Type.hs

module Bio.GB.Type
  ( GenBankSequence (..)
  , Meta (..)
  , Form (..)
  , Locus (..)
  , Version (..)
  , Source (..)
  , Reference (..)
  , Feature (..)
  ) where

import           Bio.Sequence (IsMarking, MarkedSequence)
import           Data.Text    (Text)

-- | Type that represents contents of .gb file that is used to store information about
-- genetic constructions.
--
data GenBankSequence = GenBankSequence { meta  :: Meta                        -- ^ meta-information about the sequence
                                       , gbSeq :: MarkedSequence Feature Char -- ^ sequence that is marked by 'Feature's
                                       }
  deriving (Eq, Show)

--------------------------------------------------------------------------------
-- Block with meta-information.
--------------------------------------------------------------------------------

-- | Meta-information about sequence.
--
data Meta = Meta { locus      :: Locus         -- ^ general info about sequence
                 , definition :: Maybe Text    -- ^ brief description of sequence
                 , accession  :: Maybe Text    -- ^ the unique identifier for a sequence record
                 , version    :: Maybe Version -- ^ id of sequence in GenBank database
                 , keywords   :: Maybe Text    -- ^ word or phrase describing the sequence
                 , source     :: Maybe Source  -- ^ free-format information including an abbreviated form of the organism name,
                                               --   sometimes followed by a molecule type
                 , references :: [Reference]   -- ^ publications by the authors of the sequence that discuss the data reported in the record
                 , comments   :: [Text]        -- ^ comments about the sequence (note that there can be (!!!) empty comments)
                 }
  deriving (Eq, Show)

-- | First line that should be present in every .gb file. Contains general info about sequence.
--
data Locus = Locus { name             :: Text       -- ^ name of sequence
                   , len              :: Int        -- ^ length of sequence
                   , molType          :: Text       -- ^ type of molecule that is sequenced
                   , form             :: Maybe Form -- ^ form of sequence
                   , gbDivision       :: Maybe Text -- ^ GenBank division to which a record belongs
                   , modificationDate :: Text       -- ^ date of last modification of sequence
                   }
  deriving (Eq, Show)

-- | At this moment there are two known (to me)
-- forms of seuqences that can be present in .gb file.
--
data Form = Linear | Circular
  deriving (Eq, Show)

-- | Id of sequence in GenBank database.
--
data Version = Version { versionT :: Text       -- ^ id itself
                       , gbId     :: Maybe Text -- ^ GenInfo Identifier that is assigned when sequence changes
                       }
  deriving (Eq, Show)

-- | Information about source of this sequence.
--
data Source = Source { sourceT  :: Text       -- ^ free-format (as if all this format is not too much "free format") information
                                              -- including an abbreviated form of the organism name,
                                              -- sometimes followed by a molecule type
                     , organism :: Maybe Text -- ^ the formal scientific name for the source organism
                     }
  deriving (Eq, Show)

-- | Publications by the authors of the sequence that discuss the data reported in the record.
--
data Reference = Reference { referenceT :: Text       -- ^ reference itself
                           , authors    :: Maybe Text -- ^ list of authors in the order in which they appear in the cited article
                           , title      :: Maybe Text -- ^ title of the published work
                           , journal    :: Maybe Text -- ^ MEDLINE abbreviation of the journal name
                           , pubmed     :: Maybe Text -- ^ PubMed Identifier
                           }
  deriving (Eq, Show)

--------------------------------------------------------------------------------
-- Block with FEATURES table.
--
-- FEATURES table contains information about genes and gene products, as well as regions of biological
-- significance reported in the sequence. These can include regions of the sequence
-- that code for proteins and RNA molecules, as well as a number of other features.
-- More about FEATURES table: http://www.insdc.org/documents/feature_table.html
--------------------------------------------------------------------------------

-- | One single feature.
--
data Feature = Feature { fName     :: Text           -- ^ main information about feature
                       , fStrand53 :: Bool           -- ^ set to True if sequence is contained on 5'-3' strand.
                                                     --   Set to False otherwise
                       , fProps    :: [(Text, Text)] -- ^ properties of feature (such as "label", "gene", "note" etc.)
                       }
  deriving (Eq, Show, Ord)

instance IsMarking Feature