Biobase.SubstMatrix

Documentation

data Similarity

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

data Distance

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

newtype AASubstMat t

Constructors

AASubstMat

Fields

• aaSubstMat :: Unboxed ((Z :. Letter AA) :. Letter AA) DLO

Instances

Eq (AASubstMat t)

Methods

(==) :: AASubstMat t -> AASubstMat t -> Bool

(/=) :: AASubstMat t -> AASubstMat t -> Bool

Read (AASubstMat t)

Methods

readsPrec :: Int -> ReadS (AASubstMat t)

readList :: ReadS [AASubstMat t]

readPrec :: ReadPrec (AASubstMat t)

readListPrec :: ReadPrec [AASubstMat t]

Show (AASubstMat t)

Methods

showsPrec :: Int -> AASubstMat t -> ShowS

show :: AASubstMat t -> String

showList :: [AASubstMat t] -> ShowS

Generic (AASubstMat t)

Associated Types

type Rep (AASubstMat t) :: * -> *

Methods

from :: AASubstMat t -> Rep (AASubstMat t) x

to :: Rep (AASubstMat t) x -> AASubstMat t

Binary (AASubstMat t)

Methods

put :: AASubstMat t -> Put

get :: Get (AASubstMat t)

putList :: [AASubstMat t] -> Put

Serialize (AASubstMat t)

Methods

put :: Putter (AASubstMat t)

get :: Get (AASubstMat t)

NFData (AASubstMat t)

Methods

rnf :: AASubstMat t -> ()

type Rep (AASubstMat t)

type Rep (AASubstMat t) = D1 (MetaData "AASubstMat" "Biobase.SubstMatrix" "BiobaseBlast-0.2.0.0-KX6AeL2c00KF2yhkw3Mw4U" True) (C1 (MetaCons "AASubstMat" PrefixI True) (S1 (MetaSel (Just Symbol "aaSubstMat") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 (Unboxed ((:.) ((:.) Z (Letter AA)) (Letter AA)) DLO))))

type SubstPAM = AASubstMat Similarity

PAM matrices are similarity matrices.

type SubstBLOSUM = AASubstMat Distance

BLOSUM matrices are distance matrices.

newtype ANuc3SubstMat t

Substitution matrix from amino acids to nucleotide triplets.

Constructors

ANuc3SubstMat

Fields

• anuc3SubstMat :: Unboxed ((((Z :. Letter AA) :. Letter DNA) :. Letter DNA) :. Letter DNA) DLO

Instances

Eq (ANuc3SubstMat t)

Methods

(==) :: ANuc3SubstMat t -> ANuc3SubstMat t -> Bool

(/=) :: ANuc3SubstMat t -> ANuc3SubstMat t -> Bool

Read (ANuc3SubstMat t)

Methods

readsPrec :: Int -> ReadS (ANuc3SubstMat t)

readList :: ReadS [ANuc3SubstMat t]

readPrec :: ReadPrec (ANuc3SubstMat t)

readListPrec :: ReadPrec [ANuc3SubstMat t]

Show (ANuc3SubstMat t)

Methods

showsPrec :: Int -> ANuc3SubstMat t -> ShowS

show :: ANuc3SubstMat t -> String

showList :: [ANuc3SubstMat t] -> ShowS

Generic (ANuc3SubstMat t)

Associated Types

type Rep (ANuc3SubstMat t) :: * -> *

Methods

from :: ANuc3SubstMat t -> Rep (ANuc3SubstMat t) x

to :: Rep (ANuc3SubstMat t) x -> ANuc3SubstMat t

Binary (ANuc3SubstMat t)

Methods

put :: ANuc3SubstMat t -> Put

get :: Get (ANuc3SubstMat t)

putList :: [ANuc3SubstMat t] -> Put

Serialize (ANuc3SubstMat t)

Methods

put :: Putter (ANuc3SubstMat t)

get :: Get (ANuc3SubstMat t)

NFData (ANuc3SubstMat t)

Methods

rnf :: ANuc3SubstMat t -> ()

type Rep (ANuc3SubstMat t)

type Rep (ANuc3SubstMat t) = D1 (MetaData "ANuc3SubstMat" "Biobase.SubstMatrix" "BiobaseBlast-0.2.0.0-KX6AeL2c00KF2yhkw3Mw4U" True) (C1 (MetaCons "ANuc3SubstMat" PrefixI True) (S1 (MetaSel (Just Symbol "anuc3SubstMat") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 (Unboxed ((:.) ((:.) ((:.) ((:.) Z (Letter AA)) (Letter DNA)) (Letter DNA)) (Letter DNA)) DLO))))

newtype ANuc2SubstMat t

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

Constructors

ANuc2SubstMat

Fields

• anuc2SubstMat :: Unboxed (((Z :. Letter AA) :. Letter DNA) :. Letter DNA) DLO

Instances

Eq (ANuc2SubstMat t)

Methods

(==) :: ANuc2SubstMat t -> ANuc2SubstMat t -> Bool

(/=) :: ANuc2SubstMat t -> ANuc2SubstMat t -> Bool

Read (ANuc2SubstMat t)

Methods

readsPrec :: Int -> ReadS (ANuc2SubstMat t)

readList :: ReadS [ANuc2SubstMat t]

readPrec :: ReadPrec (ANuc2SubstMat t)

readListPrec :: ReadPrec [ANuc2SubstMat t]

Show (ANuc2SubstMat t)

Methods

showsPrec :: Int -> ANuc2SubstMat t -> ShowS

show :: ANuc2SubstMat t -> String

showList :: [ANuc2SubstMat t] -> ShowS

Generic (ANuc2SubstMat t)

Associated Types

type Rep (ANuc2SubstMat t) :: * -> *

Methods

from :: ANuc2SubstMat t -> Rep (ANuc2SubstMat t) x

to :: Rep (ANuc2SubstMat t) x -> ANuc2SubstMat t

Binary (ANuc2SubstMat t)

Methods

put :: ANuc2SubstMat t -> Put

get :: Get (ANuc2SubstMat t)

putList :: [ANuc2SubstMat t] -> Put

Serialize (ANuc2SubstMat t)

Methods

put :: Putter (ANuc2SubstMat t)

get :: Get (ANuc2SubstMat t)

NFData (ANuc2SubstMat t)

Methods

rnf :: ANuc2SubstMat t -> ()

type Rep (ANuc2SubstMat t)

type Rep (ANuc2SubstMat t) = D1 (MetaData "ANuc2SubstMat" "Biobase.SubstMatrix" "BiobaseBlast-0.2.0.0-KX6AeL2c00KF2yhkw3Mw4U" True) (C1 (MetaCons "ANuc2SubstMat" PrefixI True) (S1 (MetaSel (Just Symbol "anuc2SubstMat") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 (Unboxed ((:.) ((:.) ((:.) Z (Letter AA)) (Letter DNA)) (Letter DNA)) DLO))))

newtype ANuc1SubstMat t

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) :. Letter DNA) DLO

Instances

Eq (ANuc1SubstMat t)

Methods

(==) :: ANuc1SubstMat t -> ANuc1SubstMat t -> Bool

(/=) :: ANuc1SubstMat t -> ANuc1SubstMat t -> Bool

Read (ANuc1SubstMat t)

Methods

readsPrec :: Int -> ReadS (ANuc1SubstMat t)

readList :: ReadS [ANuc1SubstMat t]

readPrec :: ReadPrec (ANuc1SubstMat t)

readListPrec :: ReadPrec [ANuc1SubstMat t]

Show (ANuc1SubstMat t)

Methods

showsPrec :: Int -> ANuc1SubstMat t -> ShowS

show :: ANuc1SubstMat t -> String

showList :: [ANuc1SubstMat t] -> ShowS

Generic (ANuc1SubstMat t)

Associated Types

type Rep (ANuc1SubstMat t) :: * -> *

Methods

from :: ANuc1SubstMat t -> Rep (ANuc1SubstMat t) x

to :: Rep (ANuc1SubstMat t) x -> ANuc1SubstMat t

Binary (ANuc1SubstMat t)

Methods

put :: ANuc1SubstMat t -> Put

get :: Get (ANuc1SubstMat t)

putList :: [ANuc1SubstMat t] -> Put

Serialize (ANuc1SubstMat t)

Methods

put :: Putter (ANuc1SubstMat t)

get :: Get (ANuc1SubstMat t)

NFData (ANuc1SubstMat t)

Methods

rnf :: ANuc1SubstMat t -> ()

type Rep (ANuc1SubstMat t)

type Rep (ANuc1SubstMat t) = D1 (MetaData "ANuc1SubstMat" "Biobase.SubstMatrix" "BiobaseBlast-0.2.0.0-KX6AeL2c00KF2yhkw3Mw4U" True) (C1 (MetaCons "ANuc1SubstMat" PrefixI True) (S1 (MetaSel (Just Symbol "anuc1SubstMat") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 (Unboxed ((:.) ((:.) Z (Letter AA)) (Letter DNA)) DLO))))

mkANuc3SubstMat :: AASubstMat t -> ANuc3SubstMat t

The usual substitution matrix, but here with a codon and an amino acid to be compared.

mkANuc2SubstMat :: (DLO -> DLO -> DLO) -> AASubstMat t -> ANuc2SubstMat t

Create a 2-tuple to amino acid substitution matrix. Here, f combines all to entries that have the same 2-tuple index.

mkANuc1SubstMat :: (DLO -> DLO -> DLO) -> AASubstMat t -> ANuc1SubstMat t

The most degenerate case, where just a single nucleotide remains in the amino-acid / nucleotide substitution. Again, f combines different entries.