xml2x-0.2: src/Tabulate.hs

-- | Tabulate
--   Data structure for tables consisting of cells with various alignments.
--   For building more generic rendering of alignments

module Tabulate where

import Prelude hiding (words)
import Bio.Alignment.BlastData
import Data.ByteString.Lazy.Char8 (ByteString,words)
import Data.List (sortBy)

type Table = (ByteString,Int,[Row])
type Row   = (ByteString,[Cell])
data Cell  = Cell { wd :: Int, color :: Int, frame :: Maybe Aux } deriving Show

tabulate :: BlastRecord -> Table
tabulate b = (head $ words $ query b, qlength b, map (row (qlength b)) (hits b))

row :: Int -> BlastHit -> Row
row wtot h = (head $ words $ subject h, go 0 $ sort_matches $ matches h)
    where
      sort_matches = sortBy (\m1 m2 -> compare (min (q_from m1) (q_to m1)) (min (q_from m2) (q_to m2)))

      go :: Int -> [BlastMatch] -> [Cell]
      go p []      = [Cell (wtot-p) 0 Nothing]
      go p (b:bs') =
          let (f',t') = (q_from b,q_to b)
              (f,t) = if f'<t' then (f',t') else (t',f')
              w1 = max (f-p) 0
              w2 = max (t-(p+w1)) 0
          in Cell w1 0 Nothing
             : Cell w2 (floor (50*bits b) `div` (t-f)) (Just $ aux b)
             : go (p+w1+w2) bs'