-}
-{-# LANGUAGE NoImplicitPrelude #-}
{-# LANGUAGE FlexibleContexts #-}
+{-# LANGUAGE NoImplicitPrelude #-}
{-# LANGUAGE OverloadedStrings #-}
+{-# LANGUAGE RankNTypes #-}
+{-# LANGUAGE ViewPatterns #-}
module Gargantext.Viz.Phylo.Tools
where
+import Control.Lens hiding (both, Level, Empty)
+import Data.List (filter, intersect, (++), sort, null, tail, last, tails, delete, nub, sortOn, nubBy, concat)
+import Data.Maybe (mapMaybe,fromMaybe)
+import Data.Map (Map, mapKeys, member, (!), restrictKeys, elems, empty, filterWithKey, unionWith)
+import Data.Set (Set)
+import Data.Text (Text,toLower,unwords)
+import Data.Tuple.Extra
+import Data.Vector (Vector,elemIndex)
+import Gargantext.Prelude
+import Gargantext.Viz.Phylo
+import qualified Data.Map as Map
+import qualified Data.Set as Set
+import qualified Data.Vector as Vector
+
+
+--------------
+-- | Misc | --
+--------------
+
+
+-- | Define a default value
+def :: a -> Maybe a -> a
+def = fromMaybe
+
+
+-- | Does a List of Sets contains at least one Set of an other List
+doesAnySetContains :: Eq a => Set a -> [Set a] -> [Set a] -> Bool
+doesAnySetContains h l l' = any (\c -> doesContains (Set.toList c) (Set.toList h)) (l' ++ l)
+
+
+-- | Does a list of A contains an other list of A
+doesContains :: Eq a => [a] -> [a] -> Bool
+doesContains l l'
+ | null l' = True
+ | length l' > length l = False
+ | elem (head' "doesContains" l') l = doesContains l (tail l')
+ | otherwise = False
+
+
+-- | Does a list of ordered A contains an other list of ordered A
+doesContainsOrd :: Eq a => Ord a => [a] -> [a] -> Bool
+doesContainsOrd l l'
+ | null l' = False
+ | last l < (head' "doesContainsOrd" l') = False
+ | (head' "doesContainsOrd" l') `elem` l = True
+ | otherwise = doesContainsOrd l (tail l')
+
+
+-- | To filter nested Sets of a
+filterNestedSets :: Eq a => Set a -> [Set a] -> [Set a] -> [Set a]
+filterNestedSets h l l'
+ | null l = if doesAnySetContains h l l'
+ then l'
+ else h : l'
+ | doesAnySetContains h l l' = filterNestedSets (head' "filterNestedSets1" l) (tail l) l'
+ | otherwise = filterNestedSets (head' "filterNestedSets2" l) (tail l) (h : l')
+
+
+
+-- | To get the good pair of keys (x,y) or (y,x) in a given Map (a,b) c
+getKeyPair :: (Int,Int) -> Map (Int,Int) a -> (Int,Int)
+getKeyPair (x,y) m = case findPair (x,y) m of
+ Nothing -> panic "[ERR][Viz.Phylo.Example.getKeyPair] Nothing"
+ Just i -> i
+ where
+ --------------------------------------
+ findPair :: (Int,Int) -> Map (Int,Int) a -> Maybe (Int,Int)
+ findPair (x',y') m'
+ | member (x',y') m' = Just (x',y')
+ | member (y',x') m' = Just (y',x')
+ | otherwise = Nothing
+ --------------------------------------
+
+
+-- | To filter Fis with small Support but by keeping non empty Periods
+keepFilled :: (Int -> [a] -> [a]) -> Int -> [a] -> [a]
+keepFilled f thr l = if (null $ f thr l) && (not $ null l)
+ then keepFilled f (thr - 1) l
+ else f thr l
+
+
+-- | To get all combinations of a list
+listToFullCombi :: Eq a => [a] -> [(a,a)]
+listToFullCombi l = [(x,y) | x <- l, y <- l]
+
+
+-- | To get all combinations of a list
+listToDirectedCombi :: Eq a => [a] -> [(a,a)]
+listToDirectedCombi l = [(x,y) | x <- l, y <- l, x /= y]
+
+
+listToEqualCombi :: Eq a => [a] -> [(a,a)]
+listToEqualCombi l = [(x,y) | x <- l, y <- l, x == y]
+
+listToPairs :: Eq a => [a] -> [(a,a)]
+listToPairs l = (listToEqualCombi l) ++ (listToUnDirectedCombi l)
+
+
+-- | To get all combinations of a list and apply a function to the resulting list of pairs
+listToDirectedCombiWith :: Eq a => forall b. (a -> b) -> [a] -> [(b,b)]
+listToDirectedCombiWith f l = [(f x,f y) | x <- l, y <- l, x /= y]
+
+
+-- | To get the sequential combinations of an order list
+listToSequentialCombi :: Eq a => [a] -> [(a,a)]
+listToSequentialCombi l = nubBy (\x y -> fst x == fst y) $ listToUnDirectedCombi l
+
+
+-- | To get all combinations of a list with no repetition
+listToUnDirectedCombi :: [a] -> [(a,a)]
+listToUnDirectedCombi l = [ (x,y) | (x:rest) <- tails l, y <- rest ]
+
+
+-- | To get all combinations of a list with no repetition and apply a function to the resulting list of pairs
+listToUnDirectedCombiWith :: forall a b. (a -> b) -> [a] -> [(b,b)]
+listToUnDirectedCombiWith f l = [ (f x, f y) | (x:rest) <- tails l, y <- rest ]
+
+
+-- | To transform a list of Ngrams Indexes into a Label
+ngramsToLabel :: Vector Ngrams -> [Int] -> Text
+ngramsToLabel ngrams l = unwords $ tail' "ngramsToLabel" $ concat $ map (\n -> ["|",n]) $ ngramsToText ngrams l
+
+
+-- | To transform a list of Ngrams Indexes into a list of Text
+ngramsToText :: Vector Ngrams -> [Int] -> [Text]
+ngramsToText ngrams l = map (\idx -> ngrams Vector.! idx) l
+
+
+-- | To transform a list of ngrams into a list of indexes
+ngramsToIdx :: [Ngrams] -> Vector Ngrams -> [Int]
+ngramsToIdx ns v = sort $ map (\n -> getIdxInVector n v) ns
+
+
+-- | To unify the keys (x,y) that Map 1 share with Map 2 such as: (x,y) <=> (y,x)
+unifySharedKeys :: Eq a => Ord a => Map (a,a) b -> Map (a,a) b -> Map (a,a) b
+unifySharedKeys m1 m2 = mapKeys (\(x,y) -> if member (y,x) m2
+ then (y,x)
+ else (x,y) ) m1
+
+
+---------------
+-- | Phylo | --
+---------------
+
+-- | An analyzer ingests a Ngrams and generates a modified version of it
+phyloAnalyzer :: Ngrams -> Ngrams
+phyloAnalyzer n = toLower n
+
+-- | To init the foundation roots of the Phylo as a Vector of Ngrams
+initFoundationsRoots :: [Ngrams] -> Vector Ngrams
+initFoundationsRoots l = Vector.fromList $ map phyloAnalyzer l
+
+-- | To init the base of a Phylo from a List of Periods and Foundations
+initPhyloBase :: [(Date, Date)] -> PhyloFoundations -> Map Date Double -> Map Date (Map (Int,Int) Double) -> Map (Date,Date) [PhyloFis] -> PhyloParam -> Phylo
+initPhyloBase pds fds nbDocs cooc fis prm = Phylo ((fst . (head' "initPhyloBase")) pds, (snd . last) pds) fds (map (\pd -> initPhyloPeriod pd []) pds) nbDocs cooc fis prm
+
+-- | To init the param of a Phylo
+initPhyloParam :: Maybe Text -> Maybe Software -> Maybe PhyloQueryBuild -> PhyloParam
+initPhyloParam (def defaultPhyloVersion -> v) (def defaultSoftware -> s) (def defaultQueryBuild -> q) = PhyloParam v s q
+
+-- | To get the last computed Level in a Phylo
+getLastLevel :: Phylo -> Level
+getLastLevel p = (last . sort)
+ $ map (snd . getPhyloLevelId)
+ $ view ( phylo_periods
+ . traverse
+ . phylo_periodLevels ) p
+
+-- | To get all the coocurency matrix of a phylo
+getPhyloCooc :: Phylo -> Map Date (Map (Int,Int) Double)
+getPhyloCooc p = p ^. phylo_cooc
+
+
+-- | To get the PhyloParam of a Phylo
+getPhyloParams :: Phylo -> PhyloParam
+getPhyloParams = _phylo_param
+
+-- | To get the title of a Phylo
+getPhyloTitle :: Phylo -> Text
+getPhyloTitle p = _q_phyloTitle $ _phyloParam_query $ getPhyloParams p
+
+-- | To get the desc of a Phylo
+getPhyloDescription :: Phylo -> Text
+getPhyloDescription p = _q_phyloTitle $ _phyloParam_query $ getPhyloParams p
+
+getPhyloMatchingFrame :: Phylo -> Int
+getPhyloMatchingFrame p = _q_interTemporalMatchingFrame $ _phyloParam_query $ getPhyloParams p
+
+getPhyloMatchingFrameTh :: Phylo -> Double
+getPhyloMatchingFrameTh p = _q_interTemporalMatchingFrameTh $ _phyloParam_query $ getPhyloParams p
+
+getPhyloProximity :: Phylo -> Proximity
+getPhyloProximity p = _q_interTemporalMatching $ _phyloParam_query $ getPhyloParams p
+
+getPhyloReBranchThr :: Phylo -> Double
+getPhyloReBranchThr p = _q_reBranchThr $ _phyloParam_query $ getPhyloParams p
+
+getPhyloReBranchNth :: Phylo -> Int
+getPhyloReBranchNth p = _q_reBranchNth $ _phyloParam_query $ getPhyloParams p
+
+getPhyloFis :: Phylo -> Map (Date,Date) [PhyloFis]
+getPhyloFis = _phylo_fis
+
+
+--------------------
+-- | PhyloRoots | --
+--------------------
+
+-- | To get the foundations of a Phylo
+getFoundations :: Phylo -> PhyloFoundations
+getFoundations = _phylo_foundations
+
+-- | To get the foundations roots of a Phylo
+getFoundationsRoots :: Phylo -> Vector Ngrams
+getFoundationsRoots p = (getFoundations p) ^. phylo_foundationsRoots
+
+-- | To get the Index of a Ngrams in the foundationsRoots of a Phylo
+getIdxInRoots :: Ngrams -> Phylo -> Int
+getIdxInRoots n p = case (elemIndex n (getFoundationsRoots p)) of
+ Nothing -> panic $ "[ERR][Viz.Phylo.Tools.getIdxInRoots] Ngrams not in foundationsRoots: " <> cs n
+ Just idx -> idx
+
+getIdxInRoots' :: Ngrams -> Vector Ngrams -> Int
+getIdxInRoots' n root = case (elemIndex n root) of
+ Nothing -> panic $ "[ERR][Viz.Phylo.Tools.getIdxInRoots] Ngrams not in foundationsRoots: " <> cs n
+ Just idx -> idx
+
+getIdxInVector :: Ngrams -> Vector Ngrams -> Int
+getIdxInVector n ns = case (elemIndex n ns) of
+ Nothing -> panic $ "[ERR][Viz.Phylo.Tools.getIdxInVector] Ngrams not in foundationsRoots: " <> cs n
+ Just idx -> idx
+
+--------------------
+-- | PhyloGroup | --
+--------------------
+
+-- | To alter a PhyloGroup matching a given Level
+alterGroupWithLevel :: (PhyloGroup -> PhyloGroup) -> Level -> Phylo -> Phylo
+alterGroupWithLevel f lvl p = over ( phylo_periods
+ . traverse
+ . phylo_periodLevels
+ . traverse
+ . phylo_levelGroups
+ . traverse
+ ) (\g -> if getGroupLevel g == lvl
+ then f g
+ else g ) p
+
+
+-- | To alter each list of PhyloGroups following a given function
+alterPhyloGroups :: ([PhyloGroup] -> [PhyloGroup]) -> Phylo -> Phylo
+alterPhyloGroups f p = over ( phylo_periods
+ . traverse
+ . phylo_periodLevels
+ . traverse
+ . phylo_levelGroups
+ ) f p
+
+
+-- | To filter the PhyloGroup of a Phylo according to a function and a value
+filterGroups :: Eq a => (PhyloGroup -> a) -> a -> [PhyloGroup] -> [PhyloGroup]
+filterGroups f x l = filter (\g -> (f g) == x) l
+
+
+-- | To maybe get the PhyloBranchId of a PhyloGroup
+getGroupBranchId :: PhyloGroup -> Maybe PhyloBranchId
+getGroupBranchId = _phylo_groupBranchId
+
+
+-- | To get the PhyloGroups Childs of a PhyloGroup
+getGroupChilds :: PhyloGroup -> Phylo -> [PhyloGroup]
+getGroupChilds g p = getGroupsFromIds (getGroupPeriodChildsId g) p
+
+
+-- | To get the id of a PhyloGroup
+getGroupId :: PhyloGroup -> PhyloGroupId
+getGroupId = _phylo_groupId
+
+
+getGroupCooc :: PhyloGroup -> Map (Int,Int) Double
+getGroupCooc = _phylo_groupCooc
+
+
+-- | To get the level out of the id of a PhyloGroup
+getGroupLevel :: PhyloGroup -> Int
+getGroupLevel = snd . fst . getGroupId
+
+
+-- | To get the level child pointers of a PhyloGroup
+getGroupLevelChilds :: PhyloGroup -> [Pointer]
+getGroupLevelChilds = _phylo_groupLevelChilds
+
+
+-- | To get the PhyloGroups Level Childs Ids of a PhyloGroup
+getGroupLevelChildsId :: PhyloGroup -> [PhyloGroupId]
+getGroupLevelChildsId g = map fst $ getGroupLevelChilds g
+
+
+-- | To get the level parent pointers of a PhyloGroup
+getGroupLevelParents :: PhyloGroup -> [Pointer]
+getGroupLevelParents = _phylo_groupLevelParents
+
+
+-- | To get the PhyloGroups Level Parents Ids of a PhyloGroup
+getGroupLevelParentsId :: PhyloGroup -> [PhyloGroupId]
+getGroupLevelParentsId g = map fst $ getGroupLevelParents g
+
+
+-- | To get the PhyloGroups Level Parents Ids of a PhyloGroup
+getGroupLevelParentId :: PhyloGroup -> PhyloGroupId
+getGroupLevelParentId g = (head' "getGroupLevelParentId") $ getGroupLevelParentsId g
+
+-- | To get the Meta value of a PhyloGroup
+getGroupMeta :: Text -> PhyloGroup -> Double
+getGroupMeta k g = (g ^. phylo_groupMeta) ! k
+
+
+-- | To get the Ngrams of a PhyloGroup
+getGroupNgrams :: PhyloGroup -> [Int]
+getGroupNgrams = _phylo_groupNgrams
+
+
+-- | To get the list of pairs (Childs & Parents) of a PhyloGroup
+getGroupPairs :: PhyloGroup -> Phylo -> [PhyloGroup]
+getGroupPairs g p = (getGroupChilds g p) ++ (getGroupParents g p)
+
+
+-- | To get the PhyloGroups Parents of a PhyloGroup
+getGroupParents :: PhyloGroup -> Phylo -> [PhyloGroup]
+getGroupParents g p = getGroupsFromIds (getGroupPeriodParentsId g) p
+
+
+-- | To get the period out of the id of a PhyloGroup
+getGroupPeriod :: PhyloGroup -> (Date,Date)
+getGroupPeriod = fst . fst . getGroupId
+
+
+-- | To get the period child pointers of a PhyloGroup
+getGroupPeriodChilds :: PhyloGroup -> [Pointer]
+getGroupPeriodChilds = _phylo_groupPeriodChilds
+
+
+-- | To get the PhyloGroups Period Parents Ids of a PhyloGroup
+getGroupPeriodChildsId :: PhyloGroup -> [PhyloGroupId]
+getGroupPeriodChildsId g = map fst $ getGroupPeriodChilds g
+
+
+-- | To get the period parent pointers of a PhyloGroup
+getGroupPeriodParents :: PhyloGroup -> [Pointer]
+getGroupPeriodParents = _phylo_groupPeriodParents
+
+
+-- | To get the PhyloGroups Period Parents Ids of a PhyloGroup
+getGroupPeriodParentsId :: PhyloGroup -> [PhyloGroupId]
+getGroupPeriodParentsId g = map fst $ getGroupPeriodParents g
+
+
+-- | To get the pointers of a given Phylogroup
+getGroupPointers :: EdgeType -> Filiation -> PhyloGroup -> [Pointer]
+getGroupPointers t f g = case t of
+ PeriodEdge -> case f of
+ Ascendant -> getGroupPeriodParents g
+ Descendant -> getGroupPeriodChilds g
+ _ -> panic "[ERR][Viz.Phylo.Tools.getGroupPointers] wrong filiation"
+ LevelEdge -> case f of
+ Ascendant -> getGroupLevelParents g
+ Descendant -> getGroupLevelChilds g
+ _ -> panic "[ERR][Viz.Phylo.Tools.getGroupPointers] wrong filiation"
+
+
+-- | To get the roots labels of a list of group ngrams
+getGroupText :: PhyloGroup -> Phylo -> [Text]
+getGroupText g p = ngramsToText (getFoundationsRoots p) (getGroupNgrams g)
+
+
+-- | To get all the PhyloGroup of a Phylo
+getGroups :: Phylo -> [PhyloGroup]
+getGroups = view ( phylo_periods
+ . traverse
+ . phylo_periodLevels
+ . traverse
+ . phylo_levelGroups
+ )
+
+
+-- | To get all PhyloGroups matching a list of PhyloGoupIds in a Phylo
+-- getGroupsFromIds :: [PhyloGroupId] -> Phylo -> [PhyloGroup]
+-- getGroupsFromIds ids p = filter (\g -> elem (getGroupId g) ids) $ getGroups p
+
+getGroupFromId :: PhyloGroupId -> Phylo -> PhyloGroup
+getGroupFromId id p =
+ let groups = Map.fromList $ map (\g -> (getGroupId g, g)) $ getGroups p
+ in groups ! id
+
+getGroupsFromIds :: [PhyloGroupId] -> Phylo -> [PhyloGroup]
+getGroupsFromIds ids p =
+ let groups = Map.fromList $ map (\g -> (getGroupId g, g)) $ getGroups p
+ in elems $ restrictKeys groups (Set.fromList ids)
+
+
+-- | To get the corresponding list of PhyloGroups from a list of PhyloNodes
+getGroupsFromNodes :: [PhyloNode] -> Phylo -> [PhyloGroup]
+getGroupsFromNodes ns p = getGroupsFromIds (map getNodeId ns) p
+
+
+-- | To get all the PhyloGroup of a Phylo with a given level and period
+getGroupsWithFilters :: Int -> (Date,Date) -> Phylo -> [PhyloGroup]
+getGroupsWithFilters lvl prd p = (getGroupsWithLevel lvl p)
+ `intersect`
+ (getGroupsWithPeriod prd p)
+
+
+-- | To get all the PhyloGroup of a Phylo with a given Level
+getGroupsWithLevel :: Int -> Phylo -> [PhyloGroup]
+getGroupsWithLevel lvl p = filterGroups getGroupLevel lvl (getGroups p)
+
+
+-- | To get all the PhyloGroup of a Phylo with a given Period
+getGroupsWithPeriod :: (Date,Date) -> Phylo -> [PhyloGroup]
+getGroupsWithPeriod prd p = filterGroups getGroupPeriod prd (getGroups p)
+
+
+-- | To create a PhyloGroup in a Phylo out of a list of Ngrams and a set of parameters
+initGroup :: [Ngrams] -> Text -> Int -> Int -> Int -> Int -> Phylo -> PhyloGroup
+initGroup ngrams lbl idx lvl from' to' p = PhyloGroup
+ (((from', to'), lvl), idx)
+ lbl
+ idxs
+ (Map.empty)
+ (Map.empty)
+ Nothing
+ (getMiniCooc (listToFullCombi idxs) (periodsToYears [(from', to')]) (getPhyloCooc p))
+ [] [] [] []
+ where
+ idxs = sort $ map (\x -> getIdxInRoots x p) ngrams
+
+
+-- | To sum two coocurency Matrix
+sumCooc :: Map (Int, Int) Double -> Map (Int, Int) Double -> Map (Int, Int) Double
+sumCooc m m' = unionWith (+) m m'
+
+-- | To build the mini cooc matrix of each group
+getMiniCooc :: [(Int,Int)] -> Set Date -> Map Date (Map (Int,Int) Double) -> Map (Int,Int) Double
+getMiniCooc pairs years cooc = filterWithKey (\(n,n') _ -> elem (n,n') pairs) cooc'
+ where
+ --------------------------------------
+ cooc' :: Map (Int,Int) Double
+ cooc' = foldl (\m m' -> sumCooc m m') empty
+ $ elems
+ $ restrictKeys cooc years
+ --------------------------------------
+
+
+---------------------
+-- | PhyloPeriod | --
+---------------------
+
+
+-- | To alter each PhyloPeriod of a Phylo following a given function
+alterPhyloPeriods :: (PhyloPeriod -> PhyloPeriod) -> Phylo -> Phylo
+alterPhyloPeriods f p = over ( phylo_periods
+ . traverse) f p
+
+
+-- | To append a list of PhyloPeriod to a Phylo
+appendToPhyloPeriods :: [PhyloPeriod] -> Phylo -> Phylo
+appendToPhyloPeriods l p = over (phylo_periods) (++ l) p
+
+
+-- | To get all the PhyloPeriodIds of a Phylo
+getPhyloPeriods :: Phylo -> [PhyloPeriodId]
+getPhyloPeriods p = map _phylo_periodId
+ $ view (phylo_periods) p
+
+
+-- | To get the id of a given PhyloPeriod
+getPhyloPeriodId :: PhyloPeriod -> PhyloPeriodId
+getPhyloPeriodId prd = _phylo_periodId prd
+
+
+-- | To create a PhyloPeriod
+initPhyloPeriod :: PhyloPeriodId -> [PhyloLevel] -> PhyloPeriod
+initPhyloPeriod id l = PhyloPeriod id l
+
+
+-- | To transform a list of periods into a set of Dates
+periodsToYears :: [(Date,Date)] -> Set Date
+periodsToYears periods = (Set.fromList . sort . concat)
+ $ map (\(d,d') -> [d..d']) periods
+
+
+--------------------
+-- | PhyloLevel | --
+--------------------
+
+
+-- | To alter a list of PhyloLevels following a given function
+alterPhyloLevels :: ([PhyloLevel] -> [PhyloLevel]) -> Phylo -> Phylo
+alterPhyloLevels f p = over ( phylo_periods
+ . traverse
+ . phylo_periodLevels) f p
+
+
+-- | To get the PhylolevelId of a given PhyloLevel
+getPhyloLevelId :: PhyloLevel -> PhyloLevelId
+getPhyloLevelId = _phylo_levelId
+
+
+-- | To get all the Phylolevels of a given PhyloPeriod
+getPhyloLevels :: PhyloPeriod -> [PhyloLevel]
+getPhyloLevels = view (phylo_periodLevels)
+
+
+-- | To create a PhyloLevel
+initPhyloLevel :: PhyloLevelId -> [PhyloGroup] -> PhyloLevel
+initPhyloLevel id groups = PhyloLevel id groups
+
+
+-- | To set the LevelId of a PhyloLevel and of all its PhyloGroups
+setPhyloLevelId :: Int -> PhyloLevel -> PhyloLevel
+setPhyloLevelId lvl' (PhyloLevel (id, _lvl) groups)
+ = PhyloLevel (id, lvl') groups'
+ where
+ groups' = over (traverse . phylo_groupId)
+ (\((period, _lvl), idx) -> ((period, lvl'), idx))
+ groups
+
+
+------------------
+-- | PhyloFis | --
+------------------
+
+
+-- | To get the clique of a PhyloFis
+getClique :: PhyloFis -> Clique
+getClique = _phyloFis_clique
+
+-- | To get the support of a PhyloFis
+getSupport :: PhyloFis -> Support
+getSupport = _phyloFis_support
+
+-- | To get the period of a PhyloFis
+getFisPeriod :: PhyloFis -> (Date,Date)
+getFisPeriod = _phyloFis_period
+
+
+----------------------------
+-- | PhyloNodes & Edges | --
+----------------------------
+
+
+-- | To alter a PhyloNode
+alterPhyloNode :: (PhyloNode -> PhyloNode) -> PhyloView -> PhyloView
+alterPhyloNode f v = over ( pv_nodes
+ . traverse
+ ) (\pn -> f pn ) v
+
+
+-- | To filter some GroupEdges with a given threshold
+filterGroupEdges :: Double -> [GroupEdge] -> [GroupEdge]
+filterGroupEdges thr edges = filter (\((_s,_t),w) -> w > thr) edges
+
+
+-- | To get the neighbours (directed/undirected) of a PhyloGroup from a list of GroupEdges
+getNeighbours :: Bool -> PhyloGroup -> [GroupEdge] -> [PhyloGroup]
+getNeighbours directed g e = case directed of
+ True -> map (\((_s,t),_w) -> t)
+ $ filter (\((s,_t),_w) -> s == g) e
+ False -> map (\((s,t),_w) -> (head' "getNeighbours") $ delete g $ nub [s,t,g])
+ $ filter (\((s,t),_w) -> s == g || t == g) e
+
+
+-- | To get the PhyloBranchId of PhyloNode if it exists
+getNodeBranchId :: PhyloNode -> PhyloBranchId
+getNodeBranchId n = case n ^. pn_bid of
+ Nothing -> panic "[ERR][Viz.Phylo.Tools.getNodeBranchId] branchId not found"
+ Just i -> i
+
+
+-- | To get the PhyloGroupId of a PhyloNode
+getNodeId :: PhyloNode -> PhyloGroupId
+getNodeId n = n ^. pn_id
+
+
+getNodePeriod :: PhyloNode -> (Date,Date)
+getNodePeriod n = fst $ fst $ getNodeId n
+
+
+-- | To get the Level of a PhyloNode
+getNodeLevel :: PhyloNode -> Level
+getNodeLevel n = (snd . fst) $ getNodeId n
+
+
+-- | To get the Parent Node of a PhyloNode in a PhyloView
+getNodeParent :: PhyloNode -> PhyloView -> [PhyloNode]
+getNodeParent n v = filter (\n' -> elem (getNodeId n') (getNodeParentsId n))
+ $ v ^. pv_nodes
+
+
+-- | To get the Parent Node id of a PhyloNode if it exists
+getNodeParentsId :: PhyloNode -> [PhyloGroupId]
+getNodeParentsId n = case n ^. pn_parents of
+ Nothing -> panic "[ERR][Viz.Phylo.Tools.getNodeParentsId] node parent not found"
+ Just ids -> ids
+
+
+-- | To get a list of PhyloNodes grouped by PhyloBranch in a PhyloView
+getNodesByBranches :: PhyloView -> [(PhyloBranchId,[PhyloNode])]
+getNodesByBranches v = zip bIds $ map (\id -> filter (\n -> (getNodeBranchId n) == id)
+ $ getNodesInBranches v ) bIds
+ where
+ --------------------------------------
+ bIds :: [PhyloBranchId]
+ bIds = getViewBranchIds v
+ --------------------------------------
+
+
+-- | To get a list of PhyloNodes owned by any PhyloBranches in a PhyloView
+getNodesInBranches :: PhyloView -> [PhyloNode]
+getNodesInBranches v = filter (\n -> isJust $ n ^. pn_bid)
+ $ v ^. pv_nodes
+
+
+-- | To get the PhyloGroupId of the Source of a PhyloEdge
+getSourceId :: PhyloEdge -> PhyloGroupId
+getSourceId e = e ^. pe_source
+
+
+-- | To get the PhyloGroupId of the Target of a PhyloEdge
+getTargetId :: PhyloEdge -> PhyloGroupId
+getTargetId e = e ^. pe_target
+
+
+---------------------
+-- | PhyloBranch | --
+---------------------
+
+
+-- | To get the PhyloBranchId of a PhyloBranch
+getBranchId :: PhyloBranch -> PhyloBranchId
+getBranchId b = b ^. pb_id
+
+-- | To get a list of PhyloBranchIds
+getBranchIds :: Phylo -> [PhyloBranchId]
+getBranchIds p = sortOn snd
+ $ nub
+ $ mapMaybe getGroupBranchId
+ $ getGroups p
+
+
+-- | To get a list of PhyloBranchIds given a Level in a Phylo
+getBranchIdsWith :: Level -> Phylo -> [PhyloBranchId]
+getBranchIdsWith lvl p = sortOn snd
+ $ mapMaybe getGroupBranchId
+ $ getGroupsWithLevel lvl p
+
+
+-- | To get the Meta value of a PhyloBranch
+getBranchMeta :: Text -> PhyloBranch -> [Double]
+getBranchMeta k b = (b ^. pb_metrics) ! k
+
+
+-- | To get all the PhyloBranchIds of a PhyloView
+getViewBranchIds :: PhyloView -> [PhyloBranchId]
+getViewBranchIds v = map getBranchId $ v ^. pv_branches
+
+
+-- | To get a list of PhyloGroup sharing the same PhyloBranchId
+getGroupsByBranches :: Phylo -> [(PhyloBranchId,[PhyloGroup])]
+getGroupsByBranches p = zip (getBranchIds p)
+ $ map (\id -> filter (\g -> (fromJust $ getGroupBranchId g) == id)
+ $ getGroupsInBranches p)
+ $ getBranchIds p
+
+
+-- | To get the sublist of all the PhyloGroups linked to a branch
+getGroupsInBranches :: Phylo -> [PhyloGroup]
+getGroupsInBranches p = filter (\g -> isJust $ g ^. phylo_groupBranchId)
+ $ getGroups p
+
+
+--------------------------------
+-- | PhyloQuery & QueryView | --
+--------------------------------
+
+
+-- | To filter PhyloView's Branches by level
+filterBranchesByLevel :: Level -> PhyloView -> [PhyloBranch]
+filterBranchesByLevel lvl pv = filter (\pb -> lvl == (fst $ pb ^. pb_id))
+ $ pv ^. pv_branches
+
+
+-- | To filter PhyloView's Edges by level
+filterEdgesByLevel :: Level -> [PhyloEdge] -> [PhyloEdge]
+filterEdgesByLevel lvl pes = filter (\pe -> (lvl == ((snd . fst) $ pe ^. pe_source))
+ && (lvl == ((snd . fst) $ pe ^. pe_target))) pes
+
+
+-- | To filter PhyloView's Edges by type
+filterEdgesByType :: EdgeType -> [PhyloEdge] -> [PhyloEdge]
+filterEdgesByType t pes = filter (\pe -> t == (pe ^. pe_type)) pes
+
+
+-- | To filter PhyloView's Nodes by the oldest Period
+filterNodesByFirstPeriod :: [PhyloNode] -> [PhyloNode]
+filterNodesByFirstPeriod pns = filter (\pn -> fstPrd == ((fst . fst) $ pn ^. pn_id)) pns
+ where
+ --------------------------------------
+ fstPrd :: (Date,Date)
+ fstPrd = (head' "filterNodesByFirstPeriod")
+ $ sortOn fst
+ $ map (\pn -> (fst . fst) $ pn ^. pn_id) pns
+ --------------------------------------
+
+
+-- | To filter PhyloView's Nodes by Branch
+filterNodesByBranch :: PhyloBranchId -> [PhyloNode] -> [PhyloNode]
+filterNodesByBranch bId pns = filter (\pn -> if isJust $ pn ^. pn_bid
+ then if bId == (fromJust $ pn ^. pn_bid)
+ then True
+ else False
+ else False ) pns
+
+
+-- | To filter PhyloView's Nodes by level
+filterNodesByLevel :: Level -> [PhyloNode] -> [PhyloNode]
+filterNodesByLevel lvl pns = filter (\pn -> lvl == ((snd . fst) $ pn ^. pn_id)) pns
+
+
+-- | To filter PhyloView's Nodes by Period
+filterNodesByPeriod :: PhyloPeriodId -> [PhyloNode] -> [PhyloNode]
+filterNodesByPeriod prd pns = filter (\pn -> prd == ((fst . fst) $ pn ^. pn_id)) pns
+
+
+-- | To get the first clustering method to apply to get the contextual units of a Phylo
+getContextualUnit :: PhyloQueryBuild -> Cluster
+getContextualUnit q = q ^. q_contextualUnit
+
+
+-- | To get the metrics to apply to contextual units
+getContextualUnitMetrics :: PhyloQueryBuild -> [Metric]
+getContextualUnitMetrics q = q ^. q_contextualUnitMetrics
+
+
+-- | To get the filters to apply to contextual units
+getContextualUnitFilters :: PhyloQueryBuild -> [Filter]
+getContextualUnitFilters q = q ^. q_contextualUnitFilters
+
+
+-- | To get the cluster methods to apply to the Nths levels of a Phylo
+getNthCluster :: PhyloQueryBuild -> Cluster
+getNthCluster q = q ^. q_nthCluster
+
+
+-- | To get the Sup Level of a reconstruction of a Phylo from a PhyloQuery
+getNthLevel :: PhyloQueryBuild -> Level
+getNthLevel q = q ^. q_nthLevel
+
+
+-- | To get the Grain of the PhyloPeriods from a PhyloQuery
+getPeriodGrain :: PhyloQueryBuild -> Int
+getPeriodGrain q = q ^. q_periodGrain
+
+
+-- | To get the intertemporal matching strategy to apply to a Phylo from a PhyloQuery
+getInterTemporalMatching :: PhyloQueryBuild -> Proximity
+getInterTemporalMatching q = q ^. q_interTemporalMatching
+
+
+-- | To get the Steps of the PhyloPeriods from a PhyloQuery
+getPeriodSteps :: PhyloQueryBuild -> Int
+getPeriodSteps q = q ^. q_periodSteps
+
+
+--------------------------------------------------
+-- | PhyloQueryBuild & PhyloQueryView Constructors | --
+--------------------------------------------------
+
+-- | To get the threshold of a Proximity
+getThreshold :: Proximity -> Double
+getThreshold prox = case prox of
+ WeightedLogJaccard (WLJParams thr _) -> thr
+ Hamming (HammingParams thr) -> thr
+ Filiation -> panic "[ERR][Viz.Phylo.Tools.getThreshold] Filiation"
+
+
+-- | To get the Proximity associated to a given Clustering method
+getProximity :: Cluster -> Proximity
+getProximity cluster = case cluster of
+ Louvain (LouvainParams proxi) -> proxi
+ RelatedComponents (RCParams proxi) -> proxi
+ _ -> panic "[ERR][Viz.Phylo.Tools.getProximity] this cluster has no associated Proximity"
+
+
+-- | To initialize all the Cluster / Proximity with their default parameters
+initFis :: Maybe Bool -> Maybe Support -> Maybe Int -> FisParams
+initFis (def True -> kmf) (def 0 -> min') (def 0 -> thr) = FisParams kmf min' thr
+
+initHamming :: Maybe Double -> HammingParams
+initHamming (def 0.01 -> sens) = HammingParams sens
+
+initLonelyBranch :: Maybe Int -> Maybe Int -> Maybe Int -> LBParams
+initLonelyBranch (def 2 -> periodsInf) (def 2 -> periodsSup) (def 1 -> minNodes) = LBParams periodsInf periodsSup minNodes
+
+initSizeBranch :: Maybe Int -> SBParams
+initSizeBranch (def 1 -> minSize) = SBParams minSize
+
+initLonelyBranch' :: Maybe Int -> Maybe Int -> Maybe Int -> LBParams
+initLonelyBranch' (def 0 -> periodsInf) (def 0 -> periodsSup) (def 1 -> minNodes) = LBParams periodsInf periodsSup minNodes
+
+initLouvain :: Maybe Proximity -> LouvainParams
+initLouvain (def defaultWeightedLogJaccard -> proxi) = LouvainParams proxi
+
+initRelatedComponents :: Maybe Proximity -> RCParams
+initRelatedComponents (def defaultWeightedLogJaccard -> proxi) = RCParams proxi
+
+-- | TODO user param in main function
+initWeightedLogJaccard :: Maybe Double -> Maybe Double -> WLJParams
+initWeightedLogJaccard (def 0.3 -> thr) (def 20.0 -> sens) = WLJParams thr sens
+
+
+-- | To initialize a PhyloQueryBuild from given and default parameters
+initPhyloQueryBuild :: Text -> Text -> Maybe Int
+ -> Maybe Int -> Maybe Cluster -> Maybe [Metric]
+ -> Maybe [Filter]-> Maybe Proximity -> Maybe Int
+ -> Maybe Double -> Maybe Double -> Maybe Int
+ -> Maybe Level -> Maybe Cluster -> PhyloQueryBuild
+initPhyloQueryBuild name desc (def 5 -> grain)
+ (def 1 -> steps) (def defaultFis -> cluster) (def [] -> metrics)
+ (def [] -> filters) (def defaultWeightedLogJaccard -> matching') (def 5 -> frame)
+ (def 0.8 -> frameThr) (def 0.5 -> reBranchThr) (def 4 -> reBranchNth)
+ (def 2 -> nthLevel) (def defaultRelatedComponents -> nthCluster) =
+ PhyloQueryBuild name desc grain
+ steps cluster metrics filters matching' frame frameThr reBranchThr reBranchNth nthLevel nthCluster
+
+
+-- | To initialize a PhyloQueryView default parameters
+initPhyloQueryView :: Maybe Level -> Maybe Filiation -> Maybe Bool -> Maybe Level -> Maybe [Metric] -> Maybe [Filter] -> Maybe [Tagger] -> Maybe (Sort, Order) -> Maybe ExportMode -> Maybe DisplayMode -> Maybe Bool -> PhyloQueryView
+initPhyloQueryView (def 2 -> lvl) (def Descendant -> f) (def False -> c) (def 1 -> d) (def [] -> ms) (def [] -> fs) (def [] -> ts) s (def Json -> em) (def Flat -> dm) (def True -> v) =
+ PhyloQueryView lvl f c d ms fs ts s em dm v
+
+
+-- | To define some obvious boolean getters
+shouldKeepMinorFis :: FisParams -> Bool
+shouldKeepMinorFis = _fis_keepMinorFis
+
+----------------------------
+-- | Default ressources | --
+----------------------------
+
+-- Clusters
+
+defaultFis :: Cluster
+defaultFis = Fis (initFis Nothing Nothing Nothing)
+
+defaultLouvain :: Cluster
+defaultLouvain = Louvain (initLouvain Nothing)
+
+defaultRelatedComponents :: Cluster
+defaultRelatedComponents = RelatedComponents (initRelatedComponents Nothing)
+
+-- Filters
+
+defaultLonelyBranch :: Filter
+defaultLonelyBranch = LonelyBranch (initLonelyBranch Nothing Nothing Nothing)
+
+defaultSizeBranch :: Filter
+defaultSizeBranch = SizeBranch (initSizeBranch Nothing)
+
+-- Params
+
+defaultPhyloParam :: PhyloParam
+defaultPhyloParam = initPhyloParam Nothing Nothing Nothing
+
+-- Proximities
+
+defaultHamming :: Proximity
+defaultHamming = Hamming (initHamming Nothing)
+
+defaultWeightedLogJaccard :: Proximity
+defaultWeightedLogJaccard = WeightedLogJaccard (initWeightedLogJaccard Nothing Nothing)
+
+-- Queries
+type Title = Text
+type Desc = Text
+
+defaultQueryBuild :: PhyloQueryBuild
+defaultQueryBuild = defaultQueryBuild'
+ "Cesar et Cleôpatre"
+ "An example of Phylomemy (french without accent)"
+
+defaultQueryBuild' :: Title -> Desc -> PhyloQueryBuild
+defaultQueryBuild' t d = initPhyloQueryBuild t d
+ Nothing Nothing Nothing
+ Nothing Nothing Nothing
+ Nothing Nothing Nothing
+ Nothing Nothing Nothing
+
+defaultQueryView :: PhyloQueryView
+defaultQueryView = initPhyloQueryView
+ Nothing Nothing Nothing
+ Nothing Nothing Nothing
+ Nothing Nothing Nothing
+ Nothing Nothing
+
+-- Software
+
+defaultSoftware :: Software
+defaultSoftware = Software "Gargantext" "v4"
+
+-- Version
+defaultPhyloVersion :: Text
+defaultPhyloVersion = "v1"