-- | This module contains data structures for the Clustal tools 
--   For more information on Clustal tools consult: <http://www.clustal.org/>

module Bio.ClustalData where
import qualified Data.Vector as V
    
-- | Data type for clustal summary, containing information about the alignment process, usually printed to STDOUT
data ClustalSummary = ClustalSummary
  {
    clustalw2version :: String,
    sequenceFormat :: String,
    parametersOfInputSequences :: [SequenceParameters],
    pairwiseAlignmentSummaries :: [PairwiseAlignmentSummary],
    guideTreeFileName :: String,
    groupNumber :: Int,
    groupSummaries :: [GroupSummary],
    alignmentScore :: Int,
    alignmentFileName :: String
  }
  deriving (Show, Eq)

data SequenceParameters = SequenceParameters
  {
     inputSequenceIndex :: Int,
     inputSequenceIdentifier :: String,
     inputSequenceLength :: Int
  }
  deriving (Show, Eq)

data PairwiseAlignmentSummary = PairwiseAlignmentSummary
  {
     firstSequenceIndex :: Int,
     secondSequenceIndex :: Int,
     pairwiseAlignmentScore :: Int
  }
  deriving (Show, Eq)

data GroupSummary = GroupSummary
  {
     alignmentGroupIndex :: Int,
     numberOfAlignedSequences :: Maybe Int,
     groupScore :: Maybe Int
  }
  deriving (Show, Eq)

-- | Data structure for Clustal alignment format
data ClustalAlignment = ClustalAlignment
  { 
    alignmentEntries :: [ClustalAlignmentEntry],
    conservationTrack :: String
  }
  deriving (Eq)

instance Show ClustalAlignment where
  show (ClustalAlignment _alignmentEntries _conservationTrack ) 
    | not (null _alignmentEntries) = header ++ alignmentString
    | otherwise = header
    where header = "CLUSTAL W (1.8) multiple sequence alignment\n\n\n" 
          longestSequenceIdLength =  (maximum (map length (map entrySequenceIdentifier _alignmentEntries))) + 1
          totalSequenceLength = length (entryAlignedSequence (head _alignmentEntries))
          alignmentString = showAlignment totalSequenceLength longestSequenceIdLength 0 _alignmentEntries _conservationTrack

showAlignment :: Int -> Int -> Int -> [ClustalAlignmentEntry] -> String -> String
showAlignment totalSequenceLength longestSequenceIdLength currentWindowPosition _alignmentEntries _conservationTrack
  | totalSequenceLength == 0 = [] 
  | currentWindowPosition <= totalSequenceLength = showAlignmentBlock longestSequenceIdLength currentWindowPosition _alignmentEntries _conservationTrack ++ (showAlignment totalSequenceLength longestSequenceIdLength (currentWindowPosition + 60) _alignmentEntries _conservationTrack)
  | otherwise = "" 

showAlignmentBlock :: Int -> Int -> [ClustalAlignmentEntry] -> String -> String
showAlignmentBlock longestSequenceIdLength currentWindowPosition _alignmentEntries _conservationTrack = blockString
  where blockString = entries ++ extraTrack ++ "\n"
        entries = concatMap (showAlignmentLine longestSequenceIdLength currentWindowPosition) _alignmentEntries
        extraTrack = concat (replicate longestSequenceIdLength " ") ++ V.toList (V.slice currentWindowPosition 60  (V.fromList _conservationTrack)) ++ "\n"

showAlignmentLine :: Int -> Int -> ClustalAlignmentEntry -> String
showAlignmentLine longestSequenceIdLength currentWindowPosition _alignmentEntry = (entrySequenceIdentifier _alignmentEntry) ++ concat (replicate (longestSequenceIdLength - length (entrySequenceIdentifier _alignmentEntry)) " ") ++ V.toList (V.slice currentWindowPosition 60  (V.fromList (entryAlignedSequence _alignmentEntry))) ++ "\n"

data ClustalAlignmentEntry = ClustalAlignmentEntry
  {
    entrySequenceIdentifier :: String,
    entryAlignedSequence :: String
  }
  deriving (Show, Eq)

data ClustalAlignmentSlice = ClustalAlignmentSlice
  {
    entrySlices :: [ClustalAlignmentEntrySlice],
    conservationTrackSlice :: String
  }
  deriving (Show, Eq)

data ClustalAlignmentEntrySlice = ClustalAlignmentEntrySlice
  {
    entrySequenceSliceIdentifier :: String,
    entryAlignedSliceSequence :: String,
    spacerLength :: Int
  }
  deriving (Show, Eq)

-- | Data structure for structural Clustal alignment format
data StructuralClustalAlignment = StructuralClustalAlignment
  { 
    structuralAlignmentEntries :: [ClustalAlignmentEntry],
    secondaryStructureTrack :: String,
    energy :: Double
  }
  deriving (Eq)

instance Show StructuralClustalAlignment where
  show (StructuralClustalAlignment _alignmentEntries _secondaryStructureTrack _energy) 
    | not (null _alignmentEntries) = header ++ alignmentString
    | otherwise = header
    where header = "CLUSTAL W \n\n" 
          longestSequenceIdLength =  (maximum (map length (map entrySequenceIdentifier _alignmentEntries))) + 1
          totalSequenceLength = length (entryAlignedSequence (head _alignmentEntries))
          alignmentString = showAlignment totalSequenceLength longestSequenceIdLength 0 _alignmentEntries _secondaryStructureTrack

data StructuralClustalAlignmentSlice = StructuralClustalAlignmentSlice
  {
    structuralEntrySlices :: [StructuralClustalAlignmentEntrySlice]
  }
  deriving (Show, Eq)

data StructuralClustalAlignmentEntrySlice = StructuralClustalAlignmentEntrySlice
  {
    structuralEntrySequenceSliceIdentifier :: String,
    structuralEntryAlignedSliceSequence :: String
  }
  deriving (Show, Eq)