{-# LANGUAGE OverloadedStrings #-}

module Currycarbon.Parsers where

import           Currycarbon.ParserHelpers
import           Currycarbon.Types
import           Currycarbon.Utils

import           Control.Exception         (throwIO)
import           Data.List                 (intercalate, transpose)
import qualified Data.Vector               as V
import qualified Data.Vector.Unboxed       as VU
import qualified Text.Parsec               as P
import qualified Text.Parsec.String        as P

-- * Parsing, rendering and writing functions
--
-- $importExport
--
-- This module contains a number of functions to manage data input and
-- output plumbing for different datatypes

-- read the calibration method

readCalibrationMethod :: String -> Either String CalibrationMethod
readCalibrationMethod :: [Char] -> Either [Char] CalibrationMethod
readCalibrationMethod [Char]
s =
    case forall s t u a.
Stream s Identity t =>
Parsec s u a -> u -> [Char] -> s -> Either ParseError a
P.runParser Parser CalibrationMethod
parseCalibrationMethod () [Char]
"" [Char]
s of
        Left ParseError
err -> forall a b. a -> Either a b
Left forall a b. (a -> b) -> a -> b
$ ParseError -> [Char]
showParsecErr ParseError
err
        Right CalibrationMethod
x  -> forall a b. b -> Either a b
Right CalibrationMethod
x

parseCalibrationMethod :: P.Parser CalibrationMethod
parseCalibrationMethod :: Parser CalibrationMethod
parseCalibrationMethod = do
    forall s u (m :: * -> *) a. ParsecT s u m a -> ParsecT s u m a
P.try Parser CalibrationMethod
bchron forall s u (m :: * -> *) a.
ParsecT s u m a -> ParsecT s u m a -> ParsecT s u m a
P.<|> forall {u}. ParsecT [Char] u Identity CalibrationMethod
matrixMultiplication
    where
        bchron :: Parser CalibrationMethod
bchron = do
            [Char]
_ <- forall s (m :: * -> *) u.
Stream s m Char =>
[Char] -> ParsecT s u m [Char]
P.string [Char]
"Bchron,"
            forall s u (m :: * -> *) a. ParsecT s u m a -> ParsecT s u m a
P.try Parser CalibrationMethod
studentT forall s u (m :: * -> *) a.
ParsecT s u m a -> ParsecT s u m a -> ParsecT s u m a
P.<|> forall {u}. ParsecT [Char] u Identity CalibrationMethod
normal
        studentT :: Parser CalibrationMethod
studentT = do
            [Char]
_ <- forall s (m :: * -> *) u.
Stream s m Char =>
[Char] -> ParsecT s u m [Char]
P.string [Char]
"StudentT,"
            Double
dof <- Parser Double
parsePositiveDouble
            forall (m :: * -> *) a. Monad m => a -> m a
return (CalibrationDistribution -> CalibrationMethod
Bchron forall a b. (a -> b) -> a -> b
$ Double -> CalibrationDistribution
StudentTDist Double
dof)
        normal :: ParsecT [Char] u Identity CalibrationMethod
normal = do
            [Char]
_ <- forall s (m :: * -> *) u.
Stream s m Char =>
[Char] -> ParsecT s u m [Char]
P.string [Char]
"Normal"
            forall (m :: * -> *) a. Monad m => a -> m a
return (CalibrationDistribution -> CalibrationMethod
Bchron CalibrationDistribution
NormalDist)
        matrixMultiplication :: ParsecT [Char] u Identity CalibrationMethod
matrixMultiplication = do
            [Char]
_ <- forall s (m :: * -> *) u.
Stream s m Char =>
[Char] -> ParsecT s u m [Char]
P.string [Char]
"MatrixMult"
            forall (m :: * -> *) a. Monad m => a -> m a
return CalibrationMethod
MatrixMultiplication

-- pretty printing

-- | Combine 'CalExpr', 'CalPDF' and 'CalC14' to render pretty command line output
-- like this:
--
-- @
-- CalEXPR: [Ex2] (S1:5000±30BP + S2:5100±100BP)
-- Calibrated: 4150BC \>\> 3941BC \> 3814BC \< 3660BC \<\< 3651BC
-- 1-sigma: 3941-3864BC, 3810-3707BC, 3667-3660BC
-- 2-sigma: 4150-4148BC, 4048-3651BC
--                                           ▁
--                                           ▒▁ ▁▁
--                                   ▁▁▁    ▁▒▒▁▒▒
--                                 ▁▁▒▒▒    ▒▒▒▒▒▒
--                               ▁▁▒▒▒▒▒▁▁▁▁▒▒▒▒▒▒▁ ▁
--                           ▁▁▁▁▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▁▒▁
--         ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▁▁▁▁▁▁▁▁
--  -4330 ┄──┬─────┬─────┬─────┬──────┬─────┬─────┬─────┬─────┄ -3530
--                    \>            \>       \^         \<
--                                 ──────  ──────── ──
--                    ─     ──────────────────────────
-- @
--
renderCalDatePretty ::
       Bool -- ^ Should the CLI plot be restricted to (boring) ASCII symbols?
    -> (NamedCalExpr, CalPDF, CalC14)
    -> String
renderCalDatePretty :: Bool -> (NamedCalExpr, CalPDF, CalC14) -> [Char]
renderCalDatePretty Bool
ascii (NamedCalExpr
calExpr, CalPDF
calPDF, CalC14
calC14) =
    [Char]
"CalEXPR: " forall a. [a] -> [a] -> [a]
++ forall a. [a] -> [[a]] -> [a]
intercalate [Char]
"\n" [
          NamedCalExpr -> [Char]
renderNamedCalExpr NamedCalExpr
calExpr
        , CalC14 -> [Char]
renderCalC14 CalC14
calC14
        , Bool -> YearBCAD -> YearBCAD -> CalPDF -> CalC14 -> [Char]
renderCLIPlotCalPDF Bool
ascii YearBCAD
6 YearBCAD
50 CalPDF
calPDF CalC14
calC14
        ]

-- write and read calibration expressions

renderNamedCalExpr :: NamedCalExpr -> String
renderNamedCalExpr :: NamedCalExpr -> [Char]
renderNamedCalExpr (NamedCalExpr [Char]
exprID CalExpr
calExpr) = [Char] -> [Char]
renderExprID [Char]
exprID forall a. [a] -> [a] -> [a]
++ [Char]
" " forall a. [a] -> [a] -> [a]
++ CalExpr -> [Char]
renderCalExpr CalExpr
calExpr

renderExprID :: String -> String
renderExprID :: [Char] -> [Char]
renderExprID [Char]
s = [Char]
"[" forall a. [a] -> [a] -> [a]
++ [Char]
s forall a. [a] -> [a] -> [a]
++ [Char]
"]"

renderCalExpr :: CalExpr -> String
renderCalExpr :: CalExpr -> [Char]
renderCalExpr (UnCalDate UncalC14
a)               = UncalC14 -> [Char]
renderUncalC14 UncalC14
a
renderCalExpr (WindowBP TimeWindowBP
a)                = TimeWindowBP -> [Char]
renderTimeWindowBP TimeWindowBP
a
renderCalExpr (WindowBCAD TimeWindowBCAD
a)              = TimeWindowBCAD -> [Char]
renderTimeWindowBCAD TimeWindowBCAD
a
renderCalExpr (CalDate (CalPDF [Char]
name Vector YearBCAD
_ Vector Float
_)) = [Char]
name
renderCalExpr (SumCal CalExpr
a CalExpr
b)                = [Char]
"(" forall a. [a] -> [a] -> [a]
++ CalExpr -> [Char]
renderCalExpr CalExpr
a forall a. [a] -> [a] -> [a]
++ [Char]
" + " forall a. [a] -> [a] -> [a]
++ CalExpr -> [Char]
renderCalExpr CalExpr
b forall a. [a] -> [a] -> [a]
++ [Char]
")"
renderCalExpr (ProductCal CalExpr
a CalExpr
b)            = [Char]
"(" forall a. [a] -> [a] -> [a]
++ CalExpr -> [Char]
renderCalExpr CalExpr
a forall a. [a] -> [a] -> [a]
++ [Char]
" * " forall a. [a] -> [a] -> [a]
++ CalExpr -> [Char]
renderCalExpr CalExpr
b forall a. [a] -> [a] -> [a]
++ [Char]
")"

renderTimeWindowBP :: TimeWindowBP -> String
renderTimeWindowBP :: TimeWindowBP -> [Char]
renderTimeWindowBP (TimeWindowBP [Char]
name YearBP
start YearBP
stop) =
    [Char]
name forall a. [a] -> [a] -> [a]
++ [Char]
":" forall a. [a] -> [a] -> [a]
++ YearBP -> [Char]
renderYearBP YearBP
start forall a. [a] -> [a] -> [a]
++ [Char]
"-" forall a. [a] -> [a] -> [a]
++ YearBP -> [Char]
renderYearBP YearBP
stop

renderTimeWindowBCAD :: TimeWindowBCAD -> String
renderTimeWindowBCAD :: TimeWindowBCAD -> [Char]
renderTimeWindowBCAD (TimeWindowBCAD [Char]
name YearBCAD
start YearBCAD
stop) =
    [Char]
name forall a. [a] -> [a] -> [a]
++ [Char]
":" forall a. [a] -> [a] -> [a]
++ YearBCAD -> [Char]
renderYearBCAD YearBCAD
start forall a. [a] -> [a] -> [a]
++ [Char]
"-" forall a. [a] -> [a] -> [a]
++ YearBCAD -> [Char]
renderYearBCAD YearBCAD
stop

parseTimeWindowBP :: P.Parser TimeWindowBP
parseTimeWindowBP :: Parser TimeWindowBP
parseTimeWindowBP = forall a. [Char] -> Parser a -> Parser a
parseRecordType [Char]
"rangeBP" forall a b. (a -> b) -> a -> b
$ forall s u (m :: * -> *) a. ParsecT s u m a -> ParsecT s u m a
P.try Parser TimeWindowBP
long forall s u (m :: * -> *) a.
ParsecT s u m a -> ParsecT s u m a -> ParsecT s u m a
P.<|> Parser TimeWindowBP
short
    where
        long :: Parser TimeWindowBP
long = do
            [Char]
name  <- forall a. [Char] -> Parser a -> Parser a
parseArgument [Char]
"id" Parser [Char]
parseAnyString
            YearBP
start <- forall a. [Char] -> Parser a -> Parser a
parseArgument [Char]
"start" Parser YearBP
parseWord
            YearBP
stop  <- forall a. [Char] -> Parser a -> Parser a
parseArgument [Char]
"stop" Parser YearBP
parseWord
            forall {m :: * -> *}.
MonadFail m =>
[Char] -> YearBP -> YearBP -> m TimeWindowBP
construct [Char]
name YearBP
start YearBP
stop
        short :: Parser TimeWindowBP
short = do
            YearBP
start <- forall a. [Char] -> Parser a -> Parser a
parseArgument [Char]
"start" Parser YearBP
parseWord
            YearBP
stop  <- forall a. [Char] -> Parser a -> Parser a
parseArgument [Char]
"stop" Parser YearBP
parseWord
            forall {m :: * -> *}.
MonadFail m =>
[Char] -> YearBP -> YearBP -> m TimeWindowBP
construct [Char]
"" YearBP
start YearBP
stop
        construct :: [Char] -> YearBP -> YearBP -> m TimeWindowBP
construct [Char]
name YearBP
start YearBP
stop = do
            if YearBP
start forall a. Ord a => a -> a -> Bool
>= YearBP
stop
            then forall (m :: * -> *) a. Monad m => a -> m a
return ([Char] -> YearBP -> YearBP -> TimeWindowBP
TimeWindowBP [Char]
name YearBP
start YearBP
stop)
            else forall (m :: * -> *) a. MonadFail m => [Char] -> m a
fail [Char]
"the BP stop date can not be larger than the start date"

parseTimeWindowBCAD :: P.Parser TimeWindowBCAD
parseTimeWindowBCAD :: Parser TimeWindowBCAD
parseTimeWindowBCAD = forall a. [Char] -> Parser a -> Parser a
parseRecordType [Char]
"rangeBCAD" forall a b. (a -> b) -> a -> b
$ forall s u (m :: * -> *) a. ParsecT s u m a -> ParsecT s u m a
P.try Parser TimeWindowBCAD
long forall s u (m :: * -> *) a.
ParsecT s u m a -> ParsecT s u m a -> ParsecT s u m a
P.<|> Parser TimeWindowBCAD
short
    where
        long :: Parser TimeWindowBCAD
long = do
            [Char]
name  <- forall a. [Char] -> Parser a -> Parser a
parseArgument [Char]
"id" Parser [Char]
parseAnyString
            YearBCAD
start <- forall a. [Char] -> Parser a -> Parser a
parseArgument [Char]
"start" Parser YearBCAD
parseInt
            YearBCAD
stop  <- forall a. [Char] -> Parser a -> Parser a
parseArgument [Char]
"stop" Parser YearBCAD
parseInt
            forall {m :: * -> *}.
MonadFail m =>
[Char] -> YearBCAD -> YearBCAD -> m TimeWindowBCAD
construct [Char]
name YearBCAD
start YearBCAD
stop
        short :: Parser TimeWindowBCAD
short = do
            YearBCAD
start <- forall a. [Char] -> Parser a -> Parser a
parseArgument [Char]
"start" Parser YearBCAD
parseInt
            YearBCAD
stop  <- forall a. [Char] -> Parser a -> Parser a
parseArgument [Char]
"stop" Parser YearBCAD
parseInt
            forall {m :: * -> *}.
MonadFail m =>
[Char] -> YearBCAD -> YearBCAD -> m TimeWindowBCAD
construct [Char]
"" YearBCAD
start YearBCAD
stop
        construct :: [Char] -> YearBCAD -> YearBCAD -> m TimeWindowBCAD
construct [Char]
name YearBCAD
start YearBCAD
stop = do
            if YearBCAD
start forall a. Ord a => a -> a -> Bool
<= YearBCAD
stop
            then forall (m :: * -> *) a. Monad m => a -> m a
return ([Char] -> YearBCAD -> YearBCAD -> TimeWindowBCAD
TimeWindowBCAD [Char]
name YearBCAD
start YearBCAD
stop)
            else forall (m :: * -> *) a. MonadFail m => [Char] -> m a
fail [Char]
"the BC/AD stop date can not be smaller than the start date"

-- https://gist.github.com/abhin4v/017a36477204a1d57745
addFun :: P.Parser CalExpr
addFun :: Parser CalExpr
addFun = forall a. [Char] -> Parser a -> Parser a
parseRecordType [Char]
"sum" forall a b. (a -> b) -> a -> b
$ do
    CalExpr
a <- forall a. [Char] -> Parser a -> Parser a
parseArgument [Char]
"a" Parser CalExpr
term
    CalExpr
b <- forall a. [Char] -> Parser a -> Parser a
parseArgument [Char]
"b" Parser CalExpr
expr
    forall (m :: * -> *) a. Monad m => a -> m a
return forall a b. (a -> b) -> a -> b
$ CalExpr -> CalExpr -> CalExpr
SumCal CalExpr
a CalExpr
b

addOperator :: P.Parser CalExpr
addOperator :: Parser CalExpr
addOperator = CalExpr -> CalExpr -> CalExpr
SumCal forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Parser CalExpr
term forall (f :: * -> *) a b. Applicative f => f (a -> b) -> f a -> f b
<*> (Char -> Parser Char
parseCharInSpace Char
'+' forall (f :: * -> *) a b. Applicative f => f a -> f b -> f b
*> Parser CalExpr
expr)

mulFun :: P.Parser CalExpr
mulFun :: Parser CalExpr
mulFun = forall a. [Char] -> Parser a -> Parser a
parseRecordType [Char]
"product" forall a b. (a -> b) -> a -> b
$ do
    CalExpr
a <- forall a. [Char] -> Parser a -> Parser a
parseArgument [Char]
"a" Parser CalExpr
factor
    CalExpr
b <- forall a. [Char] -> Parser a -> Parser a
parseArgument [Char]
"b" Parser CalExpr
term
    forall (m :: * -> *) a. Monad m => a -> m a
return forall a b. (a -> b) -> a -> b
$ CalExpr -> CalExpr -> CalExpr
ProductCal CalExpr
a CalExpr
b

mulOperator :: P.Parser CalExpr
mulOperator :: Parser CalExpr
mulOperator = CalExpr -> CalExpr -> CalExpr
ProductCal forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Parser CalExpr
factor forall (f :: * -> *) a b. Applicative f => f (a -> b) -> f a -> f b
<*> (Char -> Parser Char
parseCharInSpace Char
'*' forall (f :: * -> *) a b. Applicative f => f a -> f b -> f b
*> Parser CalExpr
term)

parens :: P.Parser CalExpr
parens :: Parser CalExpr
parens = forall s (m :: * -> *) t u open close a.
Stream s m t =>
ParsecT s u m open
-> ParsecT s u m close -> ParsecT s u m a -> ParsecT s u m a
P.between (Char -> Parser Char
parseCharInSpace Char
'(') (Char -> Parser Char
parseCharInSpace Char
')') Parser CalExpr
expr

factor :: P.Parser CalExpr
factor :: Parser CalExpr
factor =      forall s u (m :: * -> *) a. ParsecT s u m a -> ParsecT s u m a
P.try Parser CalExpr
parens
        forall s u (m :: * -> *) a.
ParsecT s u m a -> ParsecT s u m a -> ParsecT s u m a
P.<|> forall s u (m :: * -> *) a. ParsecT s u m a -> ParsecT s u m a
P.try Parser CalExpr
addFun
        forall s u (m :: * -> *) a.
ParsecT s u m a -> ParsecT s u m a -> ParsecT s u m a
P.<|> forall s u (m :: * -> *) a. ParsecT s u m a -> ParsecT s u m a
P.try Parser CalExpr
mulFun
        forall s u (m :: * -> *) a.
ParsecT s u m a -> ParsecT s u m a -> ParsecT s u m a
P.<|> forall s u (m :: * -> *) a. ParsecT s u m a -> ParsecT s u m a
P.try (TimeWindowBP -> CalExpr
WindowBP forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Parser TimeWindowBP
parseTimeWindowBP)
        forall s u (m :: * -> *) a.
ParsecT s u m a -> ParsecT s u m a -> ParsecT s u m a
P.<|> forall s u (m :: * -> *) a. ParsecT s u m a -> ParsecT s u m a
P.try (TimeWindowBCAD -> CalExpr
WindowBCAD forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Parser TimeWindowBCAD
parseTimeWindowBCAD)
        forall s u (m :: * -> *) a.
ParsecT s u m a -> ParsecT s u m a -> ParsecT s u m a
P.<|> (UncalC14 -> CalExpr
UnCalDate forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Parser UncalC14
parseUncalC14)

term :: P.Parser CalExpr
term :: Parser CalExpr
term = forall s u (m :: * -> *) a. ParsecT s u m a -> ParsecT s u m a
P.try Parser CalExpr
mulOperator forall s u (m :: * -> *) a.
ParsecT s u m a -> ParsecT s u m a -> ParsecT s u m a
P.<|> Parser CalExpr
factor

expr :: P.Parser CalExpr
expr :: Parser CalExpr
expr = forall s u (m :: * -> *) a. ParsecT s u m a -> ParsecT s u m a
P.try Parser CalExpr
addOperator forall s u (m :: * -> *) a.
ParsecT s u m a -> ParsecT s u m a -> ParsecT s u m a
P.<|> Parser CalExpr
term -- <* P.eof

namedExpr :: P.Parser NamedCalExpr
namedExpr :: Parser NamedCalExpr
namedExpr = forall s u (m :: * -> *) a. ParsecT s u m a -> ParsecT s u m a
P.try Parser NamedCalExpr
nameBeforeColon forall s u (m :: * -> *) a.
ParsecT s u m a -> ParsecT s u m a -> ParsecT s u m a
P.<|> forall s u (m :: * -> *) a. ParsecT s u m a -> ParsecT s u m a
P.try Parser NamedCalExpr
record forall s u (m :: * -> *) a.
ParsecT s u m a -> ParsecT s u m a -> ParsecT s u m a
P.<|> Parser NamedCalExpr
onlyExpr
    where
        nameBeforeColon :: Parser NamedCalExpr
nameBeforeColon = do
            [Char]
name <- Parser [Char]
parseAnyString
            Char
_ <- forall s (m :: * -> *) u.
Stream s m Char =>
Char -> ParsecT s u m Char
P.char Char
':'
            ()
_ <- forall s (m :: * -> *) u. Stream s m Char => ParsecT s u m ()
P.spaces
            CalExpr
ex <- Parser CalExpr
expr
            forall (m :: * -> *) a. Monad m => a -> m a
return ([Char] -> CalExpr -> NamedCalExpr
NamedCalExpr [Char]
name CalExpr
ex)
        record :: Parser NamedCalExpr
record = forall a. [Char] -> Parser a -> Parser a
parseRecordType [Char]
"calExpr" forall a b. (a -> b) -> a -> b
$ forall s u (m :: * -> *) a. ParsecT s u m a -> ParsecT s u m a
P.try Parser NamedCalExpr
long forall s u (m :: * -> *) a.
ParsecT s u m a -> ParsecT s u m a -> ParsecT s u m a
P.<|> Parser NamedCalExpr
short
        long :: Parser NamedCalExpr
long = do
            [Char]
name <- forall a. [Char] -> Parser a -> Parser a
parseArgument [Char]
"id" Parser [Char]
parseAnyString
            CalExpr
ex   <- forall a. [Char] -> Parser a -> Parser a
parseArgument [Char]
"expr" Parser CalExpr
expr
            forall (m :: * -> *) a. Monad m => a -> m a
return ([Char] -> CalExpr -> NamedCalExpr
NamedCalExpr [Char]
name CalExpr
ex)
        short :: Parser NamedCalExpr
short = do
            CalExpr
ex   <- forall a. [Char] -> Parser a -> Parser a
parseArgument [Char]
"expr" Parser CalExpr
expr
            forall (m :: * -> *) a. Monad m => a -> m a
return ([Char] -> CalExpr -> NamedCalExpr
NamedCalExpr [Char]
"" CalExpr
ex)
        onlyExpr :: Parser NamedCalExpr
onlyExpr = [Char] -> CalExpr -> NamedCalExpr
NamedCalExpr [Char]
"" forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Parser CalExpr
expr

readNamedCalExprs :: String -> Either String [NamedCalExpr]
readNamedCalExprs :: [Char] -> Either [Char] [NamedCalExpr]
readNamedCalExprs [Char]
s =
    case forall s t u a.
Stream s Identity t =>
Parsec s u a -> u -> [Char] -> s -> Either ParseError a
P.runParser Parser [NamedCalExpr]
parseCalExprSepBySemicolon () [Char]
"" [Char]
s of
        Left ParseError
err -> forall a b. a -> Either a b
Left forall a b. (a -> b) -> a -> b
$ ParseError -> [Char]
showParsecErr ParseError
err
        Right [NamedCalExpr]
x  -> forall a b. b -> Either a b
Right [NamedCalExpr]
x
        where
        parseCalExprSepBySemicolon :: P.Parser [NamedCalExpr]
        parseCalExprSepBySemicolon :: Parser [NamedCalExpr]
parseCalExprSepBySemicolon = forall s (m :: * -> *) t u a sep.
Stream s m t =>
ParsecT s u m a -> ParsecT s u m sep -> ParsecT s u m [a]
P.sepBy Parser NamedCalExpr
namedExpr (forall s (m :: * -> *) u.
Stream s m Char =>
Char -> ParsecT s u m Char
P.char Char
';' forall (f :: * -> *) a b. Applicative f => f a -> f b -> f a
<* forall s (m :: * -> *) u. Stream s m Char => ParsecT s u m ()
P.spaces) forall (f :: * -> *) a b. Applicative f => f a -> f b -> f a
<* forall s (m :: * -> *) t u.
(Stream s m t, Show t) =>
ParsecT s u m ()
P.eof

readOneNamedCalExpr :: String -> Either String NamedCalExpr
readOneNamedCalExpr :: [Char] -> Either [Char] NamedCalExpr
readOneNamedCalExpr [Char]
s =
    case forall s t u a.
Stream s Identity t =>
Parsec s u a -> u -> [Char] -> s -> Either ParseError a
P.runParser Parser NamedCalExpr
namedExpr () [Char]
"" [Char]
s of
        Left ParseError
err -> forall a b. a -> Either a b
Left forall a b. (a -> b) -> a -> b
$ ParseError -> [Char]
showParsecErr ParseError
err
        Right NamedCalExpr
x  -> forall a b. b -> Either a b
Right NamedCalExpr
x

readNamedCalExprsFromFile :: FilePath -> IO [NamedCalExpr]
readNamedCalExprsFromFile :: [Char] -> IO [NamedCalExpr]
readNamedCalExprsFromFile [Char]
uncalFile = do
    [[Char]]
ss <- [Char] -> [[Char]]
lines forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> [Char] -> IO [Char]
readFile [Char]
uncalFile
    forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
mapM [Char] -> IO NamedCalExpr
readOneLine [[Char]]
ss
    where
        readOneLine :: String -> IO NamedCalExpr
        readOneLine :: [Char] -> IO NamedCalExpr
readOneLine [Char]
s = case [Char] -> Either [Char] NamedCalExpr
readOneNamedCalExpr [Char]
s of
            Left [Char]
err -> forall e a. Exception e => e -> IO a
throwIO forall a b. (a -> b) -> a -> b
$ [Char] -> CurrycarbonException
CurrycarbonCLIParsingException forall a b. (a -> b) -> a -> b
$ [Char]
err forall a. [a] -> [a] -> [a]
++ [Char]
"\nin \"" forall a. [a] -> [a] -> [a]
++ [Char]
s forall a. [a] -> [a] -> [a]
++ [Char]
"\""
            Right NamedCalExpr
x  -> forall (m :: * -> *) a. Monad m => a -> m a
return NamedCalExpr
x

-- UncalC14
renderUncalC14WithoutName :: UncalC14 -> String
renderUncalC14WithoutName :: UncalC14 -> [Char]
renderUncalC14WithoutName (UncalC14 [Char]
_ YearBP
bp YearBP
sigma) = forall a. Show a => a -> [Char]
show YearBP
bp forall a. [a] -> [a] -> [a]
++ [Char]
"±" forall a. [a] -> [a] -> [a]
++ forall a. Show a => a -> [Char]
show YearBP
sigma forall a. [a] -> [a] -> [a]
++ [Char]
"BP"

renderUncalC14 :: UncalC14 -> String
renderUncalC14 :: UncalC14 -> [Char]
renderUncalC14 (UncalC14 [Char]
name YearBP
bp YearBP
sigma) = [Char]
name forall a. [a] -> [a] -> [a]
++ [Char]
":" forall a. [a] -> [a] -> [a]
++ forall a. Show a => a -> [Char]
show YearBP
bp forall a. [a] -> [a] -> [a]
++ [Char]
"±" forall a. [a] -> [a] -> [a]
++ forall a. Show a => a -> [Char]
show YearBP
sigma forall a. [a] -> [a] -> [a]
++ [Char]
"BP"

-- | Read uncalibrated radiocarbon dates from a file. The file should feature one radiocarbon date
-- per line in the form "\<sample name\>,\<mean age BP\>,\<one sigma standard deviation\>", where
-- \<sample name\> is optional. A valid file could look like this:
--
-- @
-- Sample1,5000,30
-- 6000,50
-- Sample3,4000,25
-- @
--
readUncalC14FromFile :: FilePath -> IO [UncalC14]
readUncalC14FromFile :: [Char] -> IO [UncalC14]
readUncalC14FromFile [Char]
uncalFile = do
    [Char]
s <- [Char] -> IO [Char]
readFile [Char]
uncalFile
    case forall s t u a.
Stream s Identity t =>
Parsec s u a -> u -> [Char] -> s -> Either ParseError a
P.runParser Parser [UncalC14]
uncalC14SepByNewline () [Char]
"" [Char]
s of
        Left ParseError
err -> forall e a. Exception e => e -> IO a
throwIO forall a b. (a -> b) -> a -> b
$ [Char] -> CurrycarbonException
CurrycarbonCLIParsingException forall a b. (a -> b) -> a -> b
$ ParseError -> [Char]
showParsecErr ParseError
err
        Right [UncalC14]
x  -> forall (m :: * -> *) a. Monad m => a -> m a
return [UncalC14]
x
    where
        uncalC14SepByNewline :: P.Parser [UncalC14]
        uncalC14SepByNewline :: Parser [UncalC14]
uncalC14SepByNewline = forall s (m :: * -> *) t u a sep.
Stream s m t =>
ParsecT s u m a -> ParsecT s u m sep -> ParsecT s u m [a]
P.endBy Parser UncalC14
parseUncalC14 (forall s (m :: * -> *) u. Stream s m Char => ParsecT s u m Char
P.newline forall (f :: * -> *) a b. Applicative f => f a -> f b -> f a
<* forall s (m :: * -> *) u. Stream s m Char => ParsecT s u m ()
P.spaces) forall (f :: * -> *) a b. Applicative f => f a -> f b -> f a
<* forall s (m :: * -> *) t u.
(Stream s m t, Show t) =>
ParsecT s u m ()
P.eof

readUncalC14 :: String -> Either String [UncalC14]
readUncalC14 :: [Char] -> Either [Char] [UncalC14]
readUncalC14 [Char]
s =
    case forall s t u a.
Stream s Identity t =>
Parsec s u a -> u -> [Char] -> s -> Either ParseError a
P.runParser Parser [UncalC14]
uncalC14SepBySemicolon () [Char]
"" [Char]
s of
        Left ParseError
err -> forall a b. a -> Either a b
Left forall a b. (a -> b) -> a -> b
$ ParseError -> [Char]
showParsecErr ParseError
err
        Right [UncalC14]
x  -> forall a b. b -> Either a b
Right [UncalC14]
x
    where
        uncalC14SepBySemicolon :: P.Parser [UncalC14]
        uncalC14SepBySemicolon :: Parser [UncalC14]
uncalC14SepBySemicolon = forall s (m :: * -> *) t u a sep.
Stream s m t =>
ParsecT s u m a -> ParsecT s u m sep -> ParsecT s u m [a]
P.sepBy Parser UncalC14
parseUncalC14 (forall s (m :: * -> *) u.
Stream s m Char =>
Char -> ParsecT s u m Char
P.char Char
';' forall (f :: * -> *) a b. Applicative f => f a -> f b -> f a
<* forall s (m :: * -> *) u. Stream s m Char => ParsecT s u m ()
P.spaces) forall (f :: * -> *) a b. Applicative f => f a -> f b -> f a
<* forall s (m :: * -> *) t u.
(Stream s m t, Show t) =>
ParsecT s u m ()
P.eof

parseUncalC14 :: P.Parser UncalC14
parseUncalC14 :: Parser UncalC14
parseUncalC14 = forall s u (m :: * -> *) a. ParsecT s u m a -> ParsecT s u m a
P.try Parser UncalC14
record forall s u (m :: * -> *) a.
ParsecT s u m a -> ParsecT s u m a -> ParsecT s u m a
P.<|> forall s u (m :: * -> *) a. ParsecT s u m a -> ParsecT s u m a
P.try Parser UncalC14
long forall s u (m :: * -> *) a.
ParsecT s u m a -> ParsecT s u m a -> ParsecT s u m a
P.<|> Parser UncalC14
short
    where
        record :: Parser UncalC14
record = forall a. [Char] -> Parser a -> Parser a
parseRecordType [Char]
"uncalC14" forall a b. (a -> b) -> a -> b
$ forall s u (m :: * -> *) a. ParsecT s u m a -> ParsecT s u m a
P.try Parser UncalC14
long forall s u (m :: * -> *) a.
ParsecT s u m a -> ParsecT s u m a -> ParsecT s u m a
P.<|> Parser UncalC14
short
        long :: Parser UncalC14
long = do
            [Char]
name  <- forall a. [Char] -> Parser a -> Parser a
parseArgument [Char]
"id" Parser [Char]
parseAnyString
            YearBP
age   <- forall a. [Char] -> Parser a -> Parser a
parseArgument [Char]
"yearBP" Parser YearBP
parseWord
            YearBP
sigma <- forall a. [Char] -> Parser a -> Parser a
parseArgument [Char]
"sigma" Parser YearBP
parseWord
            forall (m :: * -> *) a. Monad m => a -> m a
return ([Char] -> YearBP -> YearBP -> UncalC14
UncalC14 [Char]
name YearBP
age YearBP
sigma)
        short :: Parser UncalC14
short = do
            YearBP
age   <- forall a. [Char] -> Parser a -> Parser a
parseArgument [Char]
"yearBP" Parser YearBP
parseWord
            YearBP
sigma <- forall a. [Char] -> Parser a -> Parser a
parseArgument [Char]
"sigma" Parser YearBP
parseWord
            forall (m :: * -> *) a. Monad m => a -> m a
return ([Char] -> YearBP -> YearBP -> UncalC14
UncalC14 [Char]
"" YearBP
age YearBP
sigma)

-- CalC14
-- | Write 'CalC14's to the file system. The output file is a long .tsv file with the following structure:
--
-- @
-- id  hdrSigmaLevel  hdrStartYearBCAD  hdrStopYearBCAD
-- Sample1  1	-3797	-3709
-- Sample1  1	-3894	-3880
-- Sample1  2	-3680	-3655
-- Sample1  2	-3810	-3700
-- Sample1  2	-3941	-3864
-- Sample2  1	-1142	-1130
-- Sample2	1	-1173	-1161
-- Sample2	1	-1293	-1194
-- Sample2	1	-1368	-1356
-- Sample2	2	-1061	-1059
-- Sample2	2	-1323	-1112
-- Sample2	2	-1393	-1334
-- @
--
writeCalC14s :: FilePath -> [CalC14] -> IO ()
writeCalC14s :: [Char] -> [CalC14] -> IO ()
writeCalC14s [Char]
path [CalC14]
calC14s = [Char] -> [Char] -> IO ()
writeFile [Char]
path forall a b. (a -> b) -> a -> b
$
    [Char]
"id\thdrSigmaLevel\thdrStartYearBCAD\thdrStopYearBCAD\n"
    forall a. [a] -> [a] -> [a]
++ forall a. [a] -> [[a]] -> [a]
intercalate [Char]
"\n" (forall a b. (a -> b) -> [a] -> [b]
map CalC14 -> [Char]
renderCalC14ForFile [CalC14]
calC14s)

writeCalC14 :: FilePath -> CalC14 -> IO ()
writeCalC14 :: [Char] -> CalC14 -> IO ()
writeCalC14 [Char]
path CalC14
calC14 = [Char] -> [Char] -> IO ()
writeFile [Char]
path forall a b. (a -> b) -> a -> b
$
    [Char]
"id\thdrSigmaLevel\thdrStartYearBCAD\thdrStopYearBCAD\n"
    forall a. [a] -> [a] -> [a]
++ CalC14 -> [Char]
renderCalC14ForFile CalC14
calC14

appendCalC14 :: FilePath -> CalC14 -> IO ()
appendCalC14 :: [Char] -> CalC14 -> IO ()
appendCalC14 [Char]
path CalC14
calC14 =
    [Char] -> [Char] -> IO ()
appendFile [Char]
path forall a b. (a -> b) -> a -> b
$ [Char]
"\n" forall a. [a] -> [a] -> [a]
++ CalC14 -> [Char]
renderCalC14ForFile CalC14
calC14

renderCalC14ForFile :: CalC14 -> String
renderCalC14ForFile :: CalC14 -> [Char]
renderCalC14ForFile (CalC14 [Char]
name CalRangeSummary
_ [HDR]
hdrs68 [HDR]
hdrs95) =
    forall a. [a] -> [[a]] -> [a]
intercalate [Char]
"\n" forall a b. (a -> b) -> a -> b
$
        forall a b. (a -> b) -> [a] -> [b]
map ([Char], [Char], ([Char], [Char])) -> [Char]
renderRow forall a b. (a -> b) -> a -> b
$
        forall a b c. [a] -> [b] -> [c] -> [(a, b, c)]
zip3 (forall a. a -> [a]
repeat [Char]
name) (forall a. a -> [a]
repeat [Char]
"1") ([HDR] -> [([Char], [Char])]
renderHDRsForFile [HDR]
hdrs68) forall a. [a] -> [a] -> [a]
++
        forall a b c. [a] -> [b] -> [c] -> [(a, b, c)]
zip3 (forall a. a -> [a]
repeat [Char]
name) (forall a. a -> [a]
repeat [Char]
"2") ([HDR] -> [([Char], [Char])]
renderHDRsForFile [HDR]
hdrs95)
    where
        renderRow :: (String, String, (String, String)) -> String
        renderRow :: ([Char], [Char], ([Char], [Char])) -> [Char]
renderRow ([Char]
a, [Char]
b, ([Char]
c, [Char]
d)) = forall a. [a] -> [[a]] -> [a]
intercalate [Char]
"\t" [[Char]
a,[Char]
b,[Char]
c,[Char]
d]

renderCalC14s :: [CalC14] -> String
renderCalC14s :: [CalC14] -> [Char]
renderCalC14s [CalC14]
xs =
    [Char]
"Calibrated high density ranges (HDR):\n"
    forall a. [a] -> [a] -> [a]
++ forall a. [a] -> [[a]] -> [a]
intercalate [Char]
"\n" (forall a b. (a -> b) -> [a] -> [b]
map CalC14 -> [Char]
renderCalC14 [CalC14]
xs)

renderCalC14 :: CalC14 -> String
renderCalC14 :: CalC14 -> [Char]
renderCalC14 (CalC14 [Char]
_ CalRangeSummary
rangeSummary [HDR]
hdrs68 [HDR]
hdrs95) =
       [Char]
"Calibrated: " forall a. [a] -> [a] -> [a]
++ CalRangeSummary -> [Char]
renderCalRangeSummary CalRangeSummary
rangeSummary forall a. [a] -> [a] -> [a]
++ [Char]
"\n"
    forall a. [a] -> [a] -> [a]
++ [Char]
"1-sigma: " forall a. [a] -> [a] -> [a]
++ [HDR] -> [Char]
renderHDRs [HDR]
hdrs68 forall a. [a] -> [a] -> [a]
++ [Char]
"\n"
    forall a. [a] -> [a] -> [a]
++ [Char]
"2-sigma: " forall a. [a] -> [a] -> [a]
++ [HDR] -> [Char]
renderHDRs [HDR]
hdrs95

renderCalRangeSummary :: CalRangeSummary -> String
renderCalRangeSummary :: CalRangeSummary -> [Char]
renderCalRangeSummary CalRangeSummary
s =
       YearBCAD -> [Char]
renderYearBCAD (CalRangeSummary -> YearBCAD
_calRangeStartTwoSigma CalRangeSummary
s) forall a. [a] -> [a] -> [a]
++ [Char]
" >> "
    forall a. [a] -> [a] -> [a]
++ YearBCAD -> [Char]
renderYearBCAD (CalRangeSummary -> YearBCAD
_calRangeStartOneSigma CalRangeSummary
s) forall a. [a] -> [a] -> [a]
++ [Char]
" > "
    forall a. [a] -> [a] -> [a]
++ YearBCAD -> [Char]
renderYearBCAD (CalRangeSummary -> YearBCAD
_calRangeMedian CalRangeSummary
s) forall a. [a] -> [a] -> [a]
++ [Char]
" < "
    forall a. [a] -> [a] -> [a]
++ YearBCAD -> [Char]
renderYearBCAD (CalRangeSummary -> YearBCAD
_calRangeStopOneSigma CalRangeSummary
s) forall a. [a] -> [a] -> [a]
++ [Char]
" << "
    forall a. [a] -> [a] -> [a]
++ YearBCAD -> [Char]
renderYearBCAD (CalRangeSummary -> YearBCAD
_calRangeStopTwoSigma CalRangeSummary
s)

-- BP
renderYearBP :: YearBP -> String
renderYearBP :: YearBP -> [Char]
renderYearBP YearBP
x =
    forall a. Show a => a -> [Char]
show YearBP
x forall a. [a] -> [a] -> [a]
++ [Char]
"BP" -- ++ " (" ++ (renderYearBCAD $ bp2BCAD x) ++ ")"

-- BCAD
renderYearBCAD :: YearBCAD -> String
renderYearBCAD :: YearBCAD -> [Char]
renderYearBCAD YearBCAD
x
    | YearBCAD
x forall a. Ord a => a -> a -> Bool
< YearBCAD
0  = forall a. Show a => a -> [Char]
show (-YearBCAD
x) forall a. [a] -> [a] -> [a]
++ [Char]
"BC"
    | YearBCAD
x forall a. Ord a => a -> a -> Bool
>= YearBCAD
0 = forall a. Show a => a -> [Char]
show YearBCAD
x forall a. [a] -> [a] -> [a]
++ [Char]
"AD"
    | Bool
otherwise = forall a. HasCallStack => [Char] -> a
error forall a b. (a -> b) -> a -> b
$ [Char]
"This should never happen: " forall a. [a] -> [a] -> [a]
++ forall a. Show a => a -> [Char]
show YearBCAD
x

-- HDR
renderHDRsForFile :: [HDR] -> [(String, String)]
renderHDRsForFile :: [HDR] -> [([Char], [Char])]
renderHDRsForFile = forall a b. (a -> b) -> [a] -> [b]
map HDR -> ([Char], [Char])
renderHDRForFile

renderHDRForFile :: HDR -> (String, String)
renderHDRForFile :: HDR -> ([Char], [Char])
renderHDRForFile (HDR YearBCAD
start YearBCAD
stop) = (forall a. Show a => a -> [Char]
show YearBCAD
start, forall a. Show a => a -> [Char]
show YearBCAD
stop)

renderHDRs :: [HDR] -> String
renderHDRs :: [HDR] -> [Char]
renderHDRs [HDR]
xs = forall a. [a] -> [[a]] -> [a]
intercalate [Char]
", " (forall a b. (a -> b) -> [a] -> [b]
map HDR -> [Char]
renderHDR [HDR]
xs)

renderHDR :: HDR -> String
renderHDR :: HDR -> [Char]
renderHDR (HDR YearBCAD
start YearBCAD
stop)
    | YearBCAD
start forall a. Ord a => a -> a -> Bool
< YearBCAD
0 Bool -> Bool -> Bool
&& YearBCAD
stop forall a. Ord a => a -> a -> Bool
<= YearBCAD
0  = forall a. Show a => a -> [Char]
show (-YearBCAD
start) forall a. [a] -> [a] -> [a]
++ [Char]
"-" forall a. [a] -> [a] -> [a]
++ forall a. Show a => a -> [Char]
show (-YearBCAD
stop) forall a. [a] -> [a] -> [a]
++ [Char]
"BC"
    | YearBCAD
start forall a. Ord a => a -> a -> Bool
< YearBCAD
0 Bool -> Bool -> Bool
&& YearBCAD
stop forall a. Ord a => a -> a -> Bool
> YearBCAD
0   = forall a. Show a => a -> [Char]
show (-YearBCAD
start) forall a. [a] -> [a] -> [a]
++ [Char]
"BC-" forall a. [a] -> [a] -> [a]
++ forall a. Show a => a -> [Char]
show YearBCAD
stop forall a. [a] -> [a] -> [a]
++ [Char]
"AD"
    | YearBCAD
start forall a. Ord a => a -> a -> Bool
>= YearBCAD
0 Bool -> Bool -> Bool
&& YearBCAD
stop forall a. Ord a => a -> a -> Bool
>= YearBCAD
0 = forall a. Show a => a -> [Char]
show YearBCAD
start forall a. [a] -> [a] -> [a]
++ [Char]
"-" forall a. [a] -> [a] -> [a]
++ forall a. Show a => a -> [Char]
show YearBCAD
stop forall a. [a] -> [a] -> [a]
++ [Char]
"AD"
    | Bool
otherwise = forall a. HasCallStack => [Char] -> a
error forall a b. (a -> b) -> a -> b
$ [Char]
"This should never happen: " forall a. [a] -> [a] -> [a]
++ forall a. Show a => a -> [Char]
show YearBCAD
start forall a. [a] -> [a] -> [a]
++ [Char]
"-" forall a. [a] -> [a] -> [a]
++ forall a. Show a => a -> [Char]
show YearBCAD
stop

-- CalCurveMatrix
writeCalCurveMatrix :: FilePath -> CalCurveMatrix -> IO ()
writeCalCurveMatrix :: [Char] -> CalCurveMatrix -> IO ()
writeCalCurveMatrix [Char]
path CalCurveMatrix
calCurveMatrix =
    [Char] -> [Char] -> IO ()
writeFile [Char]
path forall a b. (a -> b) -> a -> b
$ CalCurveMatrix -> [Char]
renderCalCurveMatrix CalCurveMatrix
calCurveMatrix

renderCalCurveMatrix :: CalCurveMatrix -> String
renderCalCurveMatrix :: CalCurveMatrix -> [Char]
renderCalCurveMatrix (CalCurveMatrix Vector YearBCAD
uncals Vector YearBCAD
cals Vector (Vector Float)
curveDensities) =
    let header :: [Char]
header = [Char]
"\t" forall a. [a] -> [a] -> [a]
++ forall a. [a] -> [[a]] -> [a]
intercalate [Char]
"\t" (forall a b. (a -> b) -> [a] -> [b]
map forall a. Show a => a -> [Char]
show forall a b. (a -> b) -> a -> b
$ forall a. Unbox a => Vector a -> [a]
VU.toList Vector YearBCAD
cals) forall a. [a] -> [a] -> [a]
++ [Char]
"\n"
        body :: [[Char]]
body = forall a b c. (a -> b -> c) -> [a] -> [b] -> [c]
zipWith forall {a} {a}. (Show a, Show a) => a -> [a] -> [Char]
makeRow (forall a. Unbox a => Vector a -> [a]
VU.toList Vector YearBCAD
uncals) (forall a. [[a]] -> [[a]]
transpose forall a b. (a -> b) -> a -> b
$ forall a. Vector a -> [a]
V.toList (forall a b. (a -> b) -> Vector a -> Vector b
V.map forall a. Unbox a => Vector a -> [a]
VU.toList Vector (Vector Float)
curveDensities))
    in [Char]
header forall a. [a] -> [a] -> [a]
++ forall a. [a] -> [[a]] -> [a]
intercalate [Char]
"\n" [[Char]]
body
    where
      makeRow :: a -> [a] -> [Char]
makeRow a
uncal [a]
dens = forall a. Show a => a -> [Char]
show a
uncal forall a. [a] -> [a] -> [a]
++ [Char]
"\t" forall a. [a] -> [a] -> [a]
++ forall a. [a] -> [[a]] -> [a]
intercalate [Char]
"\t" (forall a b. (a -> b) -> [a] -> [b]
map forall a. Show a => a -> [Char]
show [a]
dens)

-- CalPDF
-- | Write 'CalPDF's to the file system. The output file is a long .tsv file with the following structure:
--
-- @
-- id  yearBCAD  density
-- ...
-- Sample1  -1391   2.8917924e-4
-- Sample1  -1390   3.3285577e-4
-- Sample1  -1389   3.5674628e-4
-- Sample1  -1388   3.750703e-4
-- ...
-- Sample2  -3678   1.8128564e-3
-- Sample2  -3677   1.9512239e-3
-- Sample2  -3676   2.0227064e-3
-- Sample2  -3675   2.095691e-3
-- ...
-- @
--
writeCalPDFs :: FilePath -> [CalPDF] -> IO ()
writeCalPDFs :: [Char] -> [CalPDF] -> IO ()
writeCalPDFs [Char]
path [CalPDF]
calPDFs =
    [Char] -> [Char] -> IO ()
writeFile [Char]
path forall a b. (a -> b) -> a -> b
$
        [Char]
"id\tyearBCAD\tdensity\n"
        forall a. [a] -> [a] -> [a]
++ [CalPDF] -> [Char]
renderCalPDFs [CalPDF]
calPDFs

writeCalPDF :: FilePath -> CalPDF -> IO ()
writeCalPDF :: [Char] -> CalPDF -> IO ()
writeCalPDF [Char]
path CalPDF
calPDF =
    [Char] -> [Char] -> IO ()
writeFile [Char]
path forall a b. (a -> b) -> a -> b
$
        [Char]
"id\tyearBCAD\tdensity\n"
        forall a. [a] -> [a] -> [a]
++ CalPDF -> [Char]
renderCalPDF CalPDF
calPDF

appendCalPDF :: FilePath -> CalPDF -> IO ()
appendCalPDF :: [Char] -> CalPDF -> IO ()
appendCalPDF [Char]
path CalPDF
calPDF =
    [Char] -> [Char] -> IO ()
appendFile [Char]
path forall a b. (a -> b) -> a -> b
$ CalPDF -> [Char]
renderCalPDF CalPDF
calPDF

renderCalPDFs :: [CalPDF] -> String
renderCalPDFs :: [CalPDF] -> [Char]
renderCalPDFs = forall (t :: * -> *) a b. Foldable t => (a -> [b]) -> t a -> [b]
concatMap CalPDF -> [Char]
renderCalPDF

renderCalPDF :: CalPDF -> String
renderCalPDF :: CalPDF -> [Char]
renderCalPDF (CalPDF [Char]
name Vector YearBCAD
cals Vector Float
dens) =
    forall (t :: * -> *) a b. Foldable t => (a -> [b]) -> t a -> [b]
concatMap forall {a} {a}. (Show a, Show a) => (a, a) -> [Char]
makeRow forall a b. (a -> b) -> a -> b
$ forall a. Unbox a => Vector a -> [a]
VU.toList forall a b. (a -> b) -> a -> b
$ forall a b.
(Unbox a, Unbox b) =>
Vector a -> Vector b -> Vector (a, b)
VU.zip Vector YearBCAD
cals Vector Float
dens
    where
      makeRow :: (a, a) -> [Char]
makeRow (a
x,a
y) = [Char]
name forall a. [a] -> [a] -> [a]
++ [Char]
"\t" forall a. [a] -> [a] -> [a]
++ forall a. Show a => a -> [Char]
show a
x forall a. [a] -> [a] -> [a]
++ [Char]
"\t" forall a. [a] -> [a] -> [a]
++ forall a. Show a => a -> [Char]
show a
y forall a. [a] -> [a] -> [a]
++ [Char]
"\n"

-- cli plot
data PlotSymbol = HistFill | HistTop | AxisEnd | AxisLine | AxisTick | HDRLine

renderCLIPlotCalPDF :: Bool -> Int -> Int -> CalPDF -> CalC14 -> String
renderCLIPlotCalPDF :: Bool -> YearBCAD -> YearBCAD -> CalPDF -> CalC14 -> [Char]
renderCLIPlotCalPDF Bool
ascii YearBCAD
rows YearBCAD
cols (CalPDF [Char]
_ Vector YearBCAD
cals Vector Float
dens) CalC14
c14 =
     let startYear :: YearBCAD
startYear = forall a. Unbox a => Vector a -> a
VU.head Vector YearBCAD
cals
         stopYear :: YearBCAD
stopYear = forall a. Unbox a => Vector a -> a
VU.last Vector YearBCAD
cals
         yearsPerCol :: YearBCAD
yearsPerCol = case forall a. Integral a => a -> a -> a
quot (forall a. Unbox a => Vector a -> YearBCAD
VU.length Vector YearBCAD
cals) YearBCAD
cols of
            YearBCAD
0 -> YearBCAD
1 -- relevant for very short PDFs
            YearBCAD
1 -> YearBCAD
2
            YearBCAD
q -> YearBCAD
q
        -- last bin will often be shorter, which renders the whole plot slightly incorrect for the last column
         meanDensPerCol :: [YearBCAD]
meanDensPerCol = YearBCAD -> Vector Float -> [YearBCAD]
calculateMeanDens YearBCAD
yearsPerCol Vector Float
dens
         effectiveCols :: YearBCAD
effectiveCols = forall (t :: * -> *) a. Foldable t => t a -> YearBCAD
length [YearBCAD]
meanDensPerCol
         plotRows :: [[Char]]
plotRows = forall a b. (a -> b) -> [a] -> [b]
map (forall a. YearBCAD -> a -> [a]
replicate YearBCAD
8 Char
' ' forall a. [a] -> [a] -> [a]
++) forall a b. (a -> b) -> a -> b
$ forall a b. (a -> b) -> [a] -> [b]
map (\YearBCAD
x -> forall a b. (a -> b) -> [a] -> [b]
map (YearBCAD -> YearBCAD -> Char
getHistSymbol YearBCAD
x) [YearBCAD]
meanDensPerCol) forall a b. (a -> b) -> a -> b
$ forall a. [a] -> [a]
reverse [YearBCAD
0..YearBCAD
rows]
         xAxis :: [Char]
xAxis = YearBCAD -> YearBCAD -> YearBCAD -> YearBCAD -> [Char]
constructXAxis YearBCAD
startYear YearBCAD
stopYear YearBCAD
effectiveCols YearBCAD
yearsPerCol
     in forall a. [a] -> [[a]] -> [a]
intercalate [Char]
"\n" [[Char]]
plotRows forall a. [a] -> [a] -> [a]
++ [Char]
"\n" forall a. [a] -> [a] -> [a]
++ [Char]
xAxis
     where
        calculateMeanDens :: Int -> VU.Vector Float -> [Int]
        calculateMeanDens :: YearBCAD -> Vector Float -> [YearBCAD]
calculateMeanDens YearBCAD
yearsPerCol Vector Float
dens_ =
            let scaling :: Float
scaling = forall a b. (Integral a, Num b) => a -> b
fromIntegral YearBCAD
rows
                meanDens :: [Float]
meanDens = forall a b. (a -> b) -> [a] -> [b]
map (\[Float]
x -> forall (t :: * -> *) a. (Foldable t, Num a) => t a -> a
sum [Float]
x forall a. Fractional a => a -> a -> a
/ forall a b. (Integral a, Num b) => a -> b
fromIntegral (forall (t :: * -> *) a. Foldable t => t a -> YearBCAD
length [Float]
x)) forall a b. (a -> b) -> a -> b
$ forall a. YearBCAD -> [a] -> [[a]]
splitEvery YearBCAD
yearsPerCol forall a b. (a -> b) -> a -> b
$ forall a. Unbox a => Vector a -> [a]
VU.toList Vector Float
dens_
                maxDens :: Float
maxDens = forall (t :: * -> *) a. (Foldable t, Ord a) => t a -> a
maximum [Float]
meanDens
            in forall a b. (a -> b) -> [a] -> [b]
map (\Float
x -> forall a b. (RealFrac a, Integral b) => a -> b
round forall a b. (a -> b) -> a -> b
$ (Float
x forall a. Fractional a => a -> a -> a
/ Float
maxDens) forall a. Num a => a -> a -> a
* Float
scaling) [Float]
meanDens
        splitEvery :: Int -> [a] -> [[a]] -- https://stackoverflow.com/a/8681226/3216883
        splitEvery :: forall a. YearBCAD -> [a] -> [[a]]
splitEvery YearBCAD
_ [] = []
        splitEvery YearBCAD
n [a]
list = [a]
first forall a. a -> [a] -> [a]
: forall a. YearBCAD -> [a] -> [[a]]
splitEvery YearBCAD
n [a]
rest
            where ([a]
first,[a]
rest) = forall a. YearBCAD -> [a] -> ([a], [a])
splitAt YearBCAD
n [a]
list
        padString :: Int -> String -> String
        padString :: YearBCAD -> [Char] -> [Char]
padString YearBCAD
l [Char]
x = forall a. YearBCAD -> a -> [a]
replicate (YearBCAD
l forall a. Num a => a -> a -> a
- forall (t :: * -> *) a. Foldable t => t a -> YearBCAD
length [Char]
x) Char
' ' forall a. [a] -> [a] -> [a]
++ [Char]
x
        getSymbol :: Bool -> PlotSymbol -> Char
        getSymbol :: Bool -> PlotSymbol -> Char
getSymbol Bool
True PlotSymbol
HistFill  = Char
'*'
        getSymbol Bool
False PlotSymbol
HistFill = Char
'▒'
        getSymbol Bool
True PlotSymbol
HistTop   = Char
'_'
        getSymbol Bool
False PlotSymbol
HistTop  = Char
'▁'
        getSymbol Bool
True PlotSymbol
AxisEnd   = Char
'+'
        getSymbol Bool
False PlotSymbol
AxisEnd  = Char
'┄'
        getSymbol Bool
True PlotSymbol
AxisLine  = Char
'-'
        getSymbol Bool
False PlotSymbol
AxisLine = Char
'─'
        getSymbol Bool
True PlotSymbol
AxisTick  = Char
'|'
        getSymbol Bool
False PlotSymbol
AxisTick = Char
'┬'
        getSymbol Bool
True PlotSymbol
HDRLine   = Char
'-'
        getSymbol Bool
False PlotSymbol
HDRLine  = Char
'─'
        getHistSymbol :: Int -> Int -> Char
        getHistSymbol :: YearBCAD -> YearBCAD -> Char
getHistSymbol YearBCAD
x YearBCAD
y
            | YearBCAD
x forall a. Eq a => a -> a -> Bool
== YearBCAD
y = Bool -> PlotSymbol -> Char
getSymbol Bool
ascii PlotSymbol
HistTop
            | YearBCAD
x forall a. Ord a => a -> a -> Bool
< YearBCAD
y  = Bool -> PlotSymbol -> Char
getSymbol Bool
ascii PlotSymbol
HistFill
            | Bool
otherwise = Char
' '
        constructXAxis :: Int -> Int -> Int -> Int -> String
        constructXAxis :: YearBCAD -> YearBCAD -> YearBCAD -> YearBCAD -> [Char]
constructXAxis YearBCAD
startYear YearBCAD
stopYear YearBCAD
effCols YearBCAD
yearsPerCol =
            let startS :: [Char]
startS = YearBCAD -> [Char] -> [Char]
padString YearBCAD
6 (forall a. Show a => a -> [Char]
show forall a b. (a -> b) -> a -> b
$ YearBCAD -> YearBCAD
roundTo10 YearBCAD
startYear)
                stopS :: [Char]
stopS = forall a. Show a => a -> [Char]
show (YearBCAD -> YearBCAD
roundTo10 YearBCAD
stopYear)
                tickFreq :: YearBCAD
tickFreq = if forall a. Num a => a -> a
abs (YearBCAD
startYear forall a. Num a => a -> a -> a
- YearBCAD
stopYear) forall a. Ord a => a -> a -> Bool
< YearBCAD
1500 then YearBCAD
100 else YearBCAD
1000
                colStartYears :: [YearBCAD]
colStartYears = forall a b. (a -> b) -> [a] -> [b]
map (\YearBCAD
a -> YearBCAD
startYear forall a. Num a => a -> a -> a
+ YearBCAD
yearsPerCol forall a. Num a => a -> a -> a
* YearBCAD
a) [YearBCAD
0..(YearBCAD
effCols forall a. Num a => a -> a -> a
- YearBCAD
1)]
                colStopYears :: [YearBCAD]
colStopYears  = forall a b. (a -> b) -> [a] -> [b]
map (\YearBCAD
b -> YearBCAD
startYear forall a. Num a => a -> a -> a
+ YearBCAD
yearsPerCol forall a. Num a => a -> a -> a
* YearBCAD
b forall a. Num a => a -> a -> a
- YearBCAD
1) [YearBCAD
1..YearBCAD
effCols]
                axis :: [Char]
axis        = forall a b c. (a -> b -> c) -> [a] -> [b] -> [c]
zipWith (YearBCAD -> YearBCAD -> YearBCAD -> Char
getAxisSymbol YearBCAD
tickFreq)                   [YearBCAD]
colStartYears [YearBCAD]
colStopYears
                simpleRange :: [Char]
simpleRange = forall a b c. (a -> b -> c) -> [a] -> [b] -> [c]
zipWith (CalRangeSummary -> YearBCAD -> YearBCAD -> Char
getRangeSymbol (CalC14 -> CalRangeSummary
_calC14RangeSummary CalC14
c14)) [YearBCAD]
colStartYears [YearBCAD]
colStopYears
                hdrOne :: [Char]
hdrOne      = forall a b c. (a -> b -> c) -> [a] -> [b] -> [c]
zipWith ([HDR] -> YearBCAD -> YearBCAD -> Char
getHDRSymbol (CalC14 -> [HDR]
_calC14HDROneSigma CalC14
c14))    [YearBCAD]
colStartYears [YearBCAD]
colStopYears
                hdrTwo :: [Char]
hdrTwo      = forall a b c. (a -> b -> c) -> [a] -> [b] -> [c]
zipWith ([HDR] -> YearBCAD -> YearBCAD -> Char
getHDRSymbol (CalC14 -> [HDR]
_calC14HDRTwoSigma CalC14
c14))    [YearBCAD]
colStartYears [YearBCAD]
colStopYears
            in  [Char]
startS forall a. [a] -> [a] -> [a]
++ ([Char]
" " forall a. [a] -> [a] -> [a]
++ [Bool -> PlotSymbol -> Char
getSymbol Bool
ascii PlotSymbol
AxisEnd]) forall a. [a] -> [a] -> [a]
++ [Char]
axis forall a. [a] -> [a] -> [a]
++ ([Bool -> PlotSymbol -> Char
getSymbol Bool
ascii PlotSymbol
AxisEnd] forall a. [a] -> [a] -> [a]
++ [Char]
" ") forall a. [a] -> [a] -> [a]
++ [Char]
stopS forall a. [a] -> [a] -> [a]
++ [Char]
"\n" forall a. [a] -> [a] -> [a]
++
                forall a. YearBCAD -> a -> [a]
replicate YearBCAD
8 Char
' ' forall a. [a] -> [a] -> [a]
++ [Char]
simpleRange forall a. [a] -> [a] -> [a]
++ [Char]
"\n" forall a. [a] -> [a] -> [a]
++
                forall a. YearBCAD -> a -> [a]
replicate YearBCAD
8 Char
' ' forall a. [a] -> [a] -> [a]
++ [Char]
hdrOne forall a. [a] -> [a] -> [a]
++ [Char]
"\n" forall a. [a] -> [a] -> [a]
++
                forall a. YearBCAD -> a -> [a]
replicate YearBCAD
8 Char
' ' forall a. [a] -> [a] -> [a]
++ [Char]
hdrTwo
            where
                roundTo10 :: Int -> Int
                roundTo10 :: YearBCAD -> YearBCAD
roundTo10 YearBCAD
x =
                    let (YearBCAD
dec,YearBCAD
rest) = forall a. Integral a => a -> a -> (a, a)
quotRem (forall a. Num a => a -> a
abs YearBCAD
x) YearBCAD
10
                        roundedDec :: YearBCAD
roundedDec = if YearBCAD
rest forall a. Ord a => a -> a -> Bool
>= YearBCAD
5 then YearBCAD
dec forall a. Num a => a -> a -> a
+ YearBCAD
1 else YearBCAD
dec
                    in YearBCAD
roundedDec forall a. Num a => a -> a -> a
* YearBCAD
10 forall a. Num a => a -> a -> a
* forall a. Num a => a -> a
signum YearBCAD
x
                getAxisSymbol :: Int -> Int -> Int -> Char
                getAxisSymbol :: YearBCAD -> YearBCAD -> YearBCAD -> Char
getAxisSymbol YearBCAD
tickFreq YearBCAD
colStartYear YearBCAD
colStopYear
                    | forall (t :: * -> *) a. Foldable t => (a -> Bool) -> t a -> Bool
any (\YearBCAD
x -> forall a. Integral a => a -> a -> a
rem YearBCAD
x YearBCAD
tickFreq forall a. Eq a => a -> a -> Bool
== YearBCAD
0) [YearBCAD
colStartYear..YearBCAD
colStopYear] = Bool -> PlotSymbol -> Char
getSymbol Bool
ascii PlotSymbol
AxisTick
                    | Bool
otherwise = Bool -> PlotSymbol -> Char
getSymbol Bool
ascii PlotSymbol
AxisLine
                getRangeSymbol :: CalRangeSummary -> Int -> Int -> Char
                getRangeSymbol :: CalRangeSummary -> YearBCAD -> YearBCAD -> Char
getRangeSymbol CalRangeSummary
range YearBCAD
colStartYear YearBCAD
colStopYear
                    | YearBCAD
colStartYear forall a. Ord a => a -> a -> Bool
<= CalRangeSummary -> YearBCAD
_calRangeMedian CalRangeSummary
range        Bool -> Bool -> Bool
&& YearBCAD
colStopYear forall a. Ord a => a -> a -> Bool
>= CalRangeSummary -> YearBCAD
_calRangeMedian CalRangeSummary
range        = Char
'^'
                    | YearBCAD
colStartYear forall a. Ord a => a -> a -> Bool
<= CalRangeSummary -> YearBCAD
_calRangeStartOneSigma CalRangeSummary
range Bool -> Bool -> Bool
&& YearBCAD
colStopYear forall a. Ord a => a -> a -> Bool
>= CalRangeSummary -> YearBCAD
_calRangeStartOneSigma CalRangeSummary
range = Char
'>'
                    | YearBCAD
colStartYear forall a. Ord a => a -> a -> Bool
<= CalRangeSummary -> YearBCAD
_calRangeStopOneSigma CalRangeSummary
range  Bool -> Bool -> Bool
&& YearBCAD
colStopYear forall a. Ord a => a -> a -> Bool
>= CalRangeSummary -> YearBCAD
_calRangeStopOneSigma CalRangeSummary
range  = Char
'<'
                    | YearBCAD
colStartYear forall a. Ord a => a -> a -> Bool
<= CalRangeSummary -> YearBCAD
_calRangeStartTwoSigma CalRangeSummary
range Bool -> Bool -> Bool
&& YearBCAD
colStopYear forall a. Ord a => a -> a -> Bool
>= CalRangeSummary -> YearBCAD
_calRangeStartTwoSigma CalRangeSummary
range = Char
'>'
                    | YearBCAD
colStartYear forall a. Ord a => a -> a -> Bool
<= CalRangeSummary -> YearBCAD
_calRangeStopTwoSigma CalRangeSummary
range  Bool -> Bool -> Bool
&& YearBCAD
colStopYear forall a. Ord a => a -> a -> Bool
>= CalRangeSummary -> YearBCAD
_calRangeStopTwoSigma CalRangeSummary
range  = Char
'<'
                    | Bool
otherwise = Char
' '
                getHDRSymbol :: [HDR] -> Int -> Int -> Char
                getHDRSymbol :: [HDR] -> YearBCAD -> YearBCAD -> Char
getHDRSymbol [HDR]
hdr YearBCAD
colStartYear YearBCAD
colStopYear
                    | forall (t :: * -> *) a. Foldable t => (a -> Bool) -> t a -> Bool
any (YearBCAD -> YearBCAD -> HDR -> Bool
doesOverlap YearBCAD
colStartYear YearBCAD
colStopYear) [HDR]
hdr = Bool -> PlotSymbol -> Char
getSymbol Bool
ascii PlotSymbol
HDRLine
                    | Bool
otherwise = Char
' '
                    where
                        doesOverlap :: Int -> Int -> HDR -> Bool
                        doesOverlap :: YearBCAD -> YearBCAD -> HDR -> Bool
doesOverlap YearBCAD
a YearBCAD
b HDR
h =
                            let ha :: YearBCAD
ha = HDR -> YearBCAD
_hdrstart HDR
h; hb :: YearBCAD
hb = HDR -> YearBCAD
_hdrstop HDR
h
                            in (YearBCAD
a forall a. Ord a => a -> a -> Bool
>= YearBCAD
ha Bool -> Bool -> Bool
&& YearBCAD
a forall a. Ord a => a -> a -> Bool
<= YearBCAD
hb) Bool -> Bool -> Bool
|| (YearBCAD
b forall a. Ord a => a -> a -> Bool
>= YearBCAD
ha Bool -> Bool -> Bool
&& YearBCAD
b forall a. Ord a => a -> a -> Bool
<= YearBCAD
hb) Bool -> Bool -> Bool
|| (YearBCAD
a forall a. Ord a => a -> a -> Bool
<= YearBCAD
ha Bool -> Bool -> Bool
&& YearBCAD
b forall a. Ord a => a -> a -> Bool
>= YearBCAD
hb)

-- CalCurve
writeCalCurve :: FilePath -> CalCurveBCAD -> IO ()
writeCalCurve :: [Char] -> CalCurveBCAD -> IO ()
writeCalCurve [Char]
path CalCurveBCAD
calCurve =
    [Char] -> [Char] -> IO ()
writeFile [Char]
path forall a b. (a -> b) -> a -> b
$ CalCurveBCAD -> [Char]
renderCalCurve CalCurveBCAD
calCurve

renderCalCurve :: CalCurveBCAD -> String
renderCalCurve :: CalCurveBCAD -> [Char]
renderCalCurve (CalCurveBCAD Vector YearBCAD
cals Vector YearBCAD
uncals Vector YearBP
sigmas) =
    let header :: [Char]
header = [Char]
"calYearBCAD\tuncalYearBCAD\tsigma\n"
        body :: [[Char]]
body = forall a b. (a -> b) -> [a] -> [b]
map forall {a} {a} {a}. (Show a, Show a, Show a) => (a, a, a) -> [Char]
makeRow forall a b. (a -> b) -> a -> b
$ forall a. Unbox a => Vector a -> [a]
VU.toList forall a b. (a -> b) -> a -> b
$ forall a b c.
(Unbox a, Unbox b, Unbox c) =>
Vector a -> Vector b -> Vector c -> Vector (a, b, c)
VU.zip3 Vector YearBCAD
cals Vector YearBCAD
uncals Vector YearBP
sigmas
    in [Char]
header forall a. [a] -> [a] -> [a]
++ forall a. [a] -> [[a]] -> [a]
intercalate [Char]
"\n" [[Char]]
body
    where
      makeRow :: (a, a, a) -> [Char]
makeRow (a
x,a
y,a
z) = forall a. Show a => a -> [Char]
show a
x forall a. [a] -> [a] -> [a]
++ [Char]
"\t" forall a. [a] -> [a] -> [a]
++ forall a. Show a => a -> [Char]
show a
y forall a. [a] -> [a] -> [a]
++ [Char]
"\t" forall a. [a] -> [a] -> [a]
++ forall a. Show a => a -> [Char]
show a
z

-- | Read a calibration curve file. The file must adhere to the current version of the
-- .c14 file format (e.g. [here](http://intcal.org/curves/intcal20.14c)). Look
-- [here](http://intcal.org/blurb.html) for other calibration curves
readCalCurveFromFile :: FilePath -> IO CalCurveBP
readCalCurveFromFile :: [Char] -> IO CalCurveBP
readCalCurveFromFile [Char]
calCurveFile = do
    [Char]
calCurve <- [Char] -> IO [Char]
readFile [Char]
calCurveFile
    forall (m :: * -> *) a. Monad m => a -> m a
return forall a b. (a -> b) -> a -> b
$ [Char] -> CalCurveBP
readCalCurve [Char]
calCurve

readCalCurve :: String -> CalCurveBP
readCalCurve :: [Char] -> CalCurveBP
readCalCurve [Char]
calCurveString = do
    case forall s t u a.
Stream s Identity t =>
Parsec s u a -> u -> [Char] -> s -> Either ParseError a
P.runParser Parser [(YearBP, YearBP, YearBP)]
parseCalCurve () [Char]
"" [Char]
calCurveString of
        Left ParseError
p  -> forall a. HasCallStack => [Char] -> a
error forall a b. (a -> b) -> a -> b
$ [Char]
"This should never happen." forall a. [a] -> [a] -> [a]
++ forall a. Show a => a -> [Char]
show ParseError
p
        Right [(YearBP, YearBP, YearBP)]
x -> Vector YearBP -> Vector YearBP -> Vector YearBP -> CalCurveBP
CalCurveBP
            (forall a. Unbox a => [a] -> Vector a
VU.fromList forall a b. (a -> b) -> a -> b
$ forall a b. (a -> b) -> [a] -> [b]
map (\(YearBP
a,YearBP
_,YearBP
_) -> YearBP
a) [(YearBP, YearBP, YearBP)]
x)
            (forall a. Unbox a => [a] -> Vector a
VU.fromList forall a b. (a -> b) -> a -> b
$ forall a b. (a -> b) -> [a] -> [b]
map (\(YearBP
_,YearBP
b,YearBP
_) -> YearBP
b) [(YearBP, YearBP, YearBP)]
x)
            (forall a. Unbox a => [a] -> Vector a
VU.fromList forall a b. (a -> b) -> a -> b
$ forall a b. (a -> b) -> [a] -> [b]
map (\(YearBP
_,YearBP
_,YearBP
c) -> YearBP
c) [(YearBP, YearBP, YearBP)]
x)

parseCalCurve :: P.Parser [(YearBP, YearBP, YearRange)]
parseCalCurve :: Parser [(YearBP, YearBP, YearBP)]
parseCalCurve = do
    forall s u (m :: * -> *) a. ParsecT s u m a -> ParsecT s u m ()
P.skipMany Parser [Char]
comments
    forall s (m :: * -> *) t u a sep.
Stream s m t =>
ParsecT s u m a -> ParsecT s u m sep -> ParsecT s u m [a]
P.sepEndBy Parser (YearBP, YearBP, YearBP)
parseCalCurveLine (forall s (m :: * -> *) t u a sep.
Stream s m t =>
ParsecT s u m a -> ParsecT s u m sep -> ParsecT s u m [a]
P.manyTill forall s (m :: * -> *) t u.
(Stream s m t, Show t) =>
ParsecT s u m t
P.anyToken (forall s u (m :: * -> *) a. ParsecT s u m a -> ParsecT s u m a
P.try forall s (m :: * -> *) u. Stream s m Char => ParsecT s u m Char
P.newline))

parseCalCurveLine :: P.Parser (YearBP, YearBP, YearRange)
parseCalCurveLine :: Parser (YearBP, YearBP, YearBP)
parseCalCurveLine = do
  YearBP
calBP <- Parser YearBP
parseWord
  Char
_ <- forall s (m :: * -> *) u.
Stream s m Char =>
[Char] -> ParsecT s u m Char
P.oneOf [Char]
","
  YearBP
bp <- Parser YearBP
parseWord
  Char
_ <- forall s (m :: * -> *) u.
Stream s m Char =>
[Char] -> ParsecT s u m Char
P.oneOf [Char]
","
  YearBP
sigma <- Parser YearBP
parseWord
  forall (m :: * -> *) a. Monad m => a -> m a
return (YearBP
calBP, YearBP
bp, YearBP
sigma)

comments :: P.Parser String
comments :: Parser [Char]
comments = do
    [Char]
_ <- forall s (m :: * -> *) u.
Stream s m Char =>
[Char] -> ParsecT s u m [Char]
P.string [Char]
"#"
    [Char]
_ <- forall s (m :: * -> *) t u a sep.
Stream s m t =>
ParsecT s u m a -> ParsecT s u m sep -> ParsecT s u m [a]
P.manyTill forall s (m :: * -> *) u. Stream s m Char => ParsecT s u m Char
P.anyChar forall s (m :: * -> *) u. Stream s m Char => ParsecT s u m Char
P.newline
    forall (m :: * -> *) a. Monad m => a -> m a
return [Char]
""

-- RandomAgeSamples
-- | Write 'RandomAgeSamples's to the file system. The output file is a long .tsv file with the following structure:
--
-- @
-- id  yearBCAD
-- ...
-- Sample1  -1221
-- Sample1  -1211
-- Sample1  -1230
-- Sample1  -1225
-- ...
-- Sample2  -3763
-- Sample2  -3788
-- Sample2  -3767
-- Sample2  -3774
-- ...
-- @
--
writeRandomAgeSamples :: FilePath -> [RandomAgeSample] -> IO ()
writeRandomAgeSamples :: [Char] -> [RandomAgeSample] -> IO ()
writeRandomAgeSamples [Char]
path [RandomAgeSample]
calPDFs =
    [Char] -> [Char] -> IO ()
writeFile [Char]
path forall a b. (a -> b) -> a -> b
$
        [Char]
"id\tyearBCAD\n"
        forall a. [a] -> [a] -> [a]
++ [RandomAgeSample] -> [Char]
renderRandomAgeSamples [RandomAgeSample]
calPDFs

writeRandomAgeSample :: FilePath -> RandomAgeSample -> IO ()
writeRandomAgeSample :: [Char] -> RandomAgeSample -> IO ()
writeRandomAgeSample [Char]
path RandomAgeSample
calPDF =
    [Char] -> [Char] -> IO ()
writeFile [Char]
path forall a b. (a -> b) -> a -> b
$
        [Char]
"id\tyearBCAD\n"
        forall a. [a] -> [a] -> [a]
++ RandomAgeSample -> [Char]
renderRandomAgeSample RandomAgeSample
calPDF

appendRandomAgeSample :: FilePath -> RandomAgeSample -> IO ()
appendRandomAgeSample :: [Char] -> RandomAgeSample -> IO ()
appendRandomAgeSample [Char]
path RandomAgeSample
calPDF =
    [Char] -> [Char] -> IO ()
appendFile [Char]
path forall a b. (a -> b) -> a -> b
$ RandomAgeSample -> [Char]
renderRandomAgeSample RandomAgeSample
calPDF

renderRandomAgeSamples :: [RandomAgeSample] -> String
renderRandomAgeSamples :: [RandomAgeSample] -> [Char]
renderRandomAgeSamples = forall (t :: * -> *) a b. Foldable t => (a -> [b]) -> t a -> [b]
concatMap RandomAgeSample -> [Char]
renderRandomAgeSample

renderRandomAgeSample :: RandomAgeSample -> String
renderRandomAgeSample :: RandomAgeSample -> [Char]
renderRandomAgeSample (RandomAgeSample [Char]
name Vector YearBCAD
samples) =
    forall (t :: * -> *) a b. Foldable t => (a -> [b]) -> t a -> [b]
concatMap forall a. Show a => a -> [Char]
makeRow forall a b. (a -> b) -> a -> b
$ forall a. Unbox a => Vector a -> [a]
VU.toList Vector YearBCAD
samples
    where
      makeRow :: a -> [Char]
makeRow a
x = [Char]
name forall a. [a] -> [a] -> [a]
++ [Char]
"\t" forall a. [a] -> [a] -> [a]
++ forall a. Show a => a -> [Char]
show a
x forall a. [a] -> [a] -> [a]
++ [Char]
"\n"