VerboseHit.hs

{-# LANGUAGE RecordWildCards #-}
{-# OPTIONS_GHC -funbox-strict-fields #-}

-- | Provides a datatype for cmsearch verbose output. The Import/Export system
-- now allows for primitive annotations using "##" as the first two characters.
-- Annotations are only accepted for individual hits.

module Biobase.Infernal.VerboseHit where

import Data.ByteString.Char8 as BS
import Text.Printf



-- | Captures a complete alignment

data VerboseHit = VerboseHit
  { vhTarget      :: !(Int,Int)     -- ^ part of target sequence (start counting at 1)
  , vhQuery       :: !(Int,Int)     -- ^ which part of the CM/stk do we align to
  , vhCM          :: !ByteString    -- ^ the CM for this alignment
  , vhStrand      :: !Strand        -- ^ should be either '+' or '-'
  , vhScore       :: !Double        -- ^ bit score
  , vhEvalue      :: !Double        -- ^ number of hits we expect to find with 'score' or higher for 'targetSequence' length
  , vhPvalue      :: !Double        -- ^ ?
  , vhGC          :: !Int           -- ^ ?
  , vhScaffold    :: !ByteString    -- ^ scaffold, chromosome, ... (the name of the sequence, not the sequence data!)
  , vhWuss        :: !ByteString    -- ^ fancy secondary structure annotation using wuss notation
  , vhConsensus   :: !ByteString    -- ^ query consensus (upper: highly, lower: weak/no)
  , vhScoring     :: !ByteString    -- ^ represents where positive and negative scores come from
  , vhSequence    :: !ByteString    -- ^ the target sequence which aligns to the model
  , vhAnnotation  :: ![ByteString]  -- ^ any annotations that could be associated (# lines)
  } deriving (Show,Read)

type Strand = Char