{-| Module : Gargantext.Core.Viz.Phylo.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 -} {-# LANGUAGE ViewPatterns #-} module Gargantext.Core.Viz.Phylo.Tools where import Control.Lens hiding (both, Level, Empty) import Data.List (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.Core.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 WeightedLogSim (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 initWeightedLogSim :: Maybe Double -> Maybe Double -> WLJParams initWeightedLogSim (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) defaultWeightedLogSim :: Proximity defaultWeightedLogSim = WeightedLogSim (initWeightedLogSim 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"