{-|
Module : Gargantext.Viz.Phylo.Tools
-Description : Phylomemy tools
+Description : Phylomemy Tools to build/manage it
Copyright : (c) CNRS, 2017-Present
License : AGPL + CECILL v3
Maintainer : team@gargantext.org
Stability : experimental
Portability : POSIX
-Phylo Toolbox:
-- functions to build a Phylo
-- functions to filter the cliques
-- functions to manage a Phylo
-
-Group Functions (TODO list)
-- cohesion sur un groupe
-- distance au dernier branchement
-- âge du groupe
-
-Futre Idea: temporal zoom on Phylo
-phyloZoomOut :: (PeriodGrain, Phylo) -> [(PeriodGrain, Phylo)]
-(from smallest granularity, it increases (zoom out) the periods of the Phylo)
-Moral idea: viz from out to in
-}
-{-# LANGUAGE NoImplicitPrelude #-}
{-# LANGUAGE FlexibleContexts #-}
+{-# LANGUAGE NoImplicitPrelude #-}
{-# LANGUAGE OverloadedStrings #-}
+{-# LANGUAGE RankNTypes #-}
+{-# LANGUAGE ViewPatterns #-}
-module Gargantext.Viz.Phylo.Tools where
+module Gargantext.Viz.Phylo.Tools
+ where
-import Data.Set (Set)
-import Data.Map (Map)
-import qualified Data.Map as Map
+import Control.Lens hiding (both, Level, Empty)
+import Data.List (filter, intersect, (++), sort, null, tail, last, tails, delete, nub, concat, sortOn)
+import Data.Maybe (mapMaybe,fromMaybe)
+import Data.Map (Map, mapKeys, member, (!))
+import Data.Set (Set)
+import Data.Text (Text, toLower)
+import Data.Tuple.Extra
+import Data.Vector (Vector,elemIndex)
import Gargantext.Prelude
import Gargantext.Viz.Phylo
-import Gargantext.Viz.Phylo.Example
+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
+listToDirectedCombi :: Eq a => [a] -> [(a,a)]
+listToDirectedCombi l = [(x,y) | x <- l, y <- l, x /= y]
+
+
+-- | 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 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 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 of the Phylo as a Vector of Ngrams
+initFoundations :: [Ngrams] -> Vector Ngrams
+initFoundations l = Vector.fromList $ map phyloAnalyzer l
+
+-- | To init the base of a Phylo from a List of Periods and Foundations
+initPhyloBase :: [(Date, Date)] -> Vector Ngrams -> PhyloPeaks -> PhyloParam -> Phylo
+initPhyloBase pds fds pks prm = Phylo ((fst . (head' "initPhyloBase")) pds, (snd . last) pds) fds pks (map (\pd -> initPhyloPeriod pd []) pds) 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 foundations of a Phylo
+getFoundations :: Phylo -> Vector Ngrams
+getFoundations = _phylo_foundations
+
+-- | To get the Index of a Ngrams in the Foundations of a Phylo
+getIdxInFoundations :: Ngrams -> Phylo -> Int
+getIdxInFoundations n p = case (elemIndex n (getFoundations p)) of
+ Nothing -> panic "[ERR][Viz.Phylo.Tools.getIdxInFoundations] Ngrams not in Foundations"
+ Just idx -> idx
+
+
+-- | 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
+
+
+--------------------
+-- | PhyloPeaks | --
+--------------------
+
+-- | To apply a fonction to each label of a Ngrams Tree
+alterLabels :: (Ngrams -> Ngrams) -> Tree Ngrams -> Tree Ngrams
+alterLabels f (Node lbl ns) = Node (f lbl) (map (\n -> alterLabels f n) ns)
+alterLabels _ Empty = panic "[ERR][Viz.Phylo.Tools.alterLabels] Empty"
+
+-- | To transform a forest of trees into a map (node,root)
+forestToMap :: [Tree Ngrams] -> Map Ngrams Ngrams
+forestToMap trees = Map.fromList $ concat $ map treeToTuples' trees
+ where
+ treeToTuples' (Node lbl ns) = treeToTuples (Node lbl ns) lbl
+ treeToTuples' Empty = panic "[ERR][Viz.Phylo.Tools.forestToMap] Empty"
+
+-- | To get the foundationsPeaks of a Phylo
+getPeaks :: Phylo -> PhyloPeaks
+getPeaks = _phylo_foundationsPeaks
+
+-- | To get the peaksLabels of a Phylo
+getPeaksLabels :: Phylo -> Vector Ngrams
+getPeaksLabels p = (getPeaks p) ^. phylo_peaksLabels
+
+-- | To get the Index of a Ngrams in the foundationsPeaks of a Phylo
+getIdxInPeaks :: Ngrams -> Phylo -> Int
+getIdxInPeaks n p = case (elemIndex n (getPeaksLabels p)) of
+ Nothing -> panic "[ERR][Viz.Phylo.Tools.getIdxInPeaks] Ngrams not in foundationsPeaks"
+ Just idx -> idx
+
+-- | To init the PhyloPeaks of a Phylo
+initPeaks :: [Tree Ngrams] -> Vector Ngrams -> PhyloPeaks
+initPeaks trees ns = PhyloPeaks labels trees
+ where
+ --------------------------------------
+ labels :: Vector Ngrams
+ labels = Vector.fromList
+ $ nub
+ $ Vector.toList
+ $ map (\n -> if member n mTrees
+ then mTrees Map.! n
+ else n ) ns
+ --------------------------------------
+ mTrees :: Map Ngrams Ngrams
+ mTrees = forestToMap trees
+ --------------------------------------
+
+-- | To transform a Ngrams Tree into a list of (node,root)
+treeToTuples :: Tree Ngrams -> Ngrams -> [(Ngrams,Ngrams)]
+treeToTuples (Node lbl ns) root = [(lbl,root)] ++ (concat $ map (\n -> treeToTuples n root) ns)
+treeToTuples Empty _ = panic "[ERR][Viz.Phylo.Tools.treeToTuples] Empty"
+
+--------------------
+-- | 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
+
+
+-- | To get the Cooc Matrix of a PhyloGroup
+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 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 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 PhyloGroupIds in a Phylo
+getGroupsFromIds :: [PhyloGroupId] -> Phylo -> [PhyloGroup]
+getGroupsFromIds ids p = filter (\g -> elem (getGroupId g) ids) $ getGroups p
+
+
+-- | 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
+ (sort $ map (\x -> getIdxInPeaks x p) ngrams)
+ (Map.empty)
+ (Map.empty)
+ Nothing
+ [] [] [] []
+
+
+---------------------
+-- | 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
+
+
+--------------------
+-- | 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 metrics of a PhyloFis
+getFisMetrics :: PhyloFis -> Map (Int,Int) (Map Text [Double])
+getFisMetrics = _phyloFis_metrics
+
+-- | To get the support of a PhyloFis
+getSupport :: PhyloFis -> Support
+getSupport = _phyloFis_support
+
+
+----------------------------
+-- | PhyloNodes & Edges | --
+----------------------------
+
+
+-- | To filter some GroupEdges with a given threshold
+filterGroupEdges :: Double -> GroupEdges -> GroupEdges
+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 -> GroupEdges -> [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
+
+
+-- | 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 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
+
+
+--------------------------------
+-- | PhyloQuery & QueryView | --
+--------------------------------
+
+-- | 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 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 -> FisParams
+initFis (def True -> kmf) (def 1 -> min') = FisParams kmf min'
+
+initHamming :: Maybe Double -> HammingParams
+initHamming (def 0.01 -> sens) = HammingParams sens
+
+initSmallBranch :: Maybe Int -> Maybe Int -> Maybe Int -> SBParams
+initSmallBranch (def 2 -> periodsInf) (def 2 -> periodsSup) (def 1 -> minNodes) = SBParams periodsInf periodsSup minNodes
+
+initLouvain :: Maybe Proximity -> LouvainParams
+initLouvain (def defaultWeightedLogJaccard -> proxi) = LouvainParams proxi
+
+initRelatedComponents :: Maybe Proximity -> RCParams
+initRelatedComponents (def Filiation -> proxi) = RCParams proxi
+
+initWeightedLogJaccard :: Maybe Double -> Maybe Double -> WLJParams
+initWeightedLogJaccard (def 0 -> thr) (def 0.01 -> sens) = WLJParams thr sens
+
+
+-- | To initialize a PhyloQuery from given and default parameters
+initPhyloQueryBuild :: Maybe Text -> Maybe Text -> Maybe Int -> Maybe Int -> Maybe Cluster -> Maybe [Metric] -> Maybe [Filter] -> Maybe Proximity -> Maybe Level -> Maybe Cluster -> PhyloQueryBuild
+initPhyloQueryBuild name desc (def 5 -> grain) (def 3 -> steps) (def defaultFis -> cluster) (def [] -> metrics) (def [] -> filters)
+ (def defaultWeightedLogJaccard -> matching') (def 2 -> nthLevel) (def defaultRelatedComponents -> nthCluster) =
+ PhyloQueryBuild name' desc' grain steps cluster metrics filters matching' nthLevel nthCluster
+ where
+ name' = maybe "Phylo Title" identity name
+ desc' = maybe "Phylo Desc" identity desc
+
+
+
+-- | 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 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 Flat -> dm) (def True -> v) =
+ PhyloQueryView lvl f c d ms fs ts s dm v
+
+
+-- | To define some obvious boolean getters
+shouldKeepMinorFis :: FisParams -> Bool
+shouldKeepMinorFis = _fis_keepMinorFis
+
+----------------------------
+-- | Default ressources | --
+----------------------------
+
+-- Clusters
-type MinSize = Int
+defaultFis :: Cluster
+defaultFis = Fis (initFis Nothing Nothing)
--- | Building a phylo
--- (Indicative and schematic function)
--- buildPhylo :: Support -> MinSize
--- -> Map Clique Support -> Phylo
--- buildPhylo s m mcs = level2Phylo
--- . groups2level
--- . clusters2group
--- . Map.map clique2cluster
--- . filterCliques s m
+defaultLouvain :: Cluster
+defaultLouvain = Louvain (initLouvain Nothing)
-level2Phylo :: PhyloLevel -> Phylo -> Phylo
-level2Phylo = undefined
+defaultRelatedComponents :: Cluster
+defaultRelatedComponents = RelatedComponents (initRelatedComponents Nothing)
-groups2level :: [PhyloGroup] -> PhyloLevel
-groups2level = undefined
+-- Filters
--- clusters2group :: [Cluster Ngrams] -> PhyloGroup
--- clusters2group = undefined
+defaultSmallBranch :: Filter
+defaultSmallBranch = SmallBranch (initSmallBranch Nothing Nothing Nothing)
--- clique2cluster :: Clique -> Cluster Ngrams
--- clique2cluster = undefined
+-- Params
--- | Filtering the cliques before bulding the Phylo
--- (Support and MinSize as parameter of the finale function to build a phylo)
--- idea: log of Corpus size (of docs)
-filterCliques :: Support -> MinSize
- -> Map Clique Support -> [Clique]
-filterCliques s ms = maximalCliques
- . filterWithSizeSet ms
- . Map.keys
- . filterWithSupport s
+defaultPhyloParam :: PhyloParam
+defaultPhyloParam = initPhyloParam Nothing Nothing Nothing
--- | Hapaxify / Threshold
--- hapax s = 1
--- ?
-filterWithSupport :: Support -> Map Clique Support -> Map Clique Support
-filterWithSupport s = Map.filter (>s)
+-- Proximities
-filterWithSizeSet :: MinSize -> [Clique] -> [Clique]
-filterWithSizeSet = undefined
+defaultHamming :: Proximity
+defaultHamming = Hamming (initHamming Nothing)
--- | filtre les cliques de ngrams compris dans une clique plus grande
--- /!\ optim inside
-maximalCliques :: [Clique] -> [Clique]
-maximalCliques = undefined
+defaultWeightedLogJaccard :: Proximity
+defaultWeightedLogJaccard = WeightedLogJaccard (initWeightedLogJaccard Nothing Nothing)
+-- Queries
+defaultQueryBuild :: PhyloQueryBuild
+defaultQueryBuild = initPhyloQueryBuild (Just "Cesar et Cleôpatre")
+ (Just "An example of Phylomemy (french without accent)")
+ Nothing Nothing Nothing
+ Nothing Nothing Nothing
+ Nothing Nothing
+defaultQueryView :: PhyloQueryView
+defaultQueryView = initPhyloQueryView Nothing Nothing Nothing Nothing Nothing Nothing Nothing Nothing Nothing Nothing
--- | Phylo management
+-- Software
--- | PhyloLevel Management
-viewGroups :: (Start,End) -> PhyloLevel -> Phylo -> [PhyloGroup]
-viewGroups = undefined
+defaultSoftware :: Software
+defaultSoftware = Software "Gargantext" "v4"
-viewLevels :: (Start,End) -> Phylo -> [PhyloLevel]
-viewLevels = undefined
+-- Version
--- | tous les terme des champs, tous les parents et les enfants
-setGroup :: PhyloGroup -> PhyloGroup -> PhyloGroup
-setGroup = undefined
---removeTerms :: recalculer les cliques pour ces termes
---addTerms
+defaultPhyloVersion :: Text
+defaultPhyloVersion = "v1"