{-# LANGUAGE GeneralizedNewtypeDeriving #-}
{-# LANGUAGE FlexibleInstances #-}
{-# LANGUAGE FlexibleContexts #-}
{-# LANGUAGE UndecidableInstances #-}
{- | Discrete Bayesian Network Library.

It is a very preliminary version. It has only been tested on very simple
examples where it worked. On bigger networks, imported from Hugin files, it was very very very slow.
So, you can use this software as a toy. Much more work is needed to validate
and optimize it. 

Look at the "Bayes.Examples" and "Bayes.Examples.Tutorial" in this package 
to see how to use the library.

-}
module Bayes(
  -- * Graph
  -- ** Graph classes
    Graph(..)
  , UndirectedGraph(..)
  , DirectedGraph(..)
  , FoldableWithVertex(..)
  , NamedGraph(..)
  -- ** Graph Monad
  , GraphMonad
  , GMState(..)
  , graphNode
  , runGraph
  , execGraph
  , evalGraph
  -- ** Support functions for Graph constructions
  , Vertex
  , Edge 
  , edge
  , newEdge
  , edgeEndPoints
  , connectedGraph
  -- * SimpleGraph implementation
  -- ** The SimpleGraph type
  , DirectedSG
  , UndirectedSG
  -- ** Bayesian network
  , SBN
  , BayesianNetwork(..)
  -- * Bayesian Monad used to ease creation of Bayesian Networks
  , BNMonad
  , runBN 
  , evalBN
  , execBN
  , variable
  , variableWithSize
  , cpt
  , proba
  , t
  , (~~)
  -- * Testing
  , testEdgeRemoval_prop
  , testVertexRemoval_prop
) where

import qualified Data.IntMap as IM
import qualified Data.Map as M
import Control.Monad.State.Strict
import Control.Monad.Writer.Strict
import Control.Applicative((<$>))
import Bayes.Factor
import Data.Maybe
import qualified Data.Map as Map
import qualified Data.Foldable as F
import qualified Data.Traversable as T 
import Control.Applicative 
import qualified Data.Set as Set

import Test.QuickCheck
import Test.QuickCheck.Arbitrary
import Data.List(sort,intercalate,nub)

--import Debug.Trace
--debug a = trace (show a) a

-- | Bayesian network. g must be a directed graph and f a factor
type BayesianNetwork g f = g () f

instance Arbitrary (DirectedSG String String) where
  arbitrary = do 
    let createVertex g i = do 
          name <- arbitrary :: Gen String
          return $ addVertex (Vertex i) name g
        createEdge g (va,vb) = do 
          name <- arbitrary :: Gen String
          return $ addEdge (edge va vb) name g 

    nbVertex <- choose (1,8) :: Gen Int
    
    g <- foldM createVertex emptyGraph [1..nbVertex]

    let allPairs = [(Vertex x,Vertex y) | x <- [1..nbVertex], y <- [1..nbVertex], x /= y]
        anEdge (x,y) = arbitrary :: Gen Bool

    edges <- filterM anEdge allPairs

    foldM createEdge g edges

instance Arbitrary (DirectedSG () String) where
  arbitrary = do 
    let createVertex g i = do 
          name <- arbitrary :: Gen String
          return $ addVertex (Vertex i) name g
        createEdge g (va,vb) = do 
          return $ addEdge (edge va vb) () g 

    nbVertex <- choose (1,8) :: Gen Int
    
    g <- foldM createVertex emptyGraph [1..nbVertex]

    let allPairs = [(Vertex x,Vertex y) | x <- [1..nbVertex], y <- [1..nbVertex], x /= y]
        anEdge (x,y) = arbitrary :: Gen Bool

    edges <- filterM anEdge allPairs

    foldM createEdge g edges   

testEdgeRemoval_prop :: DirectedSG String String -> Property
testEdgeRemoval_prop g = (not . hasNoEdges) g ==> 
  let Just e = someEdge g
      Just (vs,ve) = edgeVertices g e
      Just bi = ingoing g ve
      Just bo = outgoing g vs
      g' = removeEdge e g 
      Just bi' = ingoing g' ve
      Just bo' = outgoing g' vs
  in
  (map (sort . (:) e ) [bi', bo'] == map sort [bi,bo]) &&
   (sort (allEdges g) == sort (e:allEdges g'))

testVertexRemoval_prop :: DirectedSG String String -> Property
testVertexRemoval_prop g = (not . hasNoVertices) g ==>
    let Just v = someVertex g
        Just bi = ingoing g v 
        Just bo = outgoing g v
        g' = removeVertex v g
        srcVertices = mapMaybe (startVertex g') bi
        dstVertices = mapMaybe (endVertex g') bo 
        isNotDstVertex = not . (v `elem`) . mapMaybe (endVertex g') . fromJust . outgoing g'
        isNotStartVertex = not . (v `elem`) . mapMaybe (startVertex g') . fromJust . ingoing g'
    in 
    (sort (allVertices g) == sort (v:allVertices g')) &&
      (all isNotDstVertex srcVertices) && (all isNotStartVertex dstVertices)


-- | Graph class used for graph processing algorithms.
-- A graph processing algorithm does not have to know how the graph is implemented nor if it is
-- directed or undirected
class Graph g where
    -- | Add a new vertex
    addVertex :: Vertex -> b -> g a b -> g a b
    -- | Remove a vertex
    removeVertex :: Vertex -> g a b -> g a b
    -- | Get the vertex value if the vertex is found in the graph
    vertexValue :: g a b -> Vertex -> Maybe b
    -- | Change the vertex value if the vertex is found in the graph
    changeVertexValue :: Vertex -> b -> g a b -> Maybe (g a b)
    -- | Generate a \"random\" vertex
    someVertex :: g a b -> Maybe Vertex

    -- | Check is the graph has no vertrex
    hasNoVertices :: g a b -> Bool

    -- | Generate all vertices
    allVertices :: g a b -> [Vertex]

    -- | Get all the values
    allVertexValues :: g a b -> [b]

    -- | Get all nodes
    allNodes :: g a b -> [(Vertex,b)]

    -- | Check if two vertices are linked by a vertex
    isLinkedWithAnEdge :: g a b -> Vertex -> Vertex -> Bool

    -- | Add an edge
    addEdge :: Edge -> a -> g a b  -> g a b

    -- | Remove an dedge
    removeEdge :: Edge -> g a b -> g a b

    -- | Vertices for an edge
    edgeVertices :: g a b -> Edge -> Maybe (Vertex,Vertex)

    -- | Edge value if the edge is found in the graph
    edgeValue :: g a b -> Edge -> Maybe a

    -- | Return a \"random\" edge
    someEdge :: g a b -> Maybe Edge

    -- | Check if the graph has no edges
    hasNoEdges :: g a b -> Bool

    -- | One extremity of the edge (which is the end only for directed edge)
    endVertex :: g a b -> Edge -> Maybe Vertex
    endVertex g e = do 
      (_,ve) <- edgeVertices g e
      return ve 
        
    -- | One extremity of the edge (which is the start only for directed edge)
    startVertex :: g a b -> Edge -> Maybe Vertex
    startVertex g e = do 
      (vs,_) <- edgeVertices g e
      return vs

    -- | All edges of the graph
    allEdges :: g a b -> [Edge]

    -- | All values of the graph
    allEdgeValues :: g a b -> [a]
   
    -- | Returns an empty graph
    emptyGraph :: g a b

    -- | Check if the graph is empty
    isEmpty :: g a b -> Bool
    isEmpty g = hasNoVertices g && hasNoEdges g

    -- | Check if the graph is oriented
    oriented :: g a b -> Bool

    -- | All the neighbors of a vertex
    neighbors :: g a b -> Vertex -> Maybe [Vertex]

-- | A named graph is a graph where the vertices have a name.
-- This name is not a vertex value. Putting this name in the vertex value
-- would make algorithm less readable.
-- A vertex name is only useful to display the graph.
-- Labeled graph has a different meaning in graph theory.
class Graph g => NamedGraph g where
    -- | Add a vertex with a vertex name in addition to the value
    addLabeledVertex :: String -> Vertex -> b -> g a b -> g a b
    -- | Returns the vertex label
    vertexLabel :: g a b -> Vertex -> Maybe String


-- | Undirected graph
class Graph g => UndirectedGraph g where
    edges :: g a b -> Vertex -> Maybe [Edge]

-- | Directed graph
class Graph g => DirectedGraph g where
    ingoing :: g a b -> Vertex -> Maybe [Edge]
    outgoing :: g a b -> Vertex -> Maybe [Edge]


-- | Check if the graph is connected
connectedGraph :: Graph g => g a b -> Bool 
connectedGraph g = 
  let visited = visitVertex g (Set.empty) ([fromJust $ someVertex g])
      vertices = Set.fromList $ allVertices g
      equalSets a b = Set.isSubsetOf a b && Set.isSubsetOf b a
  in 
  equalSets visited vertices
 where 
  visitVertex _ visited [] = visited
  visitVertex theGraph visited (current:n) = 
    if Set.member current visited
      then 
        visitVertex theGraph visited n
      else
        let n' = fromJust $ neighbors theGraph current
        in
        visitVertex theGraph (Set.insert current visited) (n ++ n')



                          


-- | Edge type used to identify and edge in a graph
data Edge = Edge !Vertex !Vertex deriving(Eq,Ord,Show)

-- | Create an edge description
edge :: Vertex -> Vertex -> Edge 
edge a b = Edge a b

-- | Endpoints of an edge
edgeEndPoints :: Edge -> (Vertex,Vertex)
edgeEndPoints (Edge va vb) = (va,vb)


-- | Synonym for undefined because it is clearer to use t to set the Enum bounds of a variable
t = undefined

-- | Neighborhood structure for directed or undirected edges
-- | Directed edges
data DE = DE ![Edge] ![Edge] deriving(Eq,Show)

-- | Undirected edges
data UE = UE ![Edge] deriving(Eq,Show)

-- | Class used to share as much code as possible between
-- directed and undirected graphs without
-- implementing an undirected graph as a graph where
-- we have a directed edge in both directions 
class NeighborhoodStructure n where
  -- | Return an empty neighborhood
  emptyNeighborhood :: n 
  -- | Ingoing edges
  ingoingNeighbors :: n -> [Edge]
  -- | Outgoing edge
  outgoingNeighbors :: n -> [Edge]
  -- | Remove an edge
  removeNeighborsEdge :: Edge -> n -> n
  -- | Add an outgoing edge
  addOutgoingEdge :: Edge -> n -> n
  -- Add in ingoing edge
  addIngoingEdge :: Edge -> n -> n

-- | Directed neighborhood structure for a vertex
instance NeighborhoodStructure DE where
  emptyNeighborhood = DE [] []
  ingoingNeighbors (DE i _) = i
  outgoingNeighbors (DE _ o) = o 
  removeNeighborsEdge e (DE i o) = 
    let i' = filter (/= e) i
        o' = filter (/= e) o 
    in 
    DE i' o'
  addOutgoingEdge e (DE i o) = DE i (e:o)
  addIngoingEdge e (DE i o) = DE (e:i) o

-- | Undirected neighborhood structure for a vertex
instance NeighborhoodStructure UE where
  emptyNeighborhood = UE []
  ingoingNeighbors (UE e) = e
  outgoingNeighbors (UE e) = e
  removeNeighborsEdge e (UE l) = 
    let l' = filter (/= e) l
    in 
    UE l'
  addOutgoingEdge e (UE l) = UE (e:l)
  addIngoingEdge e (UE l) = UE (e:l)

-- | Implementtaion of a SimpleGraph
data SimpleGraph local edgedata vertexdata = SP {
 -- | Mapping of edge to edge data
    edgeMap :: !(M.Map Edge edgedata) 
 -- ^ Mapping of vertex number to vertex neighborhood and vertex data
 ,  vertexMap :: !(IM.IntMap (local, vertexdata))
 -- ^ Vertex names. Used only to generate the graphviz representtaion. Names are useless for the algorithms
 -- and I don't want them to appear in the vetex values which should only be factor. Otherwise, the algorithms
 -- are less elegant since I have to extract the factors from the values
 , nameMap :: !(IM.IntMap String)
 } 

-- | Directed simple graph
type DirectedSG = SimpleGraph DE

-- | Undirected simple graph
type UndirectedSG = SimpleGraph UE

instance (Eq a, Eq b) => Eq (SimpleGraph DE a b) where
    (==) (SP a b _) (SP a' b' _) = a == a' && b == b'

-- | An empty simple graph
emptySimpleGraph = SP M.empty IM.empty IM.empty

-- | Used to prevent adding duplicates to a graph
noRedundancy new old = old

instance Functor (SimpleGraph local edge) where 
  fmap f (SP em vm nm) = SP em (IM.map (\(l,d) -> (l, f d)) vm) nm

instance F.Foldable (SimpleGraph local edge) where
  foldr f c (SP _ vm _) = IM.foldr (\(_,d) s -> f d s) c vm

instance T.Traversable (SimpleGraph local edge) where
  traverse f (SP em vm nm) = 
    let l = IM.toList vm -- [(IM.Key, (DE, String))]
        onTriple f (k,(l,v)) = (\z -> (k,(l,z))) <$> f v
        l' = T.traverse (onTriple f) l -- f [(k,(l,z))]
        result y =  (\x -> SP em (IM.fromList x) nm) <$> y
    in 
    result l'

-- | The foldable class is limited. For a graph g we may need the vertex in addition to the value
class FoldableWithVertex g where
  -- | Fold with vertex 
  foldrWithVertex :: (Vertex -> a -> b -> b) -> b -> g c a -> b 

instance FoldableWithVertex (SimpleGraph local) where
  foldrWithVertex f s (SP _ vm _) = IM.foldrWithKey (\k (_,v) y -> f (Vertex k) v y) s vm

_addLabeledVertex vertexName vert@(Vertex v) value (SP em vm name) =
  let vm' = IM.insertWith noRedundancy v (emptyNeighborhood,value) vm
      name' = IM.insert v vertexName name 
  in
  SP em vm' name'

_vertexLabel (SP _ _ name) (Vertex v) = IM.lookup v name

instance NamedGraph DirectedSG where
      addLabeledVertex = _addLabeledVertex
      vertexLabel = _vertexLabel

instance NamedGraph UndirectedSG where
      addLabeledVertex = _addLabeledVertex
      vertexLabel = _vertexLabel

-- | SimpleGraph is an instance of Graph.
instance Graph DirectedSG where
    addVertex = _addVertex
    removeVertex = _removeVertex
    vertexValue = _vertexValue
    changeVertexValue = _changeVertexValue
    someVertex = _someVertex
    hasNoVertices = _hasNoVertices
    allVertices = _allVertices
    allVertexValues = _allVertexValues
    allNodes = _allNodes
    isLinkedWithAnEdge = _isLinkedWithAnEdge
    addEdge = _addEdge
    removeEdge = _removeEdge
    edgeVertices = _edgeVertices
    edgeValue = _edgeValue
    someEdge = _someEdge
    hasNoEdges = _hasNoEdges
    allEdges = _allEdges
    allEdgeValues = _allEdgeValues
    emptyGraph = _emptyGraph
    oriented _ = True
    neighbors g v = nub <$> liftA2 (++) 
             (map (\(Edge _ e) -> e) <$> (outgoing g v)) 
             (map (\(Edge s _) -> s) <$> (ingoing g v))

-- | Reverse edge direction
reverseEdge :: Edge -> Edge 
reverseEdge (Edge va vb) = edge vb va

-- | SimpleGraph is an instance of Graph.
instance Graph UndirectedSG where
    addVertex = _addVertex
    removeVertex = _removeVertex
    vertexValue = _vertexValue
    changeVertexValue = _changeVertexValue
    someVertex = _someVertex
    hasNoVertices = _hasNoVertices
    allVertices = _allVertices
    allVertexValues = _allVertexValues
    allNodes = _allNodes
    isLinkedWithAnEdge = _isLinkedWithAnEdge
    addEdge = _addEdge
    removeEdge e g = _removeEdge (reverseEdge e) (_removeEdge e g)
    edgeVertices = _edgeVertices
    edgeValue g e = case _edgeValue g e of 
                       Nothing -> _edgeValue g (reverseEdge e) 
                       r@(Just _) -> r
    someEdge = _someEdge
    hasNoEdges = _hasNoEdges
    allEdges = _allEdges
    allEdgeValues = _allEdgeValues
    emptyGraph = _emptyGraph
    oriented _ = False
    -- in undirected graphs the edge direction does not count so we need to get both
    -- ends to be sure we don not forget a vertex. In addition to that, an end may be the current vertex which
    -- is not part of the neighbors. So it has to be filtered out. Obviously, a better solution will
    -- have to be designed.
    neighbors g v = filter (/= v) <$> nub <$> liftA2 (++) 
       (map (\(Edge _ e) -> e) <$> (edges g v)) 
       (map (\(Edge s _) -> s) <$> (edges g v))

_emptyGraph = emptySimpleGraph

_hasNoVertices (SP _ vm _) = IM.null vm

_hasNoEdges (SP em _ _) = M.null em

_allVertices (SP _ vm _) = map Vertex . IM.keys $ vm

_allEdges (SP em _ _) = M.keys $ em

_allNodes (SP _ vm _) = map (\(k,(_,v)) -> (Vertex k,v)) . IM.assocs $ vm

_allVertexValues (SP _ vm _) = map snd (IM.elems vm)

_allEdgeValues (SP em _ _) = M.elems em

_isLinkedWithAnEdge (SP em _ _) va vb = M.member (edge va vb) em || M.member (edge vb va) em

_someVertex (SP _ vm _) = 
  if IM.null vm 
    then 
      Nothing 
    else 
      Just . Vertex . head . IM.keys $ vm

_someEdge (SP em _ _) = 
  if M.null em 
    then 
      Nothing 
    else 
      Just . head . M.keys $ em

_addVertex vert@(Vertex v) value (SP em vm nm) = SP em (IM.insertWith noRedundancy v (emptyNeighborhood,value) vm) nm

_removeVertex v@(Vertex vertex) g@(SP _ vm _)  = maybe g removeVertexWithValue (IM.lookup vertex vm)
  where
    removeVertexWithValue (n,_) = let g' = foldr _removeEdge g (ingoingNeighbors n)
                                      SP em vm' nm' = foldr _removeEdge g' (outgoingNeighbors n)
                                  in 
                                  SP em (IM.delete vertex vm') nm'
_vertexValue g@(SP _ vm _) (Vertex i) = maybe Nothing (Just . extractValue) (IM.lookup i vm)
  where
    extractValue (_,d) = d

_changeVertexValue v@(Vertex vi) newValue g@(SP e vm nm)  = 
  let newVertexMap = do
       (n,_) <- IM.lookup vi vm
       return $ IM.insert vi (n,newValue) vm
  in 
  case newVertexMap of 
    Nothing -> Just g
    Just nvm -> Just $ SP e nvm nm

_removeEdge e@(Edge (Vertex vs) (Vertex ve)) g@(SP em vm nm)  = 
  let r = do 
        _ <- M.lookup e em -- Check e is member of the graph
        (ns,vsdata) <- IM.lookup vs vm
        (ne,vedata) <- IM.lookup ve vm
        return ((vs,(removeNeighborsEdge e ns,vsdata)),(ve,(removeNeighborsEdge e ne,vedata)))
      updateGraph ((vs,vsdata),(ve,vedata)) =
        let vm' = IM.insert ve vedata . IM.insert vs vsdata $ vm
            em' = M.delete e em 
        in 
        SP em' vm' nm
  in 
  maybe g updateGraph r

_edgeVertices (SP em _ _) e@(Edge vs ve) =
     if M.member e em 
      then 
        Just (vs,ve)
      else
        Nothing

_edgeValue (SP em _ _) e = do
     v <- M.lookup e em
     return v

_addEdge newEdge@(Edge vs ve) value g@(SP em vm nm)   = 
  if testEdgeExistence g em vs ve 
    then 
      g
    else
      SP (M.insert newEdge value em) (addEdgeReference vm vs ve) nm
  where
    testEdgeExistence g em va vb = 
      if (oriented g)
        then 
          M.member (Edge va vb) em
        else 
          M.member (Edge va vb) em || M.member (Edge vb va) em 
    addEdgeReference vm (Vertex vsi) (Vertex vei) = IM.adjust addi vei (IM.adjust addo vsi vm)
    addi (n,v) = (addIngoingEdge newEdge n,v)  
    addo (n,v) = (addOutgoingEdge newEdge n,v)  

instance UndirectedGraph UndirectedSG where
  edges g@(SP _ vm _) v@(Vertex vi) =
      do 
        (n,_) <- IM.lookup vi vm
        return (ingoingNeighbors n)

instance DirectedGraph DirectedSG where
  ingoing g@(SP _ vm _) v@(Vertex vi) =
      do 
        (n,_) <- IM.lookup vi vm
        return (ingoingNeighbors n)

  outgoing g@(SP _ vm _) v@(Vertex vi) =
      do 
        (n,_) <- IM.lookup vi vm
        return (outgoingNeighbors n) 

{-
 
Following code is used to display a graph in a form adapted to humans.

-}
printNode nm (Vertex k,v) = do 
  tell "\n"
  let r = IM.lookup k nm
  when (isJust r) $ do
     tell $ fromJust r
  tell "\n"
  tell $ show v
  tell "\n"
addVertexToGraphviz nm (k,(_,v)) = do
  tell $ show k
  let r = IM.lookup k $ nm 
  when (isJust r) $ do
    tell " [label=\""
    tell $ fromJust r
    tell "\"] ;" 
  tell "\n"

instance (Show b, Show e) => Show (DirectedSG e b)where
  show g@(SP em vm nm) = execWriter $ do
  tell "digraph dot {\n"
  mapM_ (addVertexToGraphviz nm) $ IM.toList vm
  tell "\n"
  mapM_ addEdgeToGraphviz $ M.toList em
  tell "}\n"
  mapM_ (printNode nm) (allNodes g)
   where
     addEdgeToGraphviz (Edge (Vertex vs) (Vertex ve),l) = do
       tell $ show vs 
       tell " -> "
       tell $ show ve
       tell " [label=\""
       tell $ show l
       tell "\"]"
       tell ";\n"

instance (Show b, Show e) => Show (UndirectedSG e b)where
  show g@(SP em vm nm) = execWriter $ do
  tell "graph dot {\n"
  mapM_ (addVertexToGraphviz nm) $ IM.toList vm
  tell "\n"
  mapM_ addEdgeToGraphviz $ M.toList em
  tell "}\n"
  mapM_ (printNode nm) (allNodes g)
   where
     addEdgeToGraphviz (Edge (Vertex vs) (Vertex ve),l) = do
       tell $ show vs 
       tell " -- "
       tell $ show ve
       tell " [label=\""
       tell $ show l
       tell "\"]"
       tell ";\n"


-- | Bayesian variable : name,dimension, factor
-- When initialized it is using a factor with bayesian variables.
-- But the factor value are not yet set
data MaybeBNode f = UninitializedBNode String Int
                  | InitializedBNode String Int f


displayFactors :: (NeighborhoodStructure n, Show f, Factor f, Graph (SimpleGraph n)) => SimpleGraph n a f -> String
displayFactors g@(SP _ _ nm) = 
  let nodes = allNodes g
      displayFactor (Vertex i,f) = 
        let s = fromJust . IM.lookup i $ nm
        in
        s ++ "\n" ++ show f
  in
  intercalate "\n" $ map displayFactor nodes

-- | An implementation of the BayesianNetwork using the simple graph and no value of edges
type SBN f = DirectedSG () f

-- | State used for the construction of the graph in the monad and containing
-- auxiliary informations like vertex name to vertex id and vertex count
type AuxiliaryState = (M.Map String Int, Int)

emptyAuxiliaryState = (M.empty,0)

-- | The State for the monad with a mapping from variable name to variable ID.
type BNState g f = GMState g () (MaybeBNode f)

-- | The Bayesian monad
type BNMonad g f a = GraphMonad g () (MaybeBNode f) a

-- | The state of the graph monad : the graph and auxiliary data
-- useful during the construction
type GMState g e f = (AuxiliaryState,g e f)

-- | Graph monad.
-- The monad used to simplify the description of a new graph
-- g is the graph type. e the edge type. f the node type (generally a 'Factor')
newtype GraphMonad g e f a = GM {runGraphMonad :: State (GMState g e f) a} deriving(Monad, MonadState (GMState g e f))

-- | Get the Bayesian Discrete Variable for a vertex.
-- It works because we keep the variable dimension
factorVariable :: Graph g => Vertex -> BNMonad g f (Maybe DV)  
factorVariable v = do 
  g <- gets snd 
  let value = vertexValue g v
  case value of
    Nothing -> return Nothing
    Just (UninitializedBNode _ d) -> return $ Just $ DV v d
    Just (InitializedBNode _ d _) -> return $ Just $ DV v d
  

-- | Get a named vertex from the graph monad
getVertex :: Graph g => String -> GraphMonad g e f (Maybe Vertex)
getVertex a = do
  (namemap,_) <- gets fst
  return $ do
    i <- M.lookup a namemap
    return (Vertex i)

-- | Create an edge between two vertex of the Bayesian network
(<--) :: Graph g => DV -> DV -> BNMonad g f ()
DV va _ <-- DV vb _ = newEdge vb va ()

-- | Add a new labeled edge to the graph
newEdge :: Graph g => Vertex -> Vertex -> e -> GraphMonad g e f ()
newEdge va vb e = do
  (aux,g) <- get 
  let g1 = addEdge (edge va vb) e g
  put $! (aux,g1)
  return ()

whenJust Nothing _ = return ()
whenJust (Just i) f = f i >> return ()

-- | Get the node of a bayesian network under creation
getBayesianNode :: Graph g => Vertex -> BNMonad g f (Maybe (MaybeBNode f))
getBayesianNode v = do
  g <- gets snd
  return $ vertexValue g v

-- | Set the node of a bayesian network under creation
setBayesianNode :: Graph g => Vertex -> MaybeBNode f -> BNMonad g f ()
setBayesianNode v newValue = do
  (aux,oldGraph) <- get
  let newGraph = changeVertexValue v newValue oldGraph
 
  whenJust newGraph $ \nvm -> do
     put $! (aux, nvm)

-- | Initialize the values of a factor
(~~) :: (DirectedGraph g, Factor f) 
     => BNMonad g f DV -- ^ Discrete variable in the graph
     -> [Double] -- ^ List of values
     -> BNMonad g f ()
(~~) mv l = do 
  (DV v _) <- mv -- This is updating the state and so the graph
  g <- gets snd
  current <- factorVariable v
  mvalue <- getBayesianNode v
  maybe (return ()) (setCpt g v current) mvalue
 where
  setCpt g _ _ (InitializedBNode _ _ _) = return ()
  setCpt g v current (UninitializedBNode s dim) = do 
    let vertices = map (fromJust . startVertex g) . fromJust . ingoing g $ v
    fv <- mapM factorVariable vertices
    let cpt = factorWithVariables (map fromJust (current:fv)) l
        newValue r = InitializedBNode s dim r
    maybe (return ()) (setBayesianNode v . newValue) cpt

    
minBoundForEnum :: Bounded a => a -> a
minBoundForEnum _ = minBound

maxBoundForEnum :: Bounded a => a -> a
maxBoundForEnum _ = maxBound

intValue :: Enum a => a -> Int
intValue = fromEnum


-- | Set the bound of a bayesian variable (number of levels)
setVariableBoundWithSize :: Graph g
                         => Vertex -- ^ Vertex
                         -> Int -- ^ Inf limit  (0 for instance)
                         -> Int -- ^ Sup limit (1 for instance for 2 elements)
                         -> BNMonad g f ()
setVariableBoundWithSize a bmin bmax = do
    v <- getBayesianNode a
    whenJust v $ \(UninitializedBNode s _) -> do
      setBayesianNode a (UninitializedBNode s (bmax - bmin + 1))

setVariableBound :: (Enum a, Bounded a, Graph g) 
                 => Vertex -- ^ Vertex
                 -> a -- ^ Bounded variable (t :: type where t is undefined)
                 -> BNMonad g f ()
setVariableBound a e = 
  let bmin = intValue $ minBoundForEnum e
      bmax = intValue $ maxBoundForEnum e
  in 
  setVariableBoundWithSize a bmin bmax

-- | Create a new named Bayesian variable if not found.
-- Otherwise, return the found one.
addVariableIfNotFound :: NamedGraph g => String -> BNMonad g f Vertex
addVariableIfNotFound vertexName = graphNode vertexName (UninitializedBNode vertexName 0)

-- | Add a node in the graph using the graph monad
graphNode :: NamedGraph g => String -> f -> GraphMonad g e f Vertex 
graphNode vertexName initValue = do
  (aux@(namemap,_),g) <- get
  maybe (createAndReturnVertex aux g) returnVertex (M.lookup vertexName namemap)
   where
    returnVertex i = return (Vertex i)
    createAndReturnVertex (namemap,count) g = do
        let g1 = addLabeledVertex vertexName (Vertex count) initValue g
            namemap1 = M.insert vertexName count namemap
        put $! ((namemap1,count+1),g1)
        return (Vertex count)

-- | Define a Bayesian variable (name and bounds)
variable :: (Enum a, Bounded a, NamedGraph g) 
        => String -- ^ Variable name
        -> a -- ^ Variable bounds
        -> BNMonad g f DV
variable name e = do
  va <- addVariableIfNotFound name
  setVariableBound va e
  maybeValue <- getBayesianNode va 
  setBayesianNode va (fromJust maybeValue)
  case fromJust maybeValue of 
     UninitializedBNode s d -> return (DV va d)
     InitializedBNode _ d _ -> return (DV va d)

-- | Define a Bayesian variable (name and bounds)
variableWithSize :: NamedGraph g
        => String -- ^ Variable name
        -> Int -- ^ Variable size
        -> BNMonad g f DV
variableWithSize name e = do
  va <- addVariableIfNotFound name
  setVariableBoundWithSize va 0 (e-1)
  maybeValue <- getBayesianNode va 
  setBayesianNode va (fromJust maybeValue)
  case fromJust maybeValue of 
     UninitializedBNode s d -> return (DV va d)
     InitializedBNode _ d _ -> return (DV va d)

-- | Define a conditional probability between different variables
-- Variables are ordered like
-- FFF FFT FTF FTT TFF TFT TTF TTT
-- and same for other enumeration keeping enumeration order
cpt :: DirectedGraph g => DV -> [DV] -> BNMonad g f DV
cpt node conditions = do
  mapM_ (node <--) (reverse conditions)
  return node

-- | Define proba for a variable
-- Values are ordered like
-- FFF FFT FTF FTT TFF TFT TTF TTT
-- and same for other enumeration keeping enumeration order
proba :: DirectedGraph g => DV -> BNMonad g f DV
proba node = cpt node []


runGraph :: Graph g => GraphMonad g e f a -> (a,g e f)
runGraph = removeAuxiliaryState . flip runState (emptyAuxiliaryState,emptyGraph) . runGraphMonad 
 where 
  removeAuxiliaryState (r,(_,g)) = (r,g)

evalGraph :: Graph g => GraphMonad g e f a -> a
evalGraph = flip evalState (emptyAuxiliaryState,emptyGraph) . runGraphMonad 

execGraph :: Graph g => GraphMonad g e f a -> g e f
execGraph = snd . flip execState (emptyAuxiliaryState,emptyGraph) . runGraphMonad 

-- | Create a bayesian network using the simple graph implementation
-- The initialized nodes are replaced by the factor.
-- Returns the monad values and the built graph.
runBN :: BNMonad DirectedSG f a -> (a,DirectedSG () f)
runBN x = 
  let (r,g) = runGraph x
      convertBNodes (InitializedBNode s d f) = f 
      convertBNodes (UninitializedBNode s d) = error $ "All variables must be initialized with a factor: " ++ s ++ "(" ++ show d ++ ")"
  in 
  (r,fmap convertBNodes g)

-- | Create a bayesian network but only returns the monad value.
-- Mainly used for testing.
evalBN :: BNMonad DirectedSG f a -> a
evalBN = evalGraph

-- | Create a bayesian network but only returns the monad value.
-- Mainly used for testing.
execBN :: BNMonad DirectedSG f a -> DirectedSG () f
execBN x = 
  let g = execGraph x
      convertBNodes (InitializedBNode s d f) = f 
      convertBNodes (UninitializedBNode s d) = error $ "All variables must be initialized with a factor: " ++ s ++ "(" ++ show d ++ ")"
  in 
  fmap convertBNodes g