Shrub (empty) → 0.1.0.0
raw patch · 4 files changed
+456/−0 lines, 4 filesdep +basesetup-changed
Dependencies added: base
Files
- LICENSE +12/−0
- Setup.hs +2/−0
- Shrub.cabal +16/−0
- Shrub.hs +426/−0
+ LICENSE view
@@ -0,0 +1,12 @@+Copyright (c) 2014-2015, Rob O'Callahan+All rights reserved.++Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:++1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.++2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.++3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.++THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ Setup.hs view
@@ -0,0 +1,2 @@+import Distribution.Simple+main = defaultMain
+ Shrub.cabal view
@@ -0,0 +1,16 @@+name: Shrub+version: 0.1.0.0+synopsis: 4-way trie fuzzy search+description: Nucleotide sequence approximate matching+license: BSD3+license-file: LICENSE+author: Rob O'Callahan+maintainer: rcallahan@eurekagenomics.com+copyright: (c) 2014-2015 Rob O'Callahan+build-type: Simple+cabal-version: >=1.10++library+ exposed-modules: Shrub+ build-depends: base > 4 && < 5+ default-language: Haskell2010
+ Shrub.hs view
@@ -0,0 +1,426 @@+module Shrub where++import Data.List+import Data.Char++data Shrub a = Branch !(Shrub a) !(Shrub a) !(Shrub a) !(Shrub a) | Leaf !a | Empty deriving (Show)++addShrub :: Shrub a -> String -> a -> Shrub a+addShrub _ [] v = Leaf v+addShrub sb@(Branch a c g t) ('A':sq) v = Branch (addShrub a sq v) c g t+addShrub sb@(Branch a c g t) ('C':sq) v = Branch a (addShrub c sq v) g t+addShrub sb@(Branch a c g t) ('G':sq) v = Branch a c (addShrub g sq v) t+addShrub sb@(Branch a c g t) ('T':sq) v = Branch a c g (addShrub t sq v)+addShrub Empty ('A':sq) v = Branch (addShrub Empty sq v) Empty Empty Empty+addShrub Empty ('C':sq) v = Branch Empty (addShrub Empty sq v) Empty Empty+addShrub Empty ('G':sq) v = Branch Empty Empty (addShrub Empty sq v) Empty+addShrub Empty ('T':sq) v = Branch Empty Empty Empty (addShrub Empty sq v)+addShrub (Leaf _) l v = addShrub Empty l v++addShrubDegen :: Shrub a -> String -> a -> Shrub a+addShrubDegen _ [] v = Leaf v+addShrubDegen sb@(Branch a c g t) (b:sq) v | isUpper b = branch b+ | isLower b = branch $ toUpper b where+ addA = (addShrubDegen a sq v)+ addC = (addShrubDegen c sq v)+ addG = (addShrubDegen g sq v)+ addT = (addShrubDegen t sq v)+ branch b = case b of+ 'A' -> Branch addA c g t+ 'C' -> Branch a addC g t+ 'G' -> Branch a c addG t+ 'T' -> Branch a c g addT+ 'M' -> Branch addA addC g t+ 'Y' -> Branch a addC g addT+ 'R' -> Branch addA c addG t+ 'K' -> Branch a c addG addT+ 'S' -> Branch a addC addG t+ 'W' -> Branch addA c g addT+ 'B' -> Branch a addC addG addT+ 'V' -> Branch addA addC addG t+ 'D' -> Branch addA c addG addT+ 'H' -> Branch addA addC g addT+ 'I' -> Branch addA addC addG addT+ 'N' -> Branch addA addC addG addT+addShrubDegen Empty (b:sq) v | isUpper b = branch b+ | isLower b = branch $ toUpper b where+ rest = addShrubDegen Empty sq v+ branch b = case b of+ 'A' -> Branch rest Empty Empty Empty+ 'C' -> Branch Empty rest Empty Empty+ 'G' -> Branch Empty Empty rest Empty+ 'T' -> Branch Empty Empty Empty rest+ 'M' -> Branch rest rest Empty Empty+ 'Y' -> Branch Empty rest Empty rest+ 'R' -> Branch rest Empty rest Empty+ 'K' -> Branch Empty Empty rest rest+ 'S' -> Branch Empty rest rest Empty+ 'W' -> Branch rest Empty Empty rest+ 'B' -> Branch Empty rest rest rest+ 'H' -> Branch rest rest Empty rest+ 'V' -> Branch rest rest rest Empty+ 'D' -> Branch rest Empty rest rest+ 'N' -> Branch rest rest rest rest+ 'I' -> Branch rest rest rest rest+addShrubDegen (Leaf _) l v = addShrubDegen Empty l v++subtractMultiple :: Shrub a -> [String] -> Shrub a+subtractMultiple sb [] = sb+subtractMultiple sb (x:xs) = subtractMultiple (subtractShrubDegen sb x) xs++subtractShrubDegen :: Shrub a -> String -> Shrub a+subtractShrubDegen Empty _ = Empty+subtractShrubDegen v@(Leaf _) _ = Empty+subtractShrubDegen sb@(Branch _ _ _ _) [] = sb+subtractShrubDegen sb@(Branch a c g t) (b:xs) = + let empt :: Shrub a -> Shrub a+ empt (Branch Empty Empty Empty Empty) = Empty+ empt oth = oth+ in case b of+ 'A' -> empt $ Branch (subtractShrubDegen a xs) c g t+ 'C' -> empt $ Branch a (subtractShrubDegen c xs) g t+ 'G' -> empt $ Branch a c (subtractShrubDegen g xs) t+ 'T' -> empt $ Branch a c g (subtractShrubDegen t xs)+ 'I' -> empt $ Branch (subtractShrubDegen a xs) (subtractShrubDegen c xs)+ (subtractShrubDegen g xs) (subtractShrubDegen t xs)++fromListDegen :: [(String, a)] -> Shrub a+fromListDegen = loop Empty where+ loop sb [] = sb+ loop sb ((sq, v):xs) = loop (addShrubDegen sb sq v) xs++fromList :: [(String, a)] -> Shrub a+fromList = loop Empty where+ loop sb [] = sb+ loop sb ((sq, v):xs) = loop (addShrub sb sq v) xs++searchShrub sb sq m = nubMax $ searchShrub' sb sq m+searchShrub' :: Shrub a -> String -> Int -> [(Int,a)]+searchShrub' Empty _ _ = []+searchShrub' (Leaf v) [] n = [(n,v)]+searchShrub' (Branch a c g t) [] n = concatMap (\q -> searchShrub' q [] n) [a,c,g,t]+searchShrub' (Leaf v) l n = [(n,v)]+searchShrub' sb@(Branch a c g t) l@(x:xs) n =+ let perfmatch = case x of+ 'A' -> searchShrub' a xs n+ 'C' -> searchShrub' c xs n+ 'G' -> searchShrub' g xs n+ 'T' -> searchShrub' t xs n+ otherwise -> []+ indels = concatMap (\q -> searchShrub' q l (n-1)) [a,c,g,t] ++ case l of+ (_:_) -> searchShrub' sb xs (n-1)+ _ -> []+ subs = case x of+ 'A' -> concatMap (\q -> searchShrub' q xs (n-1)) [c,g,t]+ 'C' -> concatMap (\q -> searchShrub' q xs (n-1)) [a,g,t]+ 'G' -> concatMap (\q -> searchShrub' q xs (n-1)) [a,c,t]+ 'T' -> concatMap (\q -> searchShrub' q xs (n-1)) [a,c,g]+ otherwise -> concatMap (\q -> searchShrub' q xs (n-1)) [a,c,g,t]+ in perfmatch ++ if n > 0 then subs else []++perfMatch' :: Shrub a -> String -> Int -> [(Int,a)]+perfMatch' (Branch a c g t) (x:xs) n = case x of+ 'A' -> searchShrub' a xs n+ 'C' -> searchShrub' c xs n+ 'G' -> searchShrub' g xs n+ 'T' -> searchShrub' t xs n+ otherwise -> []++searchShrub'' :: Shrub a -> String -> Int -> Int -> [(Int,a)]+searchShrub'' Empty _ _ _ = []+searchShrub'' (Leaf v) [] n _ = [(n,v)]+searchShrub'' (Branch a c g t) [] n nid = concatMap (\q -> searchShrub'' q [] n nid) [a,c,g,t]+searchShrub'' (Leaf v) l n _ = [(n,v)]+searchShrub'' sb@(Branch a c g t) l@(x:xs) n nid = + let perfmatch = case x of+ 'A' -> searchShrub'' a xs n nid+ 'C' -> searchShrub'' c xs n nid+ 'G' -> searchShrub'' g xs n nid+ 'T' -> searchShrub'' t xs n nid+ otherwise -> []+ indels = concatMap (\q -> searchShrub'' q l (n-1) (nid-1)) [a,c,g,t] ++ case l of+ (_:_) -> searchShrub'' sb xs (n-1) (nid-1)+ _ -> []+ subs = case x of+ 'A' -> concatMap (\q -> searchShrub'' q xs (n-1) nid) [c,g,t]+ 'C' -> concatMap (\q -> searchShrub'' q xs (n-1) nid) [a,g,t]+ 'G' -> concatMap (\q -> searchShrub'' q xs (n-1) nid) [a,c,t]+ 'T' -> concatMap (\q -> searchShrub'' q xs (n-1) nid) [a,c,g]+ otherwise -> concatMap (\q -> searchShrub'' q xs (n-1) nid) [a,c,g,t]+ in perfmatch ++ if n > 0 then subs ++ if (nid > 0) then indels else [] else []++-- | Search Shrub with constraint to ignore a result+searchShrubNE :: Eq a => Shrub a -> String -> a -> Int -> Int -> [(Int,a)]+searchShrubNE Empty _ _ _ _ = []+searchShrubNE (Leaf v) [] om n _ | v == om = []+ |otherwise = [(n,v)]+searchShrubNE (Branch a c g t) [] om n nid = concatMap (\q -> searchShrubNE q [] om n nid) [a,c,g,t]+searchShrubNE (Leaf v) l om n _ | v == om = []+ |otherwise = [(n,v)]+searchShrubNE sb@(Branch a c g t) l@(x:xs) om n nid =+ let perfmatch = case x of+ 'A' -> searchShrubNE a xs om n nid+ 'C' -> searchShrubNE c xs om n nid+ 'G' -> searchShrubNE g xs om n nid+ 'T' -> searchShrubNE t xs om n nid+ otherwise -> []+ freeindel = nid > 0+ n' = if freeindel then n-1 else n-2+ nid' = if freeindel then nid-1 else nid'+ indels = if not freeindel && n < 2 then [] else+ if n' < 0 then [] else case l of+ (_:_:xss) -> concatMap (\q -> searchShrubNE q l om n' nid') [a, c, g, t] +++ concatMap (\q -> searchShrubNE q xss om n' nid') [a, c, g, t]+ _ -> concatMap (\q -> searchShrubNE q l om n' nid') [a, c, g, t]+ subs = case x of+ 'A' -> concatMap (\q -> searchShrubNE q xs om (n-1) nid) [c,g,t]+ 'C' -> concatMap (\q -> searchShrubNE q xs om (n-1) nid) [a,g,t]+ 'G' -> concatMap (\q -> searchShrubNE q xs om (n-1) nid) [a,c,t]+ 'T' -> concatMap (\q -> searchShrubNE q xs om (n-1) nid) [a,c,g]+ otherwise -> concatMap (\q -> searchShrubNE q xs om (n-1) nid) [a,c,g,t]+ in if n == 0 then perfmatch else perfmatch ++ subs ++ indels where++-- | Give you nid 1 cost indel, then remaining 2 cost indels+searchShrub3 :: Shrub a -> String -> Int -> Int -> [(Int,a)]+searchShrub3 Empty _ _ _ = []+searchShrub3 (Leaf v) [] n _ = [(n,v)]+searchShrub3 (Branch a c g t) [] n nid = concatMap (\q -> searchShrub3 q [] n nid) [a,c,g,t]+searchShrub3 (Leaf v) l n _ = [(n,v)]+searchShrub3 sb@(Branch a c g t) l@(x:xs) n nid =+ let perfmatch = case x of+ 'A' -> searchShrub3 a xs n nid+ 'C' -> searchShrub3 c xs n nid+ 'G' -> searchShrub3 g xs n nid+ 'T' -> searchShrub3 t xs n nid+ 'I' -> concatMap (\q -> searchShrub3 q xs n nid) [a,c,g,t]+ otherwise -> []+ freeindel = nid > 0+ n' = if freeindel then n-1 else n-2+ nid' = if freeindel then nid-1 else nid+ indels = if not freeindel && n < 2 then [] else+ if n' < 0 then [] else concatMap (\q -> searchShrub3 q l n' nid') [a,c,g,t] ++ case l of+ (_:_:xss) -> searchShrub3 sb xss n' nid'+ _ -> concatMap (\q -> searchShrub3 q l n' nid') [a,c,g,t]+ subs = case x of+ 'A' -> concatMap (\q -> searchShrub3 q xs (n-1) nid) [c,g,t]+ 'C' -> concatMap (\q -> searchShrub3 q xs (n-1) nid) [a,g,t]+ 'G' -> concatMap (\q -> searchShrub3 q xs (n-1) nid) [a,c,t]+ 'T' -> concatMap (\q -> searchShrub3 q xs (n-1) nid) [a,c,g]+ 'I' -> []+ otherwise -> concatMap (\q -> searchShrub3 q xs (n-1) nid) [a,c,g,t]+ in if n == 0 then perfmatch else perfmatch ++ subs ++ indels++-- | Melting point shrub search+searchShrubTM :: Int -> Shrub a -> String -> Int -> [(Int,a)]+searchShrubTM _ Empty _ _ = []+searchShrubTM thr (Leaf v) [] n | n >= thr = [(n,v)]+ | otherwise = []+searchShrubTM thr (Branch a c g t) [] n = concatMap (\q -> searchShrubTM thr q [] n) [a,c,g,t]+searchShrubTM thr (Leaf v) l n | n >= thr = [(n,v)]+ | otherwise = []+searchShrubTM thr sb@(Branch a c g t) l@(x:xs) n | n >= thr = concatMap (\q -> searchShrubTM thr q [] n) [a,c,g,t]+ | otherwise =+ let ssbt = searchShrubTM thr+ perfmatch = case x of+ 'A' -> ssbt a xs (n+1)+ 'C' -> ssbt c xs (n+2)+ 'G' -> ssbt g xs (n+2)+ 'T' -> ssbt t xs (n+1)+ otherwise -> []+ indels = concatMap (\q -> ssbt q l (n-3)) [a,c,g,t] ++ case l of+ (_:_:xss) -> ssbt sb xss (n-3)+ _ -> []+ subs = case x of+ 'A' -> concatMap (\q -> ssbt q xs (n-2)) [c,g,t]+ 'C' -> concatMap (\q -> ssbt q xs (n-2)) [a,g,t]+ 'G' -> concatMap (\q -> ssbt q xs (n-2)) [a,c,t]+ 'T' -> concatMap (\q -> ssbt q xs (n-2)) [a,c,g]+ 'I' -> concatMap (\q -> ssbt q xs (n-1)) [a,c,g,t]+ otherwise -> concatMap (\q -> ssbt q xs (n-2)) [a,c,g,t]+ in perfmatch ++ subs ++ indels++searchShrubPN :: Int -> Shrub a -> String -> Int -> [(Int,a)]+searchShrubPN _ Empty _ _ = []+searchShrubPN _ (Leaf v) [] n = [(n,v)]+searchShrubPN _ (Branch a c g t) [] n = concatMap (\q -> searchShrubPN 0 q [] n) [a,c,g,t]+searchShrubPN _ (Leaf v) l n = [(n,v)]+searchShrubPN pr sb@(Branch a c g t) l@(x:xs) n =+ let ssp = searchShrubPN pr'+ pr' = if pr > 0 then pr-1 else pr+ indels = concatMap (\q -> ssp q l (n-1)) [a,c,g,t] ++ case l of+ (_:_) -> ssp sb xs (n-1)+ _ -> []+ subs = case x of+ 'A' -> concatMap (\q -> ssp q xs (n-1)) [c,g,t]+ 'C' -> concatMap (\q -> ssp q xs (n-1)) [a,g,t]+ 'G' -> concatMap (\q -> ssp q xs (n-1)) [a,c,t]+ 'T' -> concatMap (\q -> ssp q xs (n-1)) [a,c,g]+ 'I' -> concatMap (\q -> ssp q xs n) [a,c,g,t]+ otherwise -> concatMap (\q -> ssp q xs (n-1)) [a,c,g,t]+ perfmatch = case x of+ 'A' -> ssp a xs n+ 'C' -> ssp c xs n+ 'G' -> ssp g xs n+ 'T' -> ssp t xs n+ otherwise -> []+ in perfmatch ++ if n == 0 || pr > 0 then [] else subs ++ indels++searchShrubTK :: Int -> Shrub a -> String -> Int -> [(Int,a)]+searchShrubTK _ Empty _ _ = []+searchShrubTK _ (Leaf v) [] n = [(n,v)]+searchShrubTK _ (Branch a c g t) [] n = concatMap (\q -> searchShrubTK 0 q [] n) [a,c,g,t]+searchShrubTK 0 (Branch a c g t) _ n = concatMap (\q -> searchShrubTK 0 q [] n) [a,c,g,t]+searchShrubTK _ (Leaf v) l n = [(n,v)]+searchShrubTK tk sb@(Branch a c g t) l@(x:xs) n =+ let ssp = searchShrubTK tk'+ tk' = tk - 1+ indels = concatMap (\q -> ssp q l (n-1)) [a,c,g,t] ++ case xs of+ (_:_) -> searchShrubTK tk sb xs (n-1)+ _ -> []+ subs = case x of+ 'A' -> concatMap (\q -> ssp q xs (n-1)) [c,g,t]+ 'C' -> concatMap (\q -> ssp q xs (n-1)) [a,g,t]+ 'G' -> concatMap (\q -> ssp q xs (n-1)) [a,c,t]+ 'T' -> concatMap (\q -> ssp q xs (n-1)) [a,c,g]+ 'I' -> concatMap (\q -> ssp q xs n) [a,c,g,t]+ otherwise -> concatMap (\q -> ssp q xs (n-1)) [a,c,g,t]+ perfmatch = case x of+ 'A' -> ssp a xs n+ 'C' -> ssp c xs n+ 'G' -> ssp g xs n+ 'T' -> ssp t xs n+ otherwise -> []+ in perfmatch ++ if n > 0 then subs ++ indels else []++searchShrubTK2 :: Int -> Shrub a -> String -> Int -> Int -> [(Int,a)]+searchShrubTK2 _ Empty _ _ _ = []+searchShrubTK2 _ (Leaf v) [] n _ = [(n,v)]+searchShrubTK2 _ (Branch a c g t) [] n nid = concatMap (\q -> searchShrubTK2 0 q [] n nid) [a,c,g,t]+searchShrubTK2 0 (Branch a c g t) _ n nid = concatMap (\q -> searchShrubTK2 0 q [] n nid) [a,c,g,t]+searchShrubTK2 _ (Leaf v) _ n _ = [(n,v)]+searchShrubTK2 tk sb@(Branch a c g t) l@(x:xs) n nid =+ let ssp = searchShrubTK2 tk'+ tk' = tk - 1+ indels = if nid < 1 then [] else concatMap (\q -> searchShrubTK2 tk q l (n-1) (nid-1)) [a,c,g,t] ++ case l of+ (_:_) -> searchShrubTK2 tk sb xs (n-1) (nid-1)+ _ -> []+ subs = case x of+ 'A' -> concatMap (\q -> ssp q xs (n-1) nid) [c,g,t]+ 'C' -> concatMap (\q -> ssp q xs (n-1) nid) [a,g,t]+ 'G' -> concatMap (\q -> ssp q xs (n-1) nid) [a,c,t]+ 'T' -> concatMap (\q -> ssp q xs (n-1) nid) [a,c,g]+ 'I' -> concatMap (\q -> ssp q xs n nid) [a,c,g,t]+ otherwise -> concatMap (\q -> ssp q xs (n-1) nid) [a,c,g,t]+ perfmatch = case x of+ 'A' -> ssp a xs n nid+ 'C' -> ssp c xs n nid+ 'G' -> ssp g xs n nid+ 'T' -> ssp t xs n nid+ otherwise -> []+ in perfmatch ++ if n > 0 then subs ++ indels else []++searchShrubTK3 :: Int -> Shrub a -> String -> Int -> Int -> [(Int,a)]+searchShrubTK3 _ Empty _ _ _ = []+searchShrubTK3 _ (Leaf v) [] n _ = [(n,v)]+searchShrubTK3 _ (Branch a c g t) [] n nid = concatMap (\q -> searchShrubTK3 0 q [] n nid) [a,c,g,t]+searchShrubTK3 0 (Branch a c g t) _ n nid = concatMap (\q -> searchShrubTK3 0 q [] n nid) [a,c,g,t]+searchShrubTK3 _ (Leaf v) _ n _ = [(n,v)]+searchShrubTK3 tk sb@(Branch a c g t) l@(x:xs) n nid =+ let ssp = searchShrubTK3 tk'+ tk' = tk - 1+ freeindel = nid > 0+ n' = if freeindel then n-1 else n-2+ nid' = if freeindel then nid-1 else nid+ indels = if n' < 0 then [] else concatMap (\q -> searchShrubTK3 tk' q l n' nid') [a,c,g,t] ++ case l of+ (_:_) -> searchShrubTK3 tk sb xs n' nid'+ _ -> []+ subs = case x of+ 'A' -> concatMap (\q -> ssp q xs (n-1) nid) [c,g,t]+ 'C' -> concatMap (\q -> ssp q xs (n-1) nid) [a,g,t]+ 'G' -> concatMap (\q -> ssp q xs (n-1) nid) [a,c,t]+ 'T' -> concatMap (\q -> ssp q xs (n-1) nid) [a,c,g]+ 'I' -> concatMap (\q -> ssp q xs n nid) [a,c,g,t]+ otherwise -> concatMap (\q -> ssp q xs (n-1) nid) [a,c,g,t]+ perfmatch = case x of+ 'A' -> ssp a xs n nid+ 'C' -> ssp c xs n nid+ 'G' -> ssp g xs n nid+ 'T' -> ssp t xs n nid+ otherwise -> []+ in perfmatch ++ if n > 0 then subs ++ indels else []++searchShrubXF :: Shrub a -> String -> Int -> Bool -> [(Int,a)]+searchShrubXF Empty _ _ _ = []+searchShrubXF (Leaf v) _ n bul = if bul then [(n,v)] else []+searchShrubXF (Branch a c g t) [] n _ = []+searchShrubXF sb@(Branch a c g t) l@(x:xs) n _ =+ let perfmatch = case x of+ 'A' -> searchShrubXF a xs n True+ 'C' -> searchShrubXF c xs n True+ 'G' -> searchShrubXF g xs n True+ 'T' -> searchShrubXF t xs n True+ otherwise -> []+ indels = concatMap (\q -> searchShrubXF q l (n-1) False) [a,c,g,t] ++ case l of+ (_:_) -> searchShrubXF sb xs (n-1) False+ _ -> []+ subs = case x of+ 'A' -> concatMap (\q -> searchShrubXF q xs (n-1) False) [c,g,t]+ 'C' -> concatMap (\q -> searchShrubXF q xs (n-1) False) [a,g,t]+ 'G' -> concatMap (\q -> searchShrubXF q xs (n-1) False) [a,c,t]+ 'T' -> concatMap (\q -> searchShrubXF q xs (n-1) False) [a,c,g]+ otherwise -> concatMap (\q -> searchShrubXF q xs (n-1) False) [a,c,g,t]+ in perfmatch ++ if n > 0 then subs else []++-- | IonTorrent Shrub search+searchShrubIT :: Shrub a -> String -> Int -> [(Int, (a, String))]+searchShrubIT Empty _ _ = []+searchShrubIT (Leaf v) s n = [(n, (v, s))]+searchShrubIT (Branch a c g t) [] n = [] --concatMap (\q -> searchShrubIT q [] n) [a,c,g,t]+searchShrubIT sb@(Branch a c g t) l@(x:xs) n | n > 0 = perfmatch ++ subs ++ indels+ | otherwise = perfmatch where+ perfmatch = case x of+ 'A' -> searchShrubIT a xs n+ 'C' -> searchShrubIT c xs n+ 'G' -> searchShrubIT g xs n+ 'T' -> searchShrubIT t xs n+ otherwise -> []+ indels = concatMap (\q -> searchShrubIT q l (n-1)) [a,c,g,t] ++ searchShrubIT sb xs (n-1)+ subs = case x of+ 'A' -> concatMap (\q -> searchShrubIT q xs (n-3)) [c,g,t]+ 'C' -> concatMap (\q -> searchShrubIT q xs (n-3)) [a,g,t]+ 'G' -> concatMap (\q -> searchShrubIT q xs (n-3)) [a,c,t]+ 'T' -> concatMap (\q -> searchShrubIT q xs (n-3)) [a,c,g]+ otherwise -> concatMap (\q -> searchShrubIT q xs (n-3)) [a,c,g,t]++nubMax :: (Ord a, Eq b) => [(a,b)] -> [(a,b)]+nubMax = foldl' go [] where+ go l i@(m, iv) = maybe (i:l) (\fn -> if m > fst (l !! fn) then i:(take fn l ++ drop (fn+1) l) else l) (findIndex (\(p, q) -> iv == q) l)++--nubMax' :: (Ord a, Eq b) => [(a,b)] -> [(a,b)]+--nubMax' = map (uncurry (flip (,))) . HM.toList $ foldl' go HM.empty where+ --go hm i@(m, iv) = maybe (HM.insert iv m hm) (\fn -> if m > fn then HM.insert iv m hm else hm) (HM.lookup iv hm)++searchShrubCount :: Shrub a -> String -> Int -> [(Int,Int,a)]+searchShrubCount sb sq mm = sshrub sb sq 0 mm where+ sshrub Empty _ _ _ = []+ sshrub (Leaf v) [] cnt n = [(n,cnt,v)]+ sshrub (Branch a c g t) [] cnt n = concatMap (\q -> sshrub q [] cnt n) [a,c,g,t]+ sshrub (Leaf v) l cnt n = [(n,cnt,v)]+ sshrub sb@(Branch a c g t) l@(x:xs) cnt n =+ let cnt' = cnt + 1+ perfmatch = case x of+ 'A' -> sshrub a xs cnt' n+ 'C' -> sshrub c xs cnt' n+ 'G' -> sshrub g xs cnt' n+ 'T' -> sshrub t xs cnt' n+ otherwise -> []+ indels = concatMap (\q -> sshrub q l cnt (n-1)) [a,c,g,t] ++ case l of+ (_:_) -> sshrub sb xs cnt' (n-1)+ _ -> []+ subs = case x of+ 'A' -> concatMap (\q -> sshrub q xs cnt' (n-1)) [c,g,t]+ 'C' -> concatMap (\q -> sshrub q xs cnt' (n-1)) [a,g,t]+ 'G' -> concatMap (\q -> sshrub q xs cnt' (n-1)) [a,c,t]+ 'T' -> concatMap (\q -> sshrub q xs cnt' (n-1)) [a,c,g]+ otherwise -> concatMap (\q -> sshrub q xs cnt' (n-1)) [a,c,g,t]+ in perfmatch ++ if n > 0 then subs else []