gsc-weighting 0.1 → 0.1.0.1

raw patch · 2 files changed

+38/−9 lines, 2 filesPVP ok

version bump matches the API change (PVP)

API changes (from Hackage documentation)

Files

• Data/Weighting/GSC.hs +37/−8
• gsc-weighting.cabal +1/−1

@@ -12,18 +12,47 @@ -- @0@ (in the leafs) and @1@.  The final weights are normalized -- to average to @1@ (i.e. sum to the number of sequences, the -- same they would sum if all weights were @1@).+--+-- For example, suppose we have+--+-- @+-- dendro = Branch 0.8+--            (Branch 0.5+--              (Branch 0.2+--                (Leaf 'A')+--                (Leaf 'B'))+--              (Leaf 'C'))+--            (Leaf 'D')+-- @+--+-- This is the same as GSC paper's example, however they used+-- similarities while we are using distances (i.e. @fmap (1-)+-- dendro@ would be exactly their example).  Then @gsc dendro@ is+--+-- @+-- gsc dendro == Branch 0.8+--                 (Branch 0.5+--                   (Branch 0.2+--                     (Leaf ('A',0.7608695652173914))+--                     (Leaf ('B',0.7608695652173914)))+--                   (Leaf ('C',1.0869565217391306)))+--                 (Leaf ('D',1.3913043478260871))+-- @+--+-- which is exactly what they calculated. gsc :: Fractional d => Dendrogram d a -> Dendrogram d (a, d)-gsc (Leaf x) = Leaf (x,1)-gsc dendro   = let (wsum, nsum, r) = go wfinal undefined [] dendro-                   wfinal = (wsum / fromIntegral nsum)-               in r+gsc (Leaf x)   = Leaf (x,1)+gsc dendrogram = ret     where+      (wsum, nsum, ret) = go undefined [] dendrogram+      wfinal            = (wsum / fromIntegral nsum)+       position (Leaf _)       = 0 -- no difference from itself       position (Branch d _ _) = d -      go wfinal _ cs (Branch d l r) =-          let (wl, nl, l') = go wfinal d ((el / wl) : cs) l-              (wr, nr, r') = go wfinal d ((er / wr) : cs) r+      go _ cs (Branch d l r) =+          let (wl, nl, l') = go d ((el / wl) : cs) l+              (wr, nr, r') = go d ((er / wr) : cs) r                el = d - position l -- edge length to left branch               er = d - position r --          ...to right branch@@ -31,7 +60,7 @@               wsum = wl + wr + el + er               nsum = nl + nr           in wsum `seq` nsum `seq` (wsum, nsum, Branch d l' r')-      go wfinal d cs (Leaf x) =+      go d cs (Leaf x) =           -- O(n) worst case, O(log n) best case (balanced dendrogram)           let w = foldl' (\curw c -> curw + curw * c) d (tail cs)           in (0, 1 :: Int, Leaf (x, w / wfinal))

@@ -1,5 +1,5 @@ Name:                gsc-weighting-Version:             0.1+Version:             0.1.0.1 Synopsis:            Generic implementation of Gerstein/Sonnhammer/Chothia weighting. License:             BSD3 License-file:        LICENSE