gsc-weighting 0.1.0.2 → 0.1.1

raw patch · 2 files changed

+27/−6 lines, 2 filesPVP: major bump suggested

API removals or changes: PVP suggests a major version bump

API changes (from Hackage documentation)

Files

• Data/Weighting/GSC.hs +20/−5
• gsc-weighting.cabal +7/−1

@@ -42,16 +42,18 @@ -- -- which is exactly what they calculated. gsc :: Fractional d => Dendrogram d a -> Dendrogram d (a, d)-gsc (Leaf x)   = Leaf (x,1)-gsc dendrogram = ret+gsc (Leaf x)                  = Leaf (x,1)+gsc b@(Branch d _ _) | d == 0 = fmap (flip (,) 1) b+gsc dendrogram                = ret     where-      (wsum, nsum, ret) = go undefined [] dendrogram-      wfinal            = (wsum / fromIntegral nsum)+      (wsumF, nsumF, ret) = go undefined [] dendrogram+      wfinal              = (wsumF / fromIntegral nsumF)        position (Leaf _)       = 0 -- no difference from itself       position (Branch d _ _) = d -      go _ cs (Branch d l r) =+      go d' cs b@(Branch d _ _) | d == 0 = zeroBranch d' cs b+      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 @@ -65,3 +67,16 @@           -- 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))++      -- special case for branches where the distance is zero.+      zeroBranch d' cs b =+          let w  = foldl' (\curw c -> curw + curw * c) d' (tail cs)+              wf = w / (wfinal * fromIntegral nsum)+              setWeights (Leaf x) = (1, Leaf (x, wf))+              setWeights (Branch d l r) =+                  let (nl, l') = setWeights l+                      (nr, r') = setWeights r+                      ns = nl + nr+                  in ns `seq` (ns, Branch d l' r')+              (nsum, ret) = setWeights b+          in (0, nsum, ret)

@@ -1,5 +1,5 @@ Name:                gsc-weighting-Version:             0.1.0.2+Version:             0.1.1 Synopsis:            Generic implementation of Gerstein/Sonnhammer/Chothia weighting. License:             BSD3 License-file:        LICENSE@@ -21,6 +21,12 @@   dendrogram.  If you want to recreate their algorithm, then just   use @UPGMA@ as linkage and residue identity as distance   function when creating the dendrogram.+  .+  Changes in version 0.1.1:+  .+  * Now works even when some (or all) branches have distance zero+    (i.e. elements below that branches are all equal with respect+    to distance metric that was used to create the dendrogram).  Library   Exposed-modules: