Biobase.Types.Structure

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.

Documentation

newtype RNAss

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

Methods

(==) :: RNAss -> RNAss -> Bool

(/=) :: RNAss -> RNAss -> Bool

Data RNAss

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

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

Methods

readsPrec :: Int -> ReadS RNAss

readList :: ReadS [RNAss]

readPrec :: ReadPrec RNAss

readListPrec :: ReadPrec [RNAss]

Show RNAss

Methods

showsPrec :: Int -> RNAss -> ShowS

show :: RNAss -> String

showList :: [RNAss] -> ShowS

Generic RNAss

Associated Types

type Rep RNAss :: * -> *

Methods

from :: RNAss -> Rep RNAss x

to :: Rep RNAss x -> RNAss

Monoid RNAss

Methods

mempty :: RNAss

mappend :: RNAss -> RNAss -> RNAss

mconcat :: [RNAss] -> RNAss

NFData RNAss

Methods

rnf :: RNAss -> ()

type Rep RNAss

type Rep RNAss = D1 (MetaData "RNAss" "Biobase.Types.Structure" "BiobaseTypes-0.1.3.0-7EMqsaldKh99G4UiC4Kzi1" True) (C1 (MetaCons "RNAss" PrefixI True) (S1 (MetaSel (Just Symbol "_rnass") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 ByteString)))

rnass :: Iso' RNAss ByteString

newtype RNAensembleStructure

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

Methods

(==) :: RNAensembleStructure -> RNAensembleStructure -> Bool

(/=) :: RNAensembleStructure -> RNAensembleStructure -> Bool

Data RNAensembleStructure

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

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

Methods

readsPrec :: Int -> ReadS RNAensembleStructure

readList :: ReadS [RNAensembleStructure]

readPrec :: ReadPrec RNAensembleStructure

readListPrec :: ReadPrec [RNAensembleStructure]

Show RNAensembleStructure

Methods

showsPrec :: Int -> RNAensembleStructure -> ShowS

show :: RNAensembleStructure -> String

showList :: [RNAensembleStructure] -> ShowS

Generic RNAensembleStructure

Associated Types

type Rep RNAensembleStructure :: * -> *

Methods

from :: RNAensembleStructure -> Rep RNAensembleStructure x

to :: Rep RNAensembleStructure x -> RNAensembleStructure

NFData RNAensembleStructure

Methods

rnf :: RNAensembleStructure -> ()

type Rep RNAensembleStructure

type Rep RNAensembleStructure = D1 (MetaData "RNAensembleStructure" "Biobase.Types.Structure" "BiobaseTypes-0.1.3.0-7EMqsaldKh99G4UiC4Kzi1" True) (C1 (MetaCons "RNAes" PrefixI True) (S1 (MetaSel (Just Symbol "_rnaes") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 ByteString)))

rnaes :: Iso' RNAensembleStructure ByteString

data RNAds

Cofolded structure.

Constructors

RNAds

Fields

• _rnadsL :: !ByteString
• _rnadsR :: !ByteString

Instances

Eq RNAds

Methods

(==) :: RNAds -> RNAds -> Bool

(/=) :: RNAds -> RNAds -> Bool

Data RNAds

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

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

Methods

readsPrec :: Int -> ReadS RNAds

readList :: ReadS [RNAds]

readPrec :: ReadPrec RNAds

readListPrec :: ReadPrec [RNAds]

Show RNAds

Methods

showsPrec :: Int -> RNAds -> ShowS

show :: RNAds -> String

showList :: [RNAds] -> ShowS

Generic RNAds

Associated Types

type Rep RNAds :: * -> *

Methods

from :: RNAds -> Rep RNAds x

to :: Rep RNAds x -> RNAds

NFData RNAds

Methods

rnf :: RNAds -> ()

type Rep RNAds

type Rep RNAds = D1 (MetaData "RNAds" "Biobase.Types.Structure" "BiobaseTypes-0.1.3.0-7EMqsaldKh99G4UiC4Kzi1" False) (C1 (MetaCons "RNAds" PrefixI True) ((:*:) (S1 (MetaSel (Just Symbol "_rnadsL") NoSourceUnpackedness SourceStrict DecidedUnpack) (Rec0 ByteString)) (S1 (MetaSel (Just Symbol "_rnadsR") NoSourceUnpackedness SourceStrict DecidedUnpack) (Rec0 ByteString))))

rnadsR :: Lens' RNAds ByteString

rnadsL :: Lens' RNAds ByteString

rnads :: Prism' ByteString RNAds

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

rnads2rnassPair :: Iso' RNAds (RNAss, RNAss)

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

Try to create a dimeric structure.

data RNAStructureError

Capture what might be wrong with the RNAss.

Constructors

RNAStructureError

Fields

• _rnaStructureError :: String
• _rnaOffender :: ByteString

Instances

Show RNAStructureError

Methods

showsPrec :: Int -> RNAStructureError -> ShowS

show :: RNAStructureError -> String

showList :: [RNAStructureError] -> ShowS

Generic RNAStructureError

Associated Types

type Rep RNAStructureError :: * -> *

Methods

from :: RNAStructureError -> Rep RNAStructureError x

to :: Rep RNAStructureError x -> RNAStructureError

NFData RNAStructureError

Methods

rnf :: RNAStructureError -> ()

type Rep RNAStructureError

type Rep RNAStructureError = D1 (MetaData "RNAStructureError" "Biobase.Types.Structure" "BiobaseTypes-0.1.3.0-7EMqsaldKh99G4UiC4Kzi1" False) (C1 (MetaCons "RNAStructureError" PrefixI True) ((:*:) (S1 (MetaSel (Just Symbol "_rnaStructureError") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 String)) (S1 (MetaSel (Just Symbol "_rnaOffender") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 ByteString))))

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

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'.

newtype RNApset

Constructors

RNApset

Fields

• _rnapset :: Set (Int, Int)

Instances

Eq RNApset

Methods

(==) :: RNApset -> RNApset -> Bool

(/=) :: RNApset -> RNApset -> Bool

Ord RNApset

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

Methods

readsPrec :: Int -> ReadS RNApset

readList :: ReadS [RNApset]

readPrec :: ReadPrec RNApset

readListPrec :: ReadPrec [RNApset]

Show RNApset

Methods

showsPrec :: Int -> RNApset -> ShowS

show :: RNApset -> String

showList :: [RNApset] -> ShowS

Generic RNApset

Associated Types

type Rep RNApset :: * -> *

Methods

from :: RNApset -> Rep RNApset x

to :: Rep RNApset x -> RNApset

NFData RNApset

Methods

rnf :: RNApset -> ()

type Rep RNApset

type Rep RNApset = D1 (MetaData "RNApset" "Biobase.Types.Structure" "BiobaseTypes-0.1.3.0-7EMqsaldKh99G4UiC4Kzi1" True) (C1 (MetaCons "RNApset" PrefixI True) (S1 (MetaSel (Just Symbol "_rnapset") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 (Set (Int, Int)))))

rnapset :: Iso' RNApset (Set (Int, Int))

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

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

rnassPairSet' :: RNAss -> RNApset

RNA pair set, but a transformation error calls error.

pairDist :: RNApset -> RNApset -> Int

Calculates the number of different base pairs betwwen two structures.