Safe Haskell	None
Language	Haskell2010

Biobase.Types.Structure

Contents

Arbitrary instances. This only creates legal instances, but does *not*

Description

Wrappers for structural data. Encoded as bytestrings. This differs from BiobaseXNA, where specialized encodings are used. These structures are supposedly "short", they need to fit into a strict bytestring.

TODO Consider where to move each type. There are merge possibilities between BiobaseXNA and BiobaseTypes.

TODO QuickCheck Arbitrary for RNAss.

Synopsis

newtype RNAss = RNAss {
- _rnass :: ByteString
}
rnass :: Iso' RNAss ByteString
newtype RNAensembleStructure = RNAes {
- _rnaes :: ByteString
}
rnaes :: Iso' RNAensembleStructure ByteString
data RNAds = RNAds {
- _rnadsL :: !ByteString
- _rnadsR :: !ByteString
}
rnadsR :: Lens' RNAds ByteString
rnadsL :: Lens' RNAds ByteString
rnads :: Prism' ByteString RNAds
rnads2rnassPair :: Iso' RNAds (RNAss, RNAss)
mkRNAds :: (Monad m, MonadError RNAStructureError m) => ByteString -> m RNAds
data RNAStructureError = RNAStructureError {
- _rnaStructureError :: String
- _rnaOffender :: ByteString
}
verifyRNAss :: (Monad m, MonadError RNAStructureError m) => RNAss -> m RNAss
data RNApset = RNApset {
- _rnapset :: !(Set (Int, Int))
- _rnapsetSLen :: !Int
}
rnapsetSLen :: Lens' RNApset Int
rnapset :: Lens' RNApset (Set (Int, Int))
rnassPairSet :: MonadError String m => RNAss -> m RNApset
rnassSPForest :: MonadError String m => RNAss -> m (SPForest ByteString Char)
compactifySPForest :: SPForest ByteString Char -> SPForest ByteString ByteString
rnassPairSet' :: RNAss -> RNApset
rnapsetRNAss :: RNApset -> RNAss
pairDist :: RNApset -> RNApset -> Int

Documentation

newtype RNAss Source #

Secondary structure using () for paired elements, and . for unpaired ones. It is assumed that the () match up. These structures from a Monoid.

Constructors

RNAss
Fields _rnass :: ByteString

Instances

Eq RNAss Source #
Instance details Defined in Biobase.Types.Structure Methods (==) :: RNAss -> RNAss -> Bool # (/=) :: RNAss -> RNAss -> Bool #
Data RNAss Source #
Instance details Defined in Biobase.Types.Structure Methods gfoldl :: (forall d b. Data d => c (d -> b) -> d -> c b) -> (forall g. g -> c g) -> RNAss -> c RNAss # gunfold :: (forall b r. Data b => c (b -> r) -> c r) -> (forall r. r -> c r) -> Constr -> c RNAss # toConstr :: RNAss -> Constr # dataTypeOf :: RNAss -> DataType # dataCast1 :: Typeable t => (forall d. Data d => c (t d)) -> Maybe (c RNAss) # dataCast2 :: Typeable t => (forall d e. (Data d, Data e) => c (t d e)) -> Maybe (c RNAss) # gmapT :: (forall b. Data b => b -> b) -> RNAss -> RNAss # gmapQl :: (r -> r' -> r) -> r -> (forall d. Data d => d -> r') -> RNAss -> r # gmapQr :: (r' -> r -> r) -> r -> (forall d. Data d => d -> r') -> RNAss -> r # gmapQ :: (forall d. Data d => d -> u) -> RNAss -> [u] # gmapQi :: Int -> (forall d. Data d => d -> u) -> RNAss -> u # gmapM :: Monad m => (forall d. Data d => d -> m d) -> RNAss -> m RNAss # gmapMp :: MonadPlus m => (forall d. Data d => d -> m d) -> RNAss -> m RNAss # gmapMo :: MonadPlus m => (forall d. Data d => d -> m d) -> RNAss -> m RNAss #
Ord RNAss Source #
Instance details Defined in Biobase.Types.Structure Methods compare :: RNAss -> RNAss -> Ordering # (<) :: RNAss -> RNAss -> Bool # (<=) :: RNAss -> RNAss -> Bool # (>) :: RNAss -> RNAss -> Bool # (>=) :: RNAss -> RNAss -> Bool # max :: RNAss -> RNAss -> RNAss # min :: RNAss -> RNAss -> RNAss #
Read RNAss Source #
Instance details Defined in Biobase.Types.Structure Methods readsPrec :: Int -> ReadS RNAss # readList :: ReadS [RNAss] # readPrec :: ReadPrec RNAss # readListPrec :: ReadPrec [RNAss] #
Show RNAss Source #
Instance details Defined in Biobase.Types.Structure Methods showsPrec :: Int -> RNAss -> ShowS # show :: RNAss -> String # showList :: [RNAss] -> ShowS #
Generic RNAss Source #
Instance details Defined in Biobase.Types.Structure Associated Types type Rep RNAss :: Type -> Type # Methods from :: RNAss -> Rep RNAss x # to :: Rep RNAss x -> RNAss #
Semigroup RNAss Source #
Instance details Defined in Biobase.Types.Structure Methods (<>) :: RNAss -> RNAss -> RNAss # sconcat :: NonEmpty RNAss -> RNAss # stimes :: Integral b => b -> RNAss -> RNAss #
Monoid RNAss Source #
Instance details Defined in Biobase.Types.Structure Methods mempty :: RNAss # mappend :: RNAss -> RNAss -> RNAss # mconcat :: [RNAss] -> RNAss #
Arbitrary RNAss Source #
Instance details Defined in Biobase.Types.Structure Methods arbitrary :: Gen RNAss # shrink :: RNAss -> [RNAss] #
NFData RNAss Source #
Instance details Defined in Biobase.Types.Structure Methods rnf :: RNAss -> () #
type Rep RNAss Source #
Instance details Defined in Biobase.Types.Structure type Rep RNAss = D1 (MetaData "RNAss" "Biobase.Types.Structure" "BiobaseTypes-0.2.0.1-B9coIbijR6NEFcCxvqIOZp" True) (C1 (MetaCons "RNAss" PrefixI True) (S1 (MetaSel (Just "_rnass") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 ByteString)))

rnass :: Iso' RNAss ByteString Source #

newtype RNAensembleStructure Source #

Ensemble structure encoding. *Very* different type ctor name chosen! The structure of this string makes verification much more complicated.

TODO describe encoding used by RNAfold for the ensemble string.

Constructors

RNAes
Fields _rnaes :: ByteString

Instances

Eq RNAensembleStructure Source #
Instance details Defined in Biobase.Types.Structure Methods (==) :: RNAensembleStructure -> RNAensembleStructure -> Bool # (/=) :: RNAensembleStructure -> RNAensembleStructure -> Bool #
Data RNAensembleStructure Source #
Instance details Defined in Biobase.Types.Structure Methods gfoldl :: (forall d b. Data d => c (d -> b) -> d -> c b) -> (forall g. g -> c g) -> RNAensembleStructure -> c RNAensembleStructure # gunfold :: (forall b r. Data b => c (b -> r) -> c r) -> (forall r. r -> c r) -> Constr -> c RNAensembleStructure # toConstr :: RNAensembleStructure -> Constr # dataTypeOf :: RNAensembleStructure -> DataType # dataCast1 :: Typeable t => (forall d. Data d => c (t d)) -> Maybe (c RNAensembleStructure) # dataCast2 :: Typeable t => (forall d e. (Data d, Data e) => c (t d e)) -> Maybe (c RNAensembleStructure) # gmapT :: (forall b. Data b => b -> b) -> RNAensembleStructure -> RNAensembleStructure # gmapQl :: (r -> r' -> r) -> r -> (forall d. Data d => d -> r') -> RNAensembleStructure -> r # gmapQr :: (r' -> r -> r) -> r -> (forall d. Data d => d -> r') -> RNAensembleStructure -> r # gmapQ :: (forall d. Data d => d -> u) -> RNAensembleStructure -> [u] # gmapQi :: Int -> (forall d. Data d => d -> u) -> RNAensembleStructure -> u # gmapM :: Monad m => (forall d. Data d => d -> m d) -> RNAensembleStructure -> m RNAensembleStructure # gmapMp :: MonadPlus m => (forall d. Data d => d -> m d) -> RNAensembleStructure -> m RNAensembleStructure # gmapMo :: MonadPlus m => (forall d. Data d => d -> m d) -> RNAensembleStructure -> m RNAensembleStructure #
Ord RNAensembleStructure Source #
Instance details Defined in Biobase.Types.Structure Methods compare :: RNAensembleStructure -> RNAensembleStructure -> Ordering # (<) :: RNAensembleStructure -> RNAensembleStructure -> Bool # (<=) :: RNAensembleStructure -> RNAensembleStructure -> Bool # (>) :: RNAensembleStructure -> RNAensembleStructure -> Bool # (>=) :: RNAensembleStructure -> RNAensembleStructure -> Bool # max :: RNAensembleStructure -> RNAensembleStructure -> RNAensembleStructure # min :: RNAensembleStructure -> RNAensembleStructure -> RNAensembleStructure #
Read RNAensembleStructure Source #
Instance details Defined in Biobase.Types.Structure Methods readsPrec :: Int -> ReadS RNAensembleStructure # readList :: ReadS [RNAensembleStructure] # readPrec :: ReadPrec RNAensembleStructure # readListPrec :: ReadPrec [RNAensembleStructure] #
Show RNAensembleStructure Source #
Instance details Defined in Biobase.Types.Structure Methods showsPrec :: Int -> RNAensembleStructure -> ShowS # show :: RNAensembleStructure -> String # showList :: [RNAensembleStructure] -> ShowS #
Generic RNAensembleStructure Source #
Instance details Defined in Biobase.Types.Structure Associated Types type Rep RNAensembleStructure :: Type -> Type # Methods from :: RNAensembleStructure -> Rep RNAensembleStructure x # to :: Rep RNAensembleStructure x -> RNAensembleStructure #
NFData RNAensembleStructure Source #
Instance details Defined in Biobase.Types.Structure Methods rnf :: RNAensembleStructure -> () #
type Rep RNAensembleStructure Source #
Instance details Defined in Biobase.Types.Structure type Rep RNAensembleStructure = D1 (MetaData "RNAensembleStructure" "Biobase.Types.Structure" "BiobaseTypes-0.2.0.1-B9coIbijR6NEFcCxvqIOZp" True) (C1 (MetaCons "RNAes" PrefixI True) (S1 (MetaSel (Just "_rnaes") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 ByteString)))

rnaes :: Iso' RNAensembleStructure ByteString Source #

data RNAds Source #

Cofolded structure.

Constructors

RNAds
Fields _rnadsL :: !ByteString _rnadsR :: !ByteString

Instances

Eq RNAds Source #
Instance details Defined in Biobase.Types.Structure Methods (==) :: RNAds -> RNAds -> Bool # (/=) :: RNAds -> RNAds -> Bool #
Data RNAds Source #
Instance details Defined in Biobase.Types.Structure Methods gfoldl :: (forall d b. Data d => c (d -> b) -> d -> c b) -> (forall g. g -> c g) -> RNAds -> c RNAds # gunfold :: (forall b r. Data b => c (b -> r) -> c r) -> (forall r. r -> c r) -> Constr -> c RNAds # toConstr :: RNAds -> Constr # dataTypeOf :: RNAds -> DataType # dataCast1 :: Typeable t => (forall d. Data d => c (t d)) -> Maybe (c RNAds) # dataCast2 :: Typeable t => (forall d e. (Data d, Data e) => c (t d e)) -> Maybe (c RNAds) # gmapT :: (forall b. Data b => b -> b) -> RNAds -> RNAds # gmapQl :: (r -> r' -> r) -> r -> (forall d. Data d => d -> r') -> RNAds -> r # gmapQr :: (r' -> r -> r) -> r -> (forall d. Data d => d -> r') -> RNAds -> r # gmapQ :: (forall d. Data d => d -> u) -> RNAds -> [u] # gmapQi :: Int -> (forall d. Data d => d -> u) -> RNAds -> u # gmapM :: Monad m => (forall d. Data d => d -> m d) -> RNAds -> m RNAds # gmapMp :: MonadPlus m => (forall d. Data d => d -> m d) -> RNAds -> m RNAds # gmapMo :: MonadPlus m => (forall d. Data d => d -> m d) -> RNAds -> m RNAds #
Ord RNAds Source #
Instance details Defined in Biobase.Types.Structure Methods compare :: RNAds -> RNAds -> Ordering # (<) :: RNAds -> RNAds -> Bool # (<=) :: RNAds -> RNAds -> Bool # (>) :: RNAds -> RNAds -> Bool # (>=) :: RNAds -> RNAds -> Bool # max :: RNAds -> RNAds -> RNAds # min :: RNAds -> RNAds -> RNAds #
Read RNAds Source #
Instance details Defined in Biobase.Types.Structure Methods readsPrec :: Int -> ReadS RNAds # readList :: ReadS [RNAds] # readPrec :: ReadPrec RNAds # readListPrec :: ReadPrec [RNAds] #
Show RNAds Source #
Instance details Defined in Biobase.Types.Structure Methods showsPrec :: Int -> RNAds -> ShowS # show :: RNAds -> String # showList :: [RNAds] -> ShowS #
Generic RNAds Source #
Instance details Defined in Biobase.Types.Structure Associated Types type Rep RNAds :: Type -> Type # Methods from :: RNAds -> Rep RNAds x # to :: Rep RNAds x -> RNAds #
NFData RNAds Source #
Instance details Defined in Biobase.Types.Structure Methods rnf :: RNAds -> () #
type Rep RNAds Source #
Instance details Defined in Biobase.Types.Structure type Rep RNAds = D1 (MetaData "RNAds" "Biobase.Types.Structure" "BiobaseTypes-0.2.0.1-B9coIbijR6NEFcCxvqIOZp" False) (C1 (MetaCons "RNAds" PrefixI True) (S1 (MetaSel (Just "_rnadsL") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 ByteString) :*: S1 (MetaSel (Just "_rnadsR") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 ByteString)))

rnadsR :: Lens' RNAds ByteString Source #

rnadsL :: Lens' RNAds ByteString Source #

rnads :: Prism' ByteString RNAds Source #

A Prism that turns ByteStrings with a single & into RNAds.

rnads2rnassPair :: Iso' RNAds (RNAss, RNAss) Source #

Isomorphism from RNAds to (RNAss,RNAss). The RNAss are only legal if taken both: rnassFromDimer . both.

mkRNAds :: (Monad m, MonadError RNAStructureError m) => ByteString -> m RNAds Source #

Try to create a dimeric structure.

data RNAStructureError Source #

Capture what might be wrong with the RNAss.

Constructors

RNAStructureError
Fields _rnaStructureError :: String _rnaOffender :: ByteString

Instances

Show RNAStructureError Source #
Instance details Defined in Biobase.Types.Structure Methods showsPrec :: Int -> RNAStructureError -> ShowS # show :: RNAStructureError -> String # showList :: [RNAStructureError] -> ShowS #
Generic RNAStructureError Source #
Instance details Defined in Biobase.Types.Structure Associated Types type Rep RNAStructureError :: Type -> Type # Methods from :: RNAStructureError -> Rep RNAStructureError x # to :: Rep RNAStructureError x -> RNAStructureError #
NFData RNAStructureError Source #
Instance details Defined in Biobase.Types.Structure Methods rnf :: RNAStructureError -> () #
type Rep RNAStructureError Source #
Instance details Defined in Biobase.Types.Structure type Rep RNAStructureError = D1 (MetaData "RNAStructureError" "Biobase.Types.Structure" "BiobaseTypes-0.2.0.1-B9coIbijR6NEFcCxvqIOZp" False) (C1 (MetaCons "RNAStructureError" PrefixI True) (S1 (MetaSel (Just "_rnaStructureError") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 String) :*: S1 (MetaSel (Just "_rnaOffender") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 ByteString)))

verifyRNAss :: (Monad m, MonadError RNAStructureError m) => RNAss -> m RNAss Source #

Verifies that the given RNAss is properly formatted. Otherwise, error out.

TODO Implement! Check with BiobaseXNA and the stack effort in there. This might influence if the verification goes into BiobaseXNA and happens via an Iso'.

data RNApset Source #

The set of nucleotide pairs, together with the sequence length.

Constructors

RNApset
Fields _rnapset :: !(Set (Int, Int)) the set of nucleotide pairs. _rnapsetSLen :: !Int length of the underlying nucleotide sequence.

Instances

Eq RNApset Source #
Instance details Defined in Biobase.Types.Structure Methods (==) :: RNApset -> RNApset -> Bool # (/=) :: RNApset -> RNApset -> Bool #
Ord RNApset Source #
Instance details Defined in Biobase.Types.Structure Methods compare :: RNApset -> RNApset -> Ordering # (<) :: RNApset -> RNApset -> Bool # (<=) :: RNApset -> RNApset -> Bool # (>) :: RNApset -> RNApset -> Bool # (>=) :: RNApset -> RNApset -> Bool # max :: RNApset -> RNApset -> RNApset # min :: RNApset -> RNApset -> RNApset #
Read RNApset Source #
Instance details Defined in Biobase.Types.Structure Methods readsPrec :: Int -> ReadS RNApset # readList :: ReadS [RNApset] # readPrec :: ReadPrec RNApset # readListPrec :: ReadPrec [RNApset] #
Show RNApset Source #
Instance details Defined in Biobase.Types.Structure Methods showsPrec :: Int -> RNApset -> ShowS # show :: RNApset -> String # showList :: [RNApset] -> ShowS #
Generic RNApset Source #
Instance details Defined in Biobase.Types.Structure Associated Types type Rep RNApset :: Type -> Type # Methods from :: RNApset -> Rep RNApset x # to :: Rep RNApset x -> RNApset #
Arbitrary RNApset Source #
Instance details Defined in Biobase.Types.Structure Methods arbitrary :: Gen RNApset # shrink :: RNApset -> [RNApset] #
NFData RNApset Source #
Instance details Defined in Biobase.Types.Structure Methods rnf :: RNApset -> () #
type Rep RNApset Source #
Instance details Defined in Biobase.Types.Structure type Rep RNApset = D1 (MetaData "RNApset" "Biobase.Types.Structure" "BiobaseTypes-0.2.0.1-B9coIbijR6NEFcCxvqIOZp" False) (C1 (MetaCons "RNApset" PrefixI True) (S1 (MetaSel (Just "_rnapset") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 (Set (Int, Int))) :*: S1 (MetaSel (Just "_rnapsetSLen") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 Int)))

rnapsetSLen :: Lens' RNApset Int Source #

rnapset :: Lens' RNApset (Set (Int, Int)) Source #

rnassPairSet :: MonadError String m => RNAss -> m RNApset Source #

Transform an RNAss into a set of base pairs (i,j). The pairs are 0-based.

rnassSPForest :: MonadError String m => RNAss -> m (SPForest ByteString Char) Source #

Genereate a simple structured/paired forest from a secondary structure string.

compactifySPForest :: SPForest ByteString Char -> SPForest ByteString ByteString Source #

Compactify such an SPForest. This means that all stems are now represented by a single SPT data constructor.

rnassPairSet' :: RNAss -> RNApset Source #

RNA pair set, but a transformation error calls error.

rnapsetRNAss :: RNApset -> RNAss Source #

pairDist :: RNApset -> RNApset -> Int Source #

Calculates the number of different base pairs between two structures. This ignores the length of the underlying sequences.

Arbitrary instances. This only creates legal instances, but does not

Documentation

Arbitrary instances. This only creates legal instances, but does *not*

Arbitrary instances. This only creates legal instances, but does not