Safe Haskell	None
Language	Haskell2010

Biobase.SubstMatrix.Types

Synopsis

data Similarity
data Distance
data AASubstMat t s a b = AASubstMat {
- _aaSubstMat :: !(Unboxed ((Z :. Letter AA a) :. Letter AA b) s)
- _aaSubstLambda :: Double
}
aaSubstMat :: forall k (t :: k) s k (a :: k) k (b :: k) k (t :: k) s k (a :: k) k (b :: k). Lens (AASubstMat (t :: k) s (a :: k) (b :: k)) (AASubstMat (t :: k) s (a :: k) (b :: k)) (Unboxed ((:.) ((:.) Z (Letter AA a)) (Letter AA b)) s) (Unboxed ((:.) ((:.) Z (Letter AA a)) (Letter AA b)) s)
aaSubstLambda :: forall k (t :: k) s k (a :: k) k (b :: k) k (t :: k). Lens (AASubstMat (t :: k) s (a :: k) (b :: k)) (AASubstMat (t :: k) s (a :: k) (b :: k)) Double Double
type SubstPAM = AASubstMat Similarity (DiscLogOdds (RTyId 1))
type SubstBLOSUM = AASubstMat Distance (DiscLogOdds (RTyId 1))
newtype ANuc3SubstMat t s a n = ANuc3SubstMat {
- _anuc3SubstMat :: Unboxed ((((Z :. Letter AA a) :. Letter DNA n) :. Letter DNA n) :. Letter DNA n) s
}
anuc3SubstMat :: forall k (t :: k) s k (a :: k) k (n :: k) k (t :: k) s k (a :: k) k (n :: k). Iso (ANuc3SubstMat (t :: k) s (a :: k) (n :: k)) (ANuc3SubstMat (t :: k) s (a :: k) (n :: k)) (Unboxed ((:.) ((:.) ((:.) ((:.) Z (Letter AA a)) (Letter DNA n)) (Letter DNA n)) (Letter DNA n)) s) (Unboxed ((:.) ((:.) ((:.) ((:.) Z (Letter AA a)) (Letter DNA n)) (Letter DNA n)) (Letter DNA n)) s)
newtype ANuc2SubstMat t s a n = ANuc2SubstMat {
- _anuc2SubstMat :: Unboxed (((Z :. Letter AA a) :. Letter DNA n) :. Letter DNA n) s
}
anuc2SubstMat :: forall k (t :: k) s k (a :: k) k (n :: k) k (t :: k) s k (a :: k) k (n :: k). Iso (ANuc2SubstMat (t :: k) s (a :: k) (n :: k)) (ANuc2SubstMat (t :: k) s (a :: k) (n :: k)) (Unboxed ((:.) ((:.) ((:.) Z (Letter AA a)) (Letter DNA n)) (Letter DNA n)) s) (Unboxed ((:.) ((:.) ((:.) Z (Letter AA a)) (Letter DNA n)) (Letter DNA n)) s)
newtype ANuc1SubstMat t s a n = ANuc1SubstMat {
- _anuc1SubstMat :: Unboxed ((Z :. Letter AA a) :. Letter DNA n) s
}
anuc1SubstMat :: forall k (t :: k) s k (a :: k) k (n :: k) k (t :: k) s k (a :: k) k (n :: k). Iso (ANuc1SubstMat (t :: k) s (a :: k) (n :: k)) (ANuc1SubstMat (t :: k) s (a :: k) (n :: k)) (Unboxed ((:.) ((:.) Z (Letter AA a)) (Letter DNA n)) s) (Unboxed ((:.) ((:.) Z (Letter AA a)) (Letter DNA n)) s)
data GapCost t = GapCost {
- gcInit :: !t
- gcCont :: !t
}

Documentation

data Similarity Source #

Denotes that we are dealing with a similarity score. Higher is more similar.

data Distance Source #

Denotes that we are dealing with a distance score. Lower is more similar.

data AASubstMat t s a b Source #

Constructors

AASubstMat
Fields _aaSubstMat :: !(Unboxed ((Z :. Letter AA a) :. Letter AA b) s) _aaSubstLambda :: Double

Instances

Instances details

(Unbox s, Eq s) => Eq (AASubstMat t s a b) Source #
Instance details Defined in Biobase.SubstMatrix.Types Methods (==) :: AASubstMat t s a b -> AASubstMat t s a b -> Bool # (/=) :: AASubstMat t s a b -> AASubstMat t s a b -> Bool #
(Read s, Unbox s) => Read (AASubstMat t s a b) Source #
Instance details Defined in Biobase.SubstMatrix.Types Methods readsPrec :: Int -> ReadS (AASubstMat t s a b) # readList :: ReadS [AASubstMat t s a b] # readPrec :: ReadPrec (AASubstMat t s a b) # readListPrec :: ReadPrec [AASubstMat t s a b] #
(Show s, Unbox s) => Show (AASubstMat t s a b) Source #
Instance details Defined in Biobase.SubstMatrix.Types Methods showsPrec :: Int -> AASubstMat t s a b -> ShowS # show :: AASubstMat t s a b -> String # showList :: [AASubstMat t s a b] -> ShowS #
Generic (AASubstMat t s a b) Source #
Instance details Defined in Biobase.SubstMatrix.Types Associated Types type Rep (AASubstMat t s a b) :: Type -> Type # Methods from :: AASubstMat t s a b -> Rep (AASubstMat t s a b) x # to :: Rep (AASubstMat t s a b) x -> AASubstMat t s a b #
type Rep (AASubstMat t s a b) Source #
Instance details Defined in Biobase.SubstMatrix.Types type Rep (AASubstMat t s a b) = D1 ('MetaData "AASubstMat" "Biobase.SubstMatrix.Types" "BiobaseBlast-0.3.3.0-8blL5vmeO2AKrfnTtE3loe" 'False) (C1 ('MetaCons "AASubstMat" 'PrefixI 'True) (S1 ('MetaSel ('Just "_aaSubstMat") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 (Unboxed ((Z :. Letter AA a) :. Letter AA b) s)) :*: S1 ('MetaSel ('Just "_aaSubstLambda") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Double)))

aaSubstMat :: forall k (t :: k) s k (a :: k) k (b :: k) k (t :: k) s k (a :: k) k (b :: k). Lens (AASubstMat (t :: k) s (a :: k) (b :: k)) (AASubstMat (t :: k) s (a :: k) (b :: k)) (Unboxed ((:.) ((:.) Z (Letter AA a)) (Letter AA b)) s) (Unboxed ((:.) ((:.) Z (Letter AA a)) (Letter AA b)) s) Source #

aaSubstLambda :: forall k (t :: k) s k (a :: k) k (b :: k) k (t :: k). Lens (AASubstMat (t :: k) s (a :: k) (b :: k)) (AASubstMat (t :: k) s (a :: k) (b :: k)) Double Double Source #

type SubstPAM = AASubstMat Similarity (DiscLogOdds (RTyId 1)) Source #

PAM matrices are similarity matrices.

type SubstBLOSUM = AASubstMat Distance (DiscLogOdds (RTyId 1)) Source #

BLOSUM matrices are distance matrices.

newtype ANuc3SubstMat t s a n Source #

Substitution matrix from amino acids to nucleotide triplets.

Constructors

ANuc3SubstMat
Fields _anuc3SubstMat :: Unboxed ((((Z :. Letter AA a) :. Letter DNA n) :. Letter DNA n) :. Letter DNA n) s

Instances

Instances details

(Unbox s, Eq s) => Eq (ANuc3SubstMat t s a n) Source #
Instance details Defined in Biobase.SubstMatrix.Types Methods (==) :: ANuc3SubstMat t s a n -> ANuc3SubstMat t s a n -> Bool # (/=) :: ANuc3SubstMat t s a n -> ANuc3SubstMat t s a n -> Bool #
(Read s, Unbox s) => Read (ANuc3SubstMat t s a n) Source #
Instance details Defined in Biobase.SubstMatrix.Types Methods readsPrec :: Int -> ReadS (ANuc3SubstMat t s a n) # readList :: ReadS [ANuc3SubstMat t s a n] # readPrec :: ReadPrec (ANuc3SubstMat t s a n) # readListPrec :: ReadPrec [ANuc3SubstMat t s a n] #
(Show s, Unbox s) => Show (ANuc3SubstMat t s a n) Source #
Instance details Defined in Biobase.SubstMatrix.Types Methods showsPrec :: Int -> ANuc3SubstMat t s a n -> ShowS # show :: ANuc3SubstMat t s a n -> String # showList :: [ANuc3SubstMat t s a n] -> ShowS #
Generic (ANuc3SubstMat t s a n) Source #
Instance details Defined in Biobase.SubstMatrix.Types Associated Types type Rep (ANuc3SubstMat t s a n) :: Type -> Type # Methods from :: ANuc3SubstMat t s a n -> Rep (ANuc3SubstMat t s a n) x # to :: Rep (ANuc3SubstMat t s a n) x -> ANuc3SubstMat t s a n #
type Rep (ANuc3SubstMat t s a n) Source #
Instance details Defined in Biobase.SubstMatrix.Types type Rep (ANuc3SubstMat t s a n) = D1 ('MetaData "ANuc3SubstMat" "Biobase.SubstMatrix.Types" "BiobaseBlast-0.3.3.0-8blL5vmeO2AKrfnTtE3loe" 'True) (C1 ('MetaCons "ANuc3SubstMat" 'PrefixI 'True) (S1 ('MetaSel ('Just "_anuc3SubstMat") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Unboxed ((((Z :. Letter AA a) :. Letter DNA n) :. Letter DNA n) :. Letter DNA n) s))))

anuc3SubstMat :: forall k (t :: k) s k (a :: k) k (n :: k) k (t :: k) s k (a :: k) k (n :: k). Iso (ANuc3SubstMat (t :: k) s (a :: k) (n :: k)) (ANuc3SubstMat (t :: k) s (a :: k) (n :: k)) (Unboxed ((:.) ((:.) ((:.) ((:.) Z (Letter AA a)) (Letter DNA n)) (Letter DNA n)) (Letter DNA n)) s) (Unboxed ((:.) ((:.) ((:.) ((:.) Z (Letter AA a)) (Letter DNA n)) (Letter DNA n)) (Letter DNA n)) s) Source #

newtype ANuc2SubstMat t s a n Source #

Substitution matrix from amino acids to degenerate nucleotide 2-tuples. The third nucleotide letter is missing.

Constructors

ANuc2SubstMat
Fields _anuc2SubstMat :: Unboxed (((Z :. Letter AA a) :. Letter DNA n) :. Letter DNA n) s

Instances

Instances details

(Unbox s, Eq s) => Eq (ANuc2SubstMat t s a n) Source #
Instance details Defined in Biobase.SubstMatrix.Types Methods (==) :: ANuc2SubstMat t s a n -> ANuc2SubstMat t s a n -> Bool # (/=) :: ANuc2SubstMat t s a n -> ANuc2SubstMat t s a n -> Bool #
(Read s, Unbox s) => Read (ANuc2SubstMat t s a n) Source #
Instance details Defined in Biobase.SubstMatrix.Types Methods readsPrec :: Int -> ReadS (ANuc2SubstMat t s a n) # readList :: ReadS [ANuc2SubstMat t s a n] # readPrec :: ReadPrec (ANuc2SubstMat t s a n) # readListPrec :: ReadPrec [ANuc2SubstMat t s a n] #
(Show s, Unbox s) => Show (ANuc2SubstMat t s a n) Source #
Instance details Defined in Biobase.SubstMatrix.Types Methods showsPrec :: Int -> ANuc2SubstMat t s a n -> ShowS # show :: ANuc2SubstMat t s a n -> String # showList :: [ANuc2SubstMat t s a n] -> ShowS #
Generic (ANuc2SubstMat t s a n) Source #
Instance details Defined in Biobase.SubstMatrix.Types Associated Types type Rep (ANuc2SubstMat t s a n) :: Type -> Type # Methods from :: ANuc2SubstMat t s a n -> Rep (ANuc2SubstMat t s a n) x # to :: Rep (ANuc2SubstMat t s a n) x -> ANuc2SubstMat t s a n #
type Rep (ANuc2SubstMat t s a n) Source #
Instance details Defined in Biobase.SubstMatrix.Types type Rep (ANuc2SubstMat t s a n) = D1 ('MetaData "ANuc2SubstMat" "Biobase.SubstMatrix.Types" "BiobaseBlast-0.3.3.0-8blL5vmeO2AKrfnTtE3loe" 'True) (C1 ('MetaCons "ANuc2SubstMat" 'PrefixI 'True) (S1 ('MetaSel ('Just "_anuc2SubstMat") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Unboxed (((Z :. Letter AA a) :. Letter DNA n) :. Letter DNA n) s))))

anuc2SubstMat :: forall k (t :: k) s k (a :: k) k (n :: k) k (t :: k) s k (a :: k) k (n :: k). Iso (ANuc2SubstMat (t :: k) s (a :: k) (n :: k)) (ANuc2SubstMat (t :: k) s (a :: k) (n :: k)) (Unboxed ((:.) ((:.) ((:.) Z (Letter AA a)) (Letter DNA n)) (Letter DNA n)) s) (Unboxed ((:.) ((:.) ((:.) Z (Letter AA a)) (Letter DNA n)) (Letter DNA n)) s) Source #

newtype ANuc1SubstMat t s a n Source #

Substitution matrix from amino acids to degenerate nucleotide 1-tuples. Two out of three nucleotides in a triplet are missing.

Constructors

ANuc1SubstMat
Fields _anuc1SubstMat :: Unboxed ((Z :. Letter AA a) :. Letter DNA n) s

Instances

Instances details

(Unbox s, Eq s) => Eq (ANuc1SubstMat t s a n) Source #
Instance details Defined in Biobase.SubstMatrix.Types Methods (==) :: ANuc1SubstMat t s a n -> ANuc1SubstMat t s a n -> Bool # (/=) :: ANuc1SubstMat t s a n -> ANuc1SubstMat t s a n -> Bool #
(Read s, Unbox s) => Read (ANuc1SubstMat t s a n) Source #
Instance details Defined in Biobase.SubstMatrix.Types Methods readsPrec :: Int -> ReadS (ANuc1SubstMat t s a n) # readList :: ReadS [ANuc1SubstMat t s a n] # readPrec :: ReadPrec (ANuc1SubstMat t s a n) # readListPrec :: ReadPrec [ANuc1SubstMat t s a n] #
(Show s, Unbox s) => Show (ANuc1SubstMat t s a n) Source #
Instance details Defined in Biobase.SubstMatrix.Types Methods showsPrec :: Int -> ANuc1SubstMat t s a n -> ShowS # show :: ANuc1SubstMat t s a n -> String # showList :: [ANuc1SubstMat t s a n] -> ShowS #
Generic (ANuc1SubstMat t s a n) Source #
Instance details Defined in Biobase.SubstMatrix.Types Associated Types type Rep (ANuc1SubstMat t s a n) :: Type -> Type # Methods from :: ANuc1SubstMat t s a n -> Rep (ANuc1SubstMat t s a n) x # to :: Rep (ANuc1SubstMat t s a n) x -> ANuc1SubstMat t s a n #
type Rep (ANuc1SubstMat t s a n) Source #
Instance details Defined in Biobase.SubstMatrix.Types type Rep (ANuc1SubstMat t s a n) = D1 ('MetaData "ANuc1SubstMat" "Biobase.SubstMatrix.Types" "BiobaseBlast-0.3.3.0-8blL5vmeO2AKrfnTtE3loe" 'True) (C1 ('MetaCons "ANuc1SubstMat" 'PrefixI 'True) (S1 ('MetaSel ('Just "_anuc1SubstMat") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Unboxed ((Z :. Letter AA a) :. Letter DNA n) s))))

anuc1SubstMat :: forall k (t :: k) s k (a :: k) k (n :: k) k (t :: k) s k (a :: k) k (n :: k). Iso (ANuc1SubstMat (t :: k) s (a :: k) (n :: k)) (ANuc1SubstMat (t :: k) s (a :: k) (n :: k)) (Unboxed ((:.) ((:.) Z (Letter AA a)) (Letter DNA n)) s) (Unboxed ((:.) ((:.) Z (Letter AA a)) (Letter DNA n)) s) Source #

data GapCost t Source #

Constructors

GapCost
Fields gcInit :: !t gcCont :: !t