-- Hoogle documentation, generated by Haddock
-- See Hoogle, http://www.haskell.org/hoogle/


-- | Handle sequence locations for bioinformatics
--   
--   Handle sequence locations for bioinformatics
@package seqloc
@version 0.2

module Bio.SeqLoc.SeqLike
class SeqLike s
length :: (SeqLike s, Integral n) => s -> n
ntAt :: (SeqLike s, Integral n) => s -> n -> Maybe Char
subseq :: (SeqLike s, Integral n, Integral m) => n -> m -> s -> Maybe s
subseqPad :: (SeqLike s, Integral n, Integral m) => n -> m -> s -> s
concat :: SeqLike s => [s] -> s
instance SeqLike ByteString
instance SeqLike ByteString
instance SeqLike [Char]

module Bio.SeqLoc.LocRepr
class LocRepr l
repr :: LocRepr l => l -> ByteString
unrepr :: LocRepr l => Parser l
reprStr :: LocRepr l => l -> String
unreprMaybe :: LocRepr l => ByteString -> Maybe l
unreprEither :: LocRepr l => ByteString -> Either String l
unreprErr :: LocRepr l => ByteString -> l


-- | Utilities for manipulating nucleotide sequences and locations on
--   nucleotide sequences that occur on a forward or a reverse-complement
--   strand.
module Bio.SeqLoc.Strand

-- | Sequence strand
data Strand
Fwd :: Strand
RevCompl :: Strand

-- | Complement of a nucleotide character, swap A<i>T and G</i>C preserving
--   case and leave all other characters unchanged.
compl :: Char -> Char

-- | A nucleotide sequence or location on a nucleotide sequence that lies
--   on a specific strand and has an orientation.
class Stranded s
revCompl :: Stranded s => s -> s

-- | Convert the orientation of a <a>Stranded</a> thing based on a
--   specified <a>Strand</a>
stranded :: Stranded s => Strand -> s -> s
instance Eq Strand
instance Ord Strand
instance Show Strand
instance Read Strand
instance Bounded Strand
instance Enum Strand
instance Stranded ByteString
instance Stranded ByteString
instance Stranded String
instance Stranded Word8
instance Stranded Char
instance Stranded Strand
instance LocRepr Strand


-- | Data type for a sequence position.
--   
--   Zero-based <a>Offset</a>indices are used throughout, to facilitate
--   direct use of indexing functions on <tt>SeqData</tt>.
module Bio.SeqLoc.Position

-- | Unstranded offset in a sequence
newtype Offset
Offset :: Int64 -> Offset
unOffset :: Offset -> Int64

-- | Stranded position in a sequence
data Pos
Pos :: !Offset -> !Strand -> Pos

-- | 0-based index of the position
offset :: Pos -> !Offset

-- | Strand of the position
strand :: Pos -> !Strand

-- | Returns a position resulting from sliding the original position along
--   the sequence by a specified offset. A positive offset will move the
--   position away from the 5' end of the forward stand of the sequence
--   regardless of the strand of the position itself. Thus,
--   
--   <pre>
--   slide (revCompl pos) off == revCompl (slide pos off)
--   </pre>
slide :: Pos -> Offset -> Pos

-- | Extract <a>Just</a> the item at a specific sequence position, or
--   <a>Nothing</a> if the position lies outside the bounds of the
--   sequence.
atPos :: SeqLike s => s -> Pos -> Maybe Char
instance Eq Offset
instance Ord Offset
instance Show Offset
instance Read Offset
instance Num Offset
instance Real Offset
instance Enum Offset
instance Integral Offset
instance Eq Pos
instance Ord Pos
instance Show Pos
instance Read Pos
instance LocRepr Pos
instance Stranded Pos
instance LocRepr Offset


-- | Data type for a sequence location consiting of a contiguous range of
--   positions on the sequence.
--   
--   Throughout, <i>sequence position</i> refers to a <a>Pos</a> which
--   includes a strand, as opposed to an <i>offset</i>, which refers to a
--   <a>Offset</a> with no strand.
module Bio.SeqLoc.Location
class Location l
strand :: Location l => l -> Strand
length :: Location l => l -> Offset
bounds :: Location l => l -> (Offset, Offset)
startPos :: Location l => l -> Pos
endPos :: Location l => l -> Pos
seqData :: (Location l, SeqLike s, Stranded s) => s -> l -> Maybe s
seqDataPad :: (Location l, SeqLike s, Stranded s) => s -> l -> s
posInto :: Location l => Pos -> l -> Maybe Pos
posOutof :: Location l => Pos -> l -> Maybe Pos
clocInto :: Location l => ContigLoc -> l -> Maybe ContigLoc
clocOutof :: Location l => ContigLoc -> l -> Maybe l
extend :: Location l => (Offset, Offset) -> l -> l
offsetWithin :: Location l => Offset -> l -> Bool
posWithin :: Location l => Pos -> l -> Bool
contigOverlaps :: Location l => ContigLoc -> l -> Bool
toContigs :: Location l => l -> [ContigLoc]
overlaps :: (Location l1, Location l2) => l1 -> l2 -> Bool

-- | Contiguous sequence location defined by a span of sequence positions,
--   lying on a specific strand of the sequence.
data ContigLoc

-- | The offset of the 5' end of the location, as a 0-based index
offset5 :: ContigLoc -> Offset

-- | Create a sequence location lying between 0-based starting and ending
--   offsets. When <tt>start &lt; end</tt>, the location be on the forward
--   strand, otherwise it will be on the reverse complement strand.
fromStartEnd :: Offset -> Offset -> ContigLoc

-- | Create a sequence location from the sequence position of the start of
--   the location and the length of the position. The strand of the
--   location, and the direction it extends from the starting position, are
--   determined by the strand of the starting position.
fromPosLen :: Pos -> Offset -> ContigLoc

-- | Create a sequence location between 0-based starting and ending bounds
--   with a specified strand.
fromBoundsStrand :: Offset -> Offset -> Strand -> ContigLoc

-- | Returns a location resulting from sliding the original location along
--   the sequence by a specified offset. A positive offset will move the
--   location away from the 5' end of the forward stand of the sequence
--   regardless of the strand of the location itself. Thus,
--   
--   <pre>
--   slide (revCompl cloc) off == revCompl (slide cloc off)
--   </pre>
slide :: Offset -> ContigLoc -> ContigLoc
instance Eq ContigLoc
instance Ord ContigLoc
instance Show ContigLoc
instance Location ContigLoc
instance LocRepr ContigLoc
instance Stranded ContigLoc


-- | Data type for a more general sequence location consiting of disjoint
--   ranges of positions on a sequence.
--   
--   Throughout, <i>sequence position</i> refers to a <a>Pos</a> which
--   includes a strand, as opposed to an <i>offset</i>, which refers to a
--   <a>Offset</a> with no strand.
module Bio.SeqLoc.SpliceLocation

-- | General (disjoint) sequence region consisting of a concatenated set of
--   one or more contiguous regions.
data SpliceLoc
fromContigs :: [ContigLoc] -> Maybe SpliceLoc
locOutof :: Location l => SpliceLoc -> l -> Maybe SpliceLoc
locInto :: Location l => SpliceLoc -> l -> Maybe SpliceLoc
mergeContigs :: [ContigLoc] -> [ContigLoc]
mergeAdjContigs :: ContigLoc -> ContigLoc -> Maybe ContigLoc
instance Eq SpliceLoc
instance Ord SpliceLoc
instance Show SpliceLoc
instance Location SpliceLoc
instance LocRepr SpliceLoc
instance Stranded SpliceLoc


-- | Data types for sequence locations and sequence positions associated
--   with specific, named sequences.
module Bio.SeqLoc.OnSeq
newtype SeqName
SeqName :: ByteString -> SeqName
unSeqName :: SeqName -> ByteString
data OnSeq s
OnSeq :: !SeqName -> !s -> OnSeq s
onSeqName :: OnSeq s -> !SeqName
unOnSeq :: OnSeq s -> !s
type SeqOffset = OnSeq Offset

-- | A position on a named sequence
type SeqPos = OnSeq Pos

-- | A location consisting of a contiguous span of positions on a named
--   sequence.
type ContigSeqLoc = OnSeq ContigLoc

-- | A general location, consisting of spans of sequence positions on a
--   specific, named sequence.
type SpliceSeqLoc = OnSeq SpliceLoc
andSameSeq :: (a -> b -> Bool) -> OnSeq a -> OnSeq b -> Bool
instance Show SeqName
instance Read SeqName
instance Eq SeqName
instance Ord SeqName
instance IsString SeqName
instance Show s => Show (OnSeq s)
instance Read s => Read (OnSeq s)
instance Eq s => Eq (OnSeq s)
instance Ord s => Ord (OnSeq s)
instance LocRepr s => LocRepr (OnSeq s)
instance Stranded s => Stranded (OnSeq s)

module Bio.SeqLoc.Transcript

-- | Splice junctions, which are isomorphic to the introns they span, but
--   which support other biologically relevant constructors and accessors.
newtype Junction
Junction :: ContigLoc -> Junction
intron :: Junction -> ContigLoc

-- | Create a splice junction from a donor position (the last position in
--   the 5' exon) and the acceptor position (the first position in the 3'
--   exon).
fromDonorAcceptor :: Pos -> Pos -> Junction

-- | Donor position, i.e., the last position in the 5' exon around a
--   junction.
donor :: Junction -> Pos

-- | Acceptor position, i.e., the first position in the 3' exon around a
--   junction.
acceptor :: Junction -> Pos

-- | List of splice junctions from a spliced location, in order.
junctions :: SpliceLoc -> [Junction]

-- | Representation of a genomic transcript, with a gene and a transcript
--   identifier, along with the genomic location of the processed
--   transcript and an optional coding sequence on that transcript.
data Transcript
Transcript :: !SeqName -> !SeqName -> !SpliceSeqLoc -> !Maybe ContigLoc -> Transcript

-- | Gene or locus name for a collection of transcripts
geneId :: Transcript -> !SeqName

-- | Specific transcript identifier
trxId :: Transcript -> !SeqName

-- | Sequence location of processed transcript
location :: Transcript -> !SpliceSeqLoc

-- | Location of CDS on the transcript
cds :: Transcript -> !Maybe ContigLoc

-- | <a>Just</a> the location of the 5' UTR on the transcript, or
--   <a>Nothing</a> if there is no <a>cds</a> on the transcript or if the
--   <a>cds</a> location begins at the first nucleotide of the
--   transcript--if a region is returned it will have positive length.
utr5 :: Transcript -> Maybe ContigLoc

-- | <a>Just</a> the location of the 3' UTR on the transcript, or
--   <a>Nothing</a> if there is no <a>cds</a> on the transcript or if the
--   <a>cds</a> location ends at the last nucleotide of the transcript--if
--   a region is returned it will have positive length.
utr3 :: Transcript -> Maybe ContigLoc

-- | Genomic location of CDS within the transcript
cdsLocation :: Transcript -> Maybe SpliceSeqLoc

-- | <a>Just</a> the input contigs sorted in stranded order, when all lie
--   on the same strand, or <a>Nothing</a> if they are not all on the same
--   strand.
sortContigs :: [ContigLoc] -> Maybe [ContigLoc]
instance Show Junction
instance Show Transcript
instance LocRepr Junction