool #
Ord JannoDateType Source #
Instance details Defined in Poseidon.Janno Methods compare :: JannoDateType -> JannoDateType -> Ordering # (<) :: JannoDateType -> JannoDateType -> Bool # (<=) :: JannoDateType -> JannoDateType -> Bool # (>) :: JannoDateType -> JannoDateType -> Bool # (>=) :: JannoDateType -> JannoDateType -> Bool # max :: JannoDateType -> JannoDateType -> JannoDateType # min :: JannoDateType -> JannoDateType -> JannoDateType #
type Rep JannoDateType Source #
Instance details Defined in Poseidon.Janno type Rep JannoDateType = D1 ('MetaData "JannoDateType" "Poseidon.Janno" "poseidon-hs-1.5.5.0-64IxIR1JUiELWCZhD8ICmR" 'False) (C1 ('MetaCons "C14" 'PrefixI 'False) (U1 :: Type -> Type) :+: (C1 ('MetaCons "Contextual" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Modern" 'PrefixI 'False) (U1 :: Type -> Type)))

data JannoCaptureType Source #

A datatype to represent Capture_Type in a janno file

Constructors

Shotgun
A1240K
ArborComplete
ArborPrimePlus
ArborAncestralPlus
TwistAncientDNA
OtherCapture
ReferenceGenome

Instances

Instances details

FromJSON JannoCaptureType Source #
Instance details Defined in Poseidon.Janno Methods parseJSON :: Value -> Parser JannoCaptureType parseJSONList :: Value -> Parser [JannoCaptureType]
ToJSON JannoCaptureType Source #
Instance details Defined in Poseidon.Janno Methods toJSON :: JannoCaptureType -> Value toEncoding :: JannoCaptureType -> Encoding toJSONList :: [JannoCaptureType] -> Value toEncodingList :: [JannoCaptureType] -> Encoding
Bounded JannoCaptureType Source #
Instance details Defined in Poseidon.Janno Methods minBound :: JannoCaptureType # maxBound :: JannoCaptureType #
Enum JannoCaptureType Source #
Instance details Defined in Poseidon.Janno Methods succ :: JannoCaptureType -> JannoCaptureType # pred :: JannoCaptureType -> JannoCaptureType # toEnum :: Int -> JannoCaptureType # fromEnum :: JannoCaptureType -> Int # enumFrom :: JannoCaptureType -> [JannoCaptureType] # enumFromThen :: JannoCaptureType -> JannoCaptureType -> [JannoCaptureType] # enumFromTo :: JannoCaptureType -> JannoCaptureType -> [JannoCaptureType] # enumFromThenTo :: JannoCaptureType -> JannoCaptureType -> JannoCaptureType -> [JannoCaptureType] #
Generic JannoCaptureType Source #
Instance details Defined in Poseidon.Janno Associated Types type Rep JannoCaptureType :: Type -> Type # Methods from :: JannoCaptureType -> Rep JannoCaptureType x # to :: Rep JannoCaptureType x -> JannoCaptureType #
Show JannoCaptureType Source #
Instance details Defined in Poseidon.Janno Methods showsPrec :: Int -> JannoCaptureType -> ShowS # show :: JannoCaptureType -> String # showList :: [JannoCaptureType] -> ShowS #
FromField JannoCaptureType Source #
Instance details Defined in Poseidon.Janno Methods parseField :: Field -> Parser JannoCaptureType
ToField JannoCaptureType Source #
Instance details Defined in Poseidon.Janno Methods toField :: JannoCaptureType -> Field
Eq JannoCaptureType Source #
Instance details Defined in Poseidon.Janno Methods (==) :: JannoCaptureType -> JannoCaptureType -> Bool # (/=) :: JannoCaptureType -> JannoCaptureType -> Bool #
Ord JannoCaptureType Source #
Instance details Defined in Poseidon.Janno Methods compare :: JannoCaptureType -> JannoCaptureType -> Ordering # (<) :: JannoCaptureType -> JannoCaptureType -> Bool # (<=) :: JannoCaptureType -> JannoCaptureType -> Bool # (>) :: JannoCaptureType -> JannoCaptureType -> Bool # (>=) :: JannoCaptureType -> JannoCaptureType -> Bool # max :: JannoCaptureType -> JannoCaptureType -> JannoCaptureType # min :: JannoCaptureType -> JannoCaptureType -> JannoCaptureType #
type Rep JannoCaptureType Source #
Instance details Defined in Poseidon.Janno type Rep JannoCaptureType = D1 ('MetaData "JannoCaptureType" "Poseidon.Janno" "poseidon-hs-1.5.5.0-64IxIR1JUiELWCZhD8ICmR" 'False) (((C1 ('MetaCons "Shotgun" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "A1240K" 'PrefixI 'False) (U1 :: Type -> Type)) :+: (C1 ('MetaCons "ArborComplete" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "ArborPrimePlus" 'PrefixI 'False) (U1 :: Type -> Type))) :+: ((C1 ('MetaCons "ArborAncestralPlus" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "TwistAncientDNA" 'PrefixI 'False) (U1 :: Type -> Type)) :+: (C1 ('MetaCons "OtherCapture" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "ReferenceGenome" 'PrefixI 'False) (U1 :: Type -> Type))))

data JannoGenotypePloidy Source #

A datatype to represent Genotype_Ploidy in a janno file

Constructors

Diploid
Haploid

Instances

Instances details

FromJSON JannoGenotypePloidy Source #
Instance details Defined in Poseidon.Janno Methods parseJSON :: Value -> Parser JannoGenotypePloidy parseJSONList :: Value -> Parser [JannoGenotypePloidy]
ToJSON JannoGenotypePloidy Source #
Instance details Defined in Poseidon.Janno Methods toJSON :: JannoGenotypePloidy -> Value toEncoding :: JannoGenotypePloidy -> Encoding toJSONList :: [JannoGenotypePloidy] -> Value toEncodingList :: [JannoGenotypePloidy] -> Encoding
Bounded JannoGenotypePloidy Source #
Instance details Defined in Poseidon.Janno Methods minBound :: JannoGenotypePloidy # maxBound :: JannoGenotypePloidy #
Enum JannoGenotypePloidy Source #
Instance details Defined in Poseidon.Janno Methods succ :: JannoGenotypePloidy -> JannoGenotypePloidy # pred :: JannoGenotypePloidy -> JannoGenotypePloidy # toEnum :: Int -> JannoGenotypePloidy # fromEnum :: JannoGenotypePloidy -> Int # enumFrom :: JannoGenotypePloidy -> [JannoGenotypePloidy] # enumFromThen :: JannoGenotypePloidy -> JannoGenotypePloidy -> [JannoGenotypePloidy] # enumFromTo :: JannoGenotypePloidy -> JannoGenotypePloidy -> [JannoGenotypePloidy] # enumFromThenTo :: JannoGenotypePloidy -> JannoGenotypePloidy -> JannoGenotypePloidy -> [JannoGenotypePloidy] #
Generic JannoGenotypePloidy Source #
Instance details Defined in Poseidon.Janno Associated Types type Rep JannoGenotypePloidy :: Type -> Type # Methods from :: JannoGenotypePloidy -> Rep JannoGenotypePloidy x # to :: Rep JannoGenotypePloidy x -> JannoGenotypePloidy #
Show JannoGenotypePloidy Source #
Instance details Defined in Poseidon.Janno Methods showsPrec :: Int -> JannoGenotypePloidy -> ShowS # show :: JannoGenotypePloidy -> String # showList :: [JannoGenotypePloidy] -> ShowS #
FromField JannoGenotypePloidy Source #
Instance details Defined in Poseidon.Janno Methods parseField :: Field -> Parser JannoGenotypePloidy
ToField JannoGenotypePloidy Source #
Instance details Defined in Poseidon.Janno Methods toField :: JannoGenotypePloidy -> Field
Eq JannoGenotypePloidy Source #
Instance details Defined in Poseidon.Janno Methods (==) :: JannoGenotypePloidy -> JannoGenotypePloidy -> Bool # (/=) :: JannoGenotypePloidy -> JannoGenotypePloidy -> Bool #
Ord JannoGenotypePloidy Source #
Instance details Defined in Poseidon.Janno Methods compare :: JannoGenotypePloidy -> JannoGenotypePloidy -> Ordering # (<) :: JannoGenotypePloidy -> JannoGenotypePloidy -> Bool # (<=) :: JannoGenotypePloidy -> JannoGenotypePloidy -> Bool # (>) :: JannoGenotypePloidy -> JannoGenotypePloidy -> Bool # (>=) :: JannoGenotypePloidy -> JannoGenotypePloidy -> Bool # max :: JannoGenotypePloidy -> JannoGenotypePloidy -> JannoGenotypePloidy # min :: JannoGenotypePloidy -> JannoGenotypePloidy -> JannoGenotypePloidy #
type Rep JannoGenotypePloidy Source #
Instance details Defined in Poseidon.Janno type Rep JannoGenotypePloidy = D1 ('MetaData "JannoGenotypePloidy" "Poseidon.Janno" "poseidon-hs-1.5.5.0-64IxIR1JUiELWCZhD8ICmR" 'False) (C1 ('MetaCons "Diploid" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Haploid" 'PrefixI 'False) (U1 :: Type -> Type))

newtype Percent Source #

A datatype for Percent values

Constructors

Percent Double

Instances

Instances details

FromJSON Percent Source #
Instance details Defined in Poseidon.Janno Methods parseJSON :: Value -> Parser Percent parseJSONList :: Value -> Parser [Percent]
ToJSON Percent Source #
Instance details Defined in Poseidon.Janno Methods toJSON :: Percent -> Value toEncoding :: Percent -> Encoding toJSONList :: [Percent] -> Value toEncodingList :: [Percent] -> Encoding
Generic Percent Source #
Instance details Defined in Poseidon.Janno Associated Types type Rep Percent :: Type -> Type # Methods from :: Percent -> Rep Percent x # to :: Rep Percent x -> Percent #
Show Percent Source #
Instance details Defined in Poseidon.Janno Methods showsPrec :: Int -> Percent -> ShowS # show :: Percent -> String # showList :: [Percent] -> ShowS #
FromField Percent Source #
Instance details Defined in Poseidon.Janno Methods parseField :: Field -> Parser Percent
ToField Percent Source #
Instance details Defined in Poseidon.Janno Methods toField :: Percent -> Field
Eq Percent Source #
Instance details Defined in Poseidon.Janno Methods (==) :: Percent -> Percent -> Bool # (/=) :: Percent -> Percent -> Bool #
Ord Percent Source #
Instance details Defined in Poseidon.Janno Methods compare :: Percent -> Percent -> Ordering # (<) :: Percent -> Percent -> Bool # (<=) :: Percent -> Percent -> Bool # (>) :: Percent -> Percent -> Bool # (>=) :: Percent -> Percent -> Bool # max :: Percent -> Percent -> Percent # min :: Percent -> Percent -> Percent #
type Rep Percent Source #
Instance details Defined in Poseidon.Janno type Rep Percent = D1 ('MetaData "Percent" "Poseidon.Janno" "poseidon-hs-1.5.5.0-64IxIR1JUiELWCZhD8ICmR" 'True) (C1 ('MetaCons "Percent" 'PrefixI 'False) (S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Double)))

data JannoUDG Source #

A datatype to represent UDG in a janno file

Constructors

Minus
Half
Plus
Mixed

Instances

Instances details

FromJSON JannoUDG Source #
Instance details Defined in Poseidon.Janno Methods parseJSON :: Value -> Parser JannoUDG parseJSONList :: Value -> Parser [JannoUDG]
ToJSON JannoUDG Source #
Instance details Defined in Poseidon.Janno Methods toJSON :: JannoUDG -> Value toEncoding :: JannoUDG -> Encoding toJSONList :: [JannoUDG] -> Value toEncodingList :: [JannoUDG] -> Encoding
Bounded JannoUDG Source #
Instance details Defined in Poseidon.Janno Methods minBound :: JannoUDG # maxBound :: JannoUDG #
Enum JannoUDG Source #
Instance details Defined in Poseidon.Janno Methods succ :: JannoUDG -> JannoUDG # pred :: JannoUDG -> JannoUDG # toEnum :: Int -> JannoUDG # fromEnum :: JannoUDG -> Int # enumFrom :: JannoUDG -> [JannoUDG] # enumFromThen :: JannoUDG -> JannoUDG -> [JannoUDG] # enumFromTo :: JannoUDG -> JannoUDG -> [JannoUDG] # enumFromThenTo :: JannoUDG -> JannoUDG -> JannoUDG -> [JannoUDG] #
Generic JannoUDG Source #
Instance details Defined in Poseidon.Janno Associated Types type Rep JannoUDG :: Type -> Type # Methods from :: JannoUDG -> Rep JannoUDG x # to :: Rep JannoUDG x -> JannoUDG #
Show JannoUDG Source #
Instance details Defined in Poseidon.Janno Methods showsPrec :: Int -> JannoUDG -> ShowS # show :: JannoUDG -> String # showList :: [JannoUDG] -> ShowS #
FromField JannoUDG Source #
Instance details Defined in Poseidon.Janno Methods parseField :: Field -> Parser JannoUDG
ToField JannoUDG Source #
Instance details Defined in Poseidon.Janno Methods toField :: JannoUDG -> Field
Eq JannoUDG Source #
Instance details Defined in Poseidon.Janno Methods (==) :: JannoUDG -> JannoUDG -> Bool # (/=) :: JannoUDG -> JannoUDG -> Bool #
Ord JannoUDG Source #
Instance details Defined in Poseidon.Janno Methods compare :: JannoUDG -> JannoUDG -> Ordering # (<) :: JannoUDG -> JannoUDG -> Bool # (<=) :: JannoUDG -> JannoUDG -> Bool # (>) :: JannoUDG -> JannoUDG -> Bool # (>=) :: JannoUDG -> JannoUDG -> Bool # max :: JannoUDG -> JannoUDG -> JannoUDG # min :: JannoUDG -> JannoUDG -> JannoUDG #
type Rep JannoUDG Source #
Instance details Defined in Poseidon.Janno type Rep JannoUDG = D1 ('MetaData "JannoUDG" "Poseidon.Janno" "poseidon-hs-1.5.5.0-64IxIR1JUiELWCZhD8ICmR" 'False) ((C1 ('MetaCons "Minus" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Half" 'PrefixI 'False) (U1 :: Type -> Type)) :+: (C1 ('MetaCons "Plus" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Mixed" 'PrefixI 'False) (U1 :: Type -> Type)))

newtype JURI Source #

A datatype to represent URIs in a janno file

Constructors

JURI String

Instances

Instances details

FromJSON JURI Source #
Instance details Defined in Poseidon.Janno Methods parseJSON :: Value -> Parser JURI parseJSONList :: Value -> Parser [JURI]
ToJSON JURI Source #
Instance details Defined in Poseidon.Janno Methods toJSON :: JURI -> Value toEncoding :: JURI -> Encoding toJSONList :: [JURI] -> Value toEncodingList :: [JURI] -> Encoding
Generic JURI Source #
Instance details Defined in Poseidon.Janno Associated Types type Rep JURI :: Type -> Type # Methods from :: JURI -> Rep JURI x # to :: Rep JURI x -> JURI #
Show JURI Source #
Instance details Defined in Poseidon.Janno Methods showsPrec :: Int -> JURI -> ShowS # show :: JURI -> String # showList :: [JURI] -> ShowS #
FromField JURI Source #
Instance details Defined in Poseidon.Janno Methods parseField :: Field -> Parser JURI
ToField JURI Source #
Instance details Defined in Poseidon.Janno Methods toField :: JURI -> Field
Eq JURI Source #
Instance details Defined in Poseidon.Janno Methods (==) :: JURI -> JURI -> Bool # (/=) :: JURI -> JURI -> Bool #
Ord JURI Source #
Instance details Defined in Poseidon.Janno Methods compare :: JURI -> JURI -> Ordering # (<) :: JURI -> JURI -> Bool # (<=) :: JURI -> JURI -> Bool # (>) :: JURI -> JURI -> Bool # (>=) :: JURI -> JURI -> Bool # max :: JURI -> JURI -> JURI # min :: JURI -> JURI -> JURI #
type Rep JURI Source #
Instance details Defined in Poseidon.Janno type Rep JURI = D1 ('MetaData "JURI" "Poseidon.Janno" "poseidon-hs-1.5.5.0-64IxIR1JUiELWCZhD8ICmR" 'True) (C1 ('MetaCons "JURI" 'PrefixI 'False) (S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 String)))

data RelationDegree Source #

Constructors

Identical
First
Second
ThirdToFifth
SixthToTenth
Unrelated
OtherDegree

Instances

Instances details

FromJSON RelationDegree Source #
Instance details Defined in Poseidon.Janno Methods parseJSON :: Value -> Parser RelationDegree parseJSONList :: Value -> Parser [RelationDegree]
ToJSON RelationDegree Source #
Instance details Defined in Poseidon.Janno Methods toJSON :: RelationDegree -> Value toEncoding :: RelationDegree -> Encoding toJSONList :: [RelationDegree] -> Value toEncodingList :: [RelationDegree] -> Encoding
Bounded RelationDegree Source #
Instance details Defined in Poseidon.Janno Methods minBound :: RelationDegree # maxBound :: RelationDegree #
Enum RelationDegree Source #
Instance details Defined in Poseidon.Janno Methods succ :: RelationDegree -> RelationDegree # pred :: RelationDegree -> RelationDegree # toEnum :: Int -> RelationDegree # fromEnum :: RelationDegree -> Int # enumFrom :: RelationDegree -> [RelationDegree] # enumFromThen :: RelationDegree -> RelationDegree -> [RelationDegree] # enumFromTo :: RelationDegree -> RelationDegree -> [RelationDegree] # enumFromThenTo :: RelationDegree -> RelationDegree -> RelationDegree -> [RelationDegree] #
Generic RelationDegree Source #
Instance details Defined in Poseidon.Janno Associated Types type Rep RelationDegree :: Type -> Type # Methods from :: RelationDegree -> Rep RelationDegree x # to :: Rep RelationDegree x -> RelationDegree #
Show RelationDegree Source #
Instance details Defined in Poseidon.Janno Methods showsPrec :: Int -> RelationDegree -> ShowS # show :: RelationDegree -> String # showList :: [RelationDegree] -> ShowS #
FromField RelationDegree Source #
Instance details Defined in Poseidon.Janno Methods parseField :: Field -> Parser RelationDegree
ToField RelationDegree Source #
Instance details Defined in Poseidon.Janno Methods toField :: RelationDegree -> Field
Eq RelationDegree Source #
Instance details Defined in Poseidon.Janno Methods (==) :: RelationDegree -> RelationDegree -> Bool # (/=) :: RelationDegree -> RelationDegree -> Bool #
Ord RelationDegree Source #
Instance details Defined in Poseidon.Janno Methods compare :: RelationDegree -> RelationDegree -> Ordering # (<) :: RelationDegree -> RelationDegree -> Bool # (<=) :: RelationDegree -> RelationDegree -> Bool # (>) :: RelationDegree -> RelationDegree -> Bool # (>=) :: RelationDegree -> RelationDegree -> Bool # max :: RelationDegree -> RelationDegree -> RelationDegree # min :: RelationDegree -> RelationDegree -> RelationDegree #
type Rep RelationDegree Source #
Instance details Defined in Poseidon.Janno type Rep RelationDegree = D1 ('MetaData "RelationDegree" "Poseidon.Janno" "poseidon-hs-1.5.5.0-64IxIR1JUiELWCZhD8ICmR" 'False) ((C1 ('MetaCons "Identical" 'PrefixI 'False) (U1 :: Type -> Type) :+: (C1 ('MetaCons "First" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Second" 'PrefixI 'False) (U1 :: Type -> Type))) :+: ((C1 ('MetaCons "ThirdToFifth" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "SixthToTenth" 'PrefixI 'False) (U1 :: Type -> Type)) :+: (C1 ('MetaCons "Unrelated" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "OtherDegree" 'PrefixI 'False) (U1 :: Type -> Type))))

data JannoLibraryBuilt Source #

A datatype to represent Library_Built in a janno file

Constructors

DS
SS
MixedSSDS
Other

Instances

Instances details

FromJSON JannoLibraryBuilt Source #
Instance details Defined in Poseidon.Janno Methods parseJSON :: Value -> Parser JannoLibraryBuilt parseJSONList :: Value -> Parser [JannoLibraryBuilt]
ToJSON JannoLibraryBuilt Source #
Instance details Defined in Poseidon.Janno Methods toJSON :: JannoLibraryBuilt -> Value toEncoding :: JannoLibraryBuilt -> Encoding toJSONList :: [JannoLibraryBuilt] -> Value toEncodingList :: [JannoLibraryBuilt] -> Encoding
Bounded JannoLibraryBuilt Source #
Instance details Defined in Poseidon.Janno Methods minBound :: JannoLibraryBuilt # maxBound :: JannoLibraryBuilt #
Enum JannoLibraryBuilt Source #
Instance details Defined in Poseidon.Janno Methods succ :: JannoLibraryBuilt -> JannoLibraryBuilt # pred :: JannoLibraryBuilt -> JannoLibraryBuilt # toEnum :: Int -> JannoLibraryBuilt # fromEnum :: JannoLibraryBuilt -> Int # enumFrom :: JannoLibraryBuilt -> [JannoLibraryBuilt] # enumFromThen :: JannoLibraryBuilt -> JannoLibraryBuilt -> [JannoLibraryBuilt] # enumFromTo :: JannoLibraryBuilt -> JannoLibraryBuilt -> [JannoLibraryBuilt] # enumFromThenTo :: JannoLibraryBuilt -> JannoLibraryBuilt -> JannoLibraryBuilt -> [JannoLibraryBuilt] #
Generic JannoLibraryBuilt Source #
Instance details Defined in Poseidon.Janno Associated Types type Rep JannoLibraryBuilt :: Type -> Type # Methods from :: JannoLibraryBuilt -> Rep JannoLibraryBuilt x # to :: Rep JannoLibraryBuilt x -> JannoLibraryBuilt #
Show JannoLibraryBuilt Source #
Instance details Defined in Poseidon.Janno Methods showsPrec :: Int -> JannoLibraryBuilt -> ShowS # show :: JannoLibraryBuilt -> String # showList :: [JannoLibraryBuilt] -> ShowS #
FromField JannoLibraryBuilt Source #
Instance details Defined in Poseidon.Janno Methods parseField :: Field -> Parser JannoLibraryBuilt
ToField JannoLibraryBuilt Source #
Instance details Defined in Poseidon.Janno Methods toField :: JannoLibraryBuilt -> Field
Eq JannoLibraryBuilt Source #
Instance details Defined in Poseidon.Janno Methods (==) :: JannoLibraryBuilt -> JannoLibraryBuilt -> Bool # (/=) :: JannoLibraryBuilt -> JannoLibraryBuilt -> Bool #
Ord JannoLibraryBuilt Source #
Instance details Defined in Poseidon.Janno Methods compare :: JannoLibraryBuilt -> JannoLibraryBuilt -> Ordering # (<) :: JannoLibraryBuilt -> JannoLibraryBuilt -> Bool # (<=) :: JannoLibraryBuilt -> JannoLibraryBuilt -> Bool # (>) :: JannoLibraryBuilt -> JannoLibraryBuilt -> Bool # (>=) :: JannoLibraryBuilt -> JannoLibraryBuilt -> Bool # max :: JannoLibraryBuilt -> JannoLibraryBuilt -> JannoLibraryBuilt # min :: JannoLibraryBuilt -> JannoLibraryBuilt -> JannoLibraryBuilt #
type Rep JannoLibraryBuilt Source #
Instance details Defined in Poseidon.Janno type Rep JannoLibraryBuilt = D1 ('MetaData "JannoLibraryBuilt" "Poseidon.Janno" "poseidon-hs-1.5.5.0-64IxIR1JUiELWCZhD8ICmR" 'False) ((C1 ('MetaCons "DS" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "SS" 'PrefixI 'False) (U1 :: Type -> Type)) :+: (C1 ('MetaCons "MixedSSDS" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Other" 'PrefixI 'False) (U1 :: Type -> Type)))

data AccessionID Source #

A datatype to represent AccessionIDs in a janno file

Constructors

INSDCProject String
INSDCStudy String
INSDCBioSample String
INSDCSample String
INSDCExperiment String
INSDCRun String
INSDCAnalysis String
OtherID String

Instances

Instances details

FromJSON AccessionID Source #
Instance details Defined in Poseidon.Janno Methods parseJSON :: Value -> Parser AccessionID parseJSONList :: Value -> Parser [AccessionID]
ToJSON AccessionID Source #
Instance details Defined in Poseidon.Janno Methods toJSON :: AccessionID -> Value toEncoding :: AccessionID -> Encoding toJSONList :: [AccessionID] -> Value toEncodingList :: [AccessionID] -> Encoding
Generic AccessionID Source #
Instance details Defined in Poseidon.Janno Associated Types type Rep AccessionID :: Type -> Type # Methods from :: AccessionID -> Rep AccessionID x # to :: Rep AccessionID x -> AccessionID #
Show AccessionID Source #
Instance details Defined in Poseidon.Janno Methods showsPrec :: Int -> AccessionID -> ShowS # show :: AccessionID -> String # showList :: [AccessionID] -> ShowS #
FromField AccessionID Source #
Instance details Defined in Poseidon.Janno Methods parseField :: Field -> Parser AccessionID
ToField AccessionID Source #
Instance details Defined in Poseidon.Janno Methods toField :: AccessionID -> Field
Eq AccessionID Source #
Instance details Defined in Poseidon.Janno Methods (==) :: AccessionID -> AccessionID -> Bool # (/=) :: AccessionID -> AccessionID -> Bool #
Ord AccessionID Source #
Instance details Defined in Poseidon.Janno Methods compare :: AccessionID -> AccessionID -> Ordering # (<) :: AccessionID -> AccessionID -> Bool # (<=) :: AccessionID -> AccessionID -> Bool # (>) :: AccessionID -> AccessionID -> Bool # (>=) :: AccessionID -> AccessionID -> Bool # max :: AccessionID -> AccessionID -> AccessionID # min :: AccessionID -> AccessionID -> AccessionID #
type Rep AccessionID Source #
Instance details Defined in Poseidon.Janno type Rep AccessionID = D1 ('MetaData "AccessionID" "Poseidon.Janno" "poseidon-hs-1.5.5.0-64IxIR1JUiELWCZhD8ICmR" 'False) (((C1 ('MetaCons "INSDCProject" 'PrefixI 'False) (S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 String)) :+: C1 ('MetaCons "INSDCStudy" 'PrefixI 'False) (S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 String))) :+: (C1 ('MetaCons "INSDCBioSample" 'PrefixI 'False) (S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 String)) :+: C1 ('MetaCons "INSDCSample" 'PrefixI 'False) (S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 String)))) :+: ((C1 ('MetaCons "INSDCExperiment" 'PrefixI 'False) (S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 String)) :+: C1 ('MetaCons "INSDCRun" 'PrefixI 'False) (S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 String))) :+: (C1 ('MetaCons "INSDCAnalysis" 'PrefixI 'False) (S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 String)) :+: C1 ('MetaCons "OtherID" 'PrefixI 'False) (S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 String)))))

makeAccessionID :: MonadFail m => String -> m AccessionID Source #

makeLatitude :: MonadFail m => Double -> m Latitude Source #

makeLongitude :: MonadFail m => Double -> m Longitude Source #

writeJannoFile :: FilePath -> JannoRows -> IO () Source #

readJannoFile :: FilePath -> PoseidonIO JannoRows Source #

A function to load one janno file

createMinimalJanno :: [EigenstratIndEntry] -> JannoRows Source #

A function to create empty janno rows for a set of individuals

createMinimalSample :: EigenstratIndEntry -> JannoRow Source #

A function to create an empty janno row for an individual

jannoHeaderString :: [String] Source #

newtype CsvNamedRecord Source #

A datatype to collect additional, unpecified .janno file columns (a hashmap in cassava/Data.Csv)

Constructors

CsvNamedRecord NamedRecord

Instances

Instances details

FromJSON CsvNamedRecord Source #
Instance details Defined in Poseidon.Janno Methods parseJSON :: Value -> Parser CsvNamedRecord parseJSONList :: Value -> Parser [CsvNamedRecord]
ToJSON CsvNamedRecord Source #
Instance details Defined in Poseidon.Janno Methods toJSON :: CsvNamedRecord -> Value toEncoding :: CsvNamedRecord -> Encoding toJSONList :: [CsvNamedRecord] -> Value toEncodingList :: [CsvNamedRecord] -> Encoding
Generic CsvNamedRecord Source #
Instance details Defined in Poseidon.Janno Associated Types type Rep CsvNamedRecord :: Type -> Type # Methods from :: CsvNamedRecord -> Rep CsvNamedRecord x # to :: Rep CsvNamedRecord x -> CsvNamedRecord #
Show CsvNamedRecord Source #
Instance details Defined in Poseidon.Janno Methods showsPrec :: Int -> CsvNamedRecord -> ShowS # show :: CsvNamedRecord -> String # showList :: [CsvNamedRecord] -> ShowS #
Eq CsvNamedRecord Source #
Instance details Defined in Poseidon.Janno Methods (==) :: CsvNamedRecord -> CsvNamedRecord -> Bool # (/=) :: CsvNamedRecord -> CsvNamedRecord -> Bool #
PresenceCountable CsvNamedRecord Source #
Instance details Defined in Poseidon.CLI.Survey Methods countPresence :: CsvNamedRecord -> Int Source #
type Rep CsvNamedRecord Source #
Instance details Defined in Poseidon.Janno type Rep CsvNamedRecord = D1 ('MetaData "CsvNamedRecord" "Poseidon.Janno" "poseidon-hs-1.5.5.0-64IxIR1JUiELWCZhD8ICmR" 'True) (C1 ('MetaCons "CsvNamedRecord" 'PrefixI 'False) (S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 NamedRecord)))

newtype JannoRows Source #

A data type to represent a janno file

Constructors

JannoRows [JannoRow]

Instances

Instances details

FromJSON JannoRows Source #
Instance details Defined in Poseidon.Janno Methods parseJSON :: Value -> Parser JannoRows parseJSONList :: Value -> Parser [JannoRows]
ToJSON JannoRows Source #
Instance details Defined in Poseidon.Janno Methods toJSON :: JannoRows -> Value toEncoding :: JannoRows -> Encoding toJSONList :: [JannoRows] -> Value toEncodingList :: [JannoRows] -> Encoding
Monoid JannoRows Source #
Instance details Defined in Poseidon.Janno Methods mempty :: JannoRows # mappend :: JannoRows -> JannoRows -> JannoRows # mconcat :: [JannoRows] -> JannoRows #
Semigroup JannoRows Source #
Instance details Defined in Poseidon.Janno Methods (<>) :: JannoRows -> JannoRows -> JannoRows # sconcat :: NonEmpty JannoRows -> JannoRows # stimes :: Integral b => b -> JannoRows -> JannoRows #
Generic JannoRows Source #
Instance details Defined in Poseidon.Janno Associated Types type Rep JannoRows :: Type -> Type # Methods from :: JannoRows -> Rep JannoRows x # to :: Rep JannoRows x -> JannoRows #
Show JannoRows Source #
Instance details Defined in Poseidon.Janno Methods showsPrec :: Int -> JannoRows -> ShowS # show :: JannoRows -> String # showList :: [JannoRows] -> ShowS #
Eq JannoRows Source #
Instance details Defined in Poseidon.Janno Methods (==) :: JannoRows -> JannoRows -> Bool # (/=) :: JannoRows -> JannoRows -> Bool #
type Rep JannoRows Source #
Instance details Defined in Poseidon.Janno type Rep JannoRows = D1 ('MetaData "JannoRows" "Poseidon.Janno" "poseidon-hs-1.5.5.0-64IxIR1JUiELWCZhD8ICmR" 'True) (C1 ('MetaCons "JannoRows" 'PrefixI 'False) (S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 [JannoRow])))

type JannoStringList = JannoList String Source #

filterLookup :: FromField a => NamedRecord -> ByteString -> Parser a Source #

filterLookupOptional :: FromField a => NamedRecord -> ByteString -> Parser (Maybe a) Source #

getCsvNR :: CsvNamedRecord -> NamedRecord Source #

encodingOptions :: EncodeOptions Source #

decodingOptions :: DecodeOptions Source #

explicitNA :: ByteString -> ByteString Source #

A helper functions to replace empty bytestrings values in janno files with explicit "n/a"

removeUselessSuffix :: String -> String Source #

parseCsvParseError :: Parser CsvParseError Source #

renderCsvParseError :: CsvParseError -> String Source #

getMaybeJannoList :: Maybe (JannoList a) -> [a] Source #