Safe Haskell	None
Language	Haskell2010

Bio.FASTA.Type

Synopsis

type Fasta a = [FastaItem a]
data FastaItem a = FastaItem {
- name :: Text
- sequ :: BareSequence a
}
class ParsableFastaToken a where
- parseToken :: (Char -> Bool) -> Parser a
data Modification
- = Mod_A_Star
- | Mod_C_Star
- | Mod_G_Star
- | Mod_T_Star
- | Mod_rA
- | Mod_rC
- | Mod_rG
- | Mod_rU
- | Mod_Plus_A
- | Mod_Plus_C
- | Mod_Plus_G
- | Mod_Plus_T
- | Mod_rAf
- | Mod_rCf
- | Mod_rGf
- | Mod_rUf
- | Mod_mA
- | Mod_mC
- | Mod_mG
- | Mod_mU
- | Mod_mA_Star
- | Mod_mC_Star
- | Mod_mG_Star
- | Mod_mU_Star
- | Mod_dU
- | Mod_5Bio
- | Mod_iBio
- | Mod_56FAM
- | Mod_36FAM
- | Mod_5HEX
- | Mod_5TMR
- | Mod_3BHQ1
- | Mod_3BHQ2
- | Mod_5NH2
- | Mod_3NH2
- | Mod_5PO4
- | Mod_3PO4
- | Mod_3BioTEG
- | Mod_C12
- | Mod_NHSdT
- | Mod_5Mal
- | Mod_5thio
- | Mod_3thio
- | Mod_3azide
- | Mod_3alkine
- | Mod_5CholTEG
- | Mod_3CholTEG
- | Mod_5C10
- | Mod_5Alk
- | Mod_GC
- | Mod_GT
- | Mod_AT
- | Mod_TG
- | Mod_AC
- | Mod_CC
- | Mod_AA
- | Mod_TC
- | Mod_TT
- | Mod_CG
- | Mod_GG
- | Mod_AG
- | Mod_GA
- | Mod_CA
- | Mod_CT
- | Mod_TA
- | Mod_AAA
- | Mod_AAC
- | Mod_ACT
- | Mod_ATC
- | Mod_ATG
- | Mod_CAG
- | Mod_AGA
- | Mod_CAT
- | Mod_CCG
- | Mod_CGT
- | Mod_CTG
- | Mod_GAA
- | Mod_GAC
- | Mod_GCT
- | Mod_GGT
- | Mod_GTT
- | Mod_TAC
- | Mod_TCT
- | Mod_TGC
- | Mod_TGG
- | Mod_TTC
- | Mod_TTT
- | Unknown String
data ModItem
- = Mod Modification
- | Letter Char
modificationToString :: Modification -> String

Documentation

type Fasta a = [FastaItem a] Source #

Type alias for FASTA file. satisfies the following format : >(s|t)*[^nr]+(s|t)*(n|r)*((w|s)(n|r)*)*

data FastaItem a Source #

One record in FASTA file.

Constructors

FastaItem
Fields name :: Text name of the sequence sequ :: BareSequence a bare sequence

Instances

Instances details

Functor FastaItem Source #
Instance details Defined in Bio.FASTA.Type Methods fmap :: (a -> b) -> FastaItem a -> FastaItem b # (<$) :: a -> FastaItem b -> FastaItem a #
Eq a => Eq (FastaItem a) Source #
Instance details Defined in Bio.FASTA.Type Methods (==) :: FastaItem a -> FastaItem a -> Bool # (/=) :: FastaItem a -> FastaItem a -> Bool #
Show a => Show (FastaItem a) Source #
Instance details Defined in Bio.FASTA.Type Methods showsPrec :: Int -> FastaItem a -> ShowS # show :: FastaItem a -> String # showList :: [FastaItem a] -> ShowS #

class ParsableFastaToken a where Source #

Methods

parseToken :: (Char -> Bool) -> Parser a Source #

Instances

Instances details

ParsableFastaToken Char Source #
Instance details Defined in Bio.FASTA.Parser Methods parseToken :: (Char -> Bool) -> Parser Char Source #
ParsableFastaToken ModItem Source #
Instance details Defined in Bio.FASTA.Parser Methods parseToken :: (Char -> Bool) -> Parser ModItem Source #

data Modification Source #

Constructors

Mod_A_Star
Mod_C_Star
Mod_G_Star
Mod_T_Star
Mod_rA
Mod_rC
Mod_rG
Mod_rU
Mod_Plus_A
Mod_Plus_C
Mod_Plus_G
Mod_Plus_T
Mod_rAf
Mod_rCf
Mod_rGf
Mod_rUf
Mod_mA
Mod_mC
Mod_mG
Mod_mU
Mod_mA_Star
Mod_mC_Star
Mod_mG_Star
Mod_mU_Star
Mod_dU
Mod_5Bio
Mod_iBio
Mod_56FAM
Mod_36FAM
Mod_5HEX
Mod_5TMR
Mod_3BHQ1
Mod_3BHQ2
Mod_5NH2
Mod_3NH2
Mod_5PO4
Mod_3PO4
Mod_3BioTEG
Mod_C12
Mod_NHSdT
Mod_5Mal
Mod_5thio
Mod_3thio
Mod_3azide
Mod_3alkine
Mod_5CholTEG
Mod_3CholTEG
Mod_5C10
Mod_5Alk
Mod_GC
Mod_GT
Mod_AT
Mod_TG
Mod_AC
Mod_CC
Mod_AA
Mod_TC
Mod_TT
Mod_CG
Mod_GG
Mod_AG
Mod_GA
Mod_CA
Mod_CT
Mod_TA
Mod_AAA
Mod_AAC
Mod_ACT
Mod_ATC
Mod_ATG
Mod_CAG
Mod_AGA
Mod_CAT
Mod_CCG
Mod_CGT
Mod_CTG
Mod_GAA
Mod_GAC
Mod_GCT
Mod_GGT
Mod_GTT
Mod_TAC
Mod_TCT
Mod_TGC
Mod_TGG
Mod_TTC
Mod_TTT
Unknown String

Instances

Instances details

Eq Modification Source #
Instance details Defined in Bio.FASTA.Type Methods (==) :: Modification -> Modification -> Bool # (/=) :: Modification -> Modification -> Bool #
Ord Modification Source #
Instance details Defined in Bio.FASTA.Type Methods compare :: Modification -> Modification -> Ordering # (<) :: Modification -> Modification -> Bool # (<=) :: Modification -> Modification -> Bool # (>) :: Modification -> Modification -> Bool # (>=) :: Modification -> Modification -> Bool # max :: Modification -> Modification -> Modification # min :: Modification -> Modification -> Modification #
Show Modification Source #
Instance details Defined in Bio.FASTA.Type Methods showsPrec :: Int -> Modification -> ShowS # show :: Modification -> String # showList :: [Modification] -> ShowS #
Generic Modification Source #
Instance details Defined in Bio.FASTA.Type Associated Types type Rep Modification :: Type -> Type # Methods from :: Modification -> Rep Modification x # to :: Rep Modification x -> Modification #
type Rep Modification Source #
Instance details Defined in Bio.FASTA.Type type Rep Modification = D1 ('MetaData "Modification" "Bio.FASTA.Type" "cobot-io-0.1.4.3-FtR1iZLExqtGkRGhoXEUKM" 'False) ((((((C1 ('MetaCons "Mod_A_Star" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Mod_C_Star" 'PrefixI 'False) (U1 :: Type -> Type)) :+: (C1 ('MetaCons "Mod_G_Star" 'PrefixI 'False) (U1 :: Type -> Type) :+: (C1 ('MetaCons "Mod_T_Star" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Mod_rA" 'PrefixI 'False) (U1 :: Type -> Type)))) :+: ((C1 ('MetaCons "Mod_rC" 'PrefixI 'False) (U1 :: Type -> Type) :+: (C1 ('MetaCons "Mod_rG" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Mod_rU" 'PrefixI 'False) (U1 :: Type -> Type))) :+: (C1 ('MetaCons "Mod_Plus_A" 'PrefixI 'False) (U1 :: Type -> Type) :+: (C1 ('MetaCons "Mod_Plus_C" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Mod_Plus_G" 'PrefixI 'False) (U1 :: Type -> Type))))) :+: (((C1 ('MetaCons "Mod_Plus_T" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Mod_rAf" 'PrefixI 'False) (U1 :: Type -> Type)) :+: (C1 ('MetaCons "Mod_rCf" 'PrefixI 'False) (U1 :: Type -> Type) :+: (C1 ('MetaCons "Mod_rGf" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Mod_rUf" 'PrefixI 'False) (U1 :: Type -> Type)))) :+: ((C1 ('MetaCons "Mod_mA" 'PrefixI 'False) (U1 :: Type -> Type) :+: (C1 ('MetaCons "Mod_mC" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Mod_mG" 'PrefixI 'False) (U1 :: Type -> Type))) :+: (C1 ('MetaCons "Mod_mU" 'PrefixI 'False) (U1 :: Type -> Type) :+: (C1 ('MetaCons "Mod_mA_Star" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Mod_mC_Star" 'PrefixI 'False) (U1 :: Type -> Type)))))) :+: ((((C1 ('MetaCons "Mod_mG_Star" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Mod_mU_Star" 'PrefixI 'False) (U1 :: Type -> Type)) :+: (C1 ('MetaCons "Mod_dU" 'PrefixI 'False) (U1 :: Type -> Type) :+: (C1 ('MetaCons "Mod_5Bio" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Mod_iBio" 'PrefixI 'False) (U1 :: Type -> Type)))) :+: ((C1 ('MetaCons "Mod_56FAM" 'PrefixI 'False) (U1 :: Type -> Type) :+: (C1 ('MetaCons "Mod_36FAM" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Mod_5HEX" 'PrefixI 'False) (U1 :: Type -> Type))) :+: (C1 ('MetaCons "Mod_5TMR" 'PrefixI 'False) (U1 :: Type -> Type) :+: (C1 ('MetaCons "Mod_3BHQ1" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Mod_3BHQ2" 'PrefixI 'False) (U1 :: Type -> Type))))) :+: (((C1 ('MetaCons "Mod_5NH2" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Mod_3NH2" 'PrefixI 'False) (U1 :: Type -> Type)) :+: (C1 ('MetaCons "Mod_5PO4" 'PrefixI 'False) (U1 :: Type -> Type) :+: (C1 ('MetaCons "Mod_3PO4" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Mod_3BioTEG" 'PrefixI 'False) (U1 :: Type -> Type)))) :+: ((C1 ('MetaCons "Mod_C12" 'PrefixI 'False) (U1 :: Type -> Type) :+: (C1 ('MetaCons "Mod_NHSdT" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Mod_5Mal" 'PrefixI 'False) (U1 :: Type -> Type))) :+: (C1 ('MetaCons "Mod_5thio" 'PrefixI 'False) (U1 :: Type -> Type) :+: (C1 ('MetaCons "Mod_3thio" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Mod_3azide" 'PrefixI 'False) (U1 :: Type -> Type))))))) :+: (((((C1 ('MetaCons "Mod_3alkine" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Mod_5CholTEG" 'PrefixI 'False) (U1 :: Type -> Type)) :+: (C1 ('MetaCons "Mod_3CholTEG" 'PrefixI 'False) (U1 :: Type -> Type) :+: (C1 ('MetaCons "Mod_5C10" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Mod_5Alk" 'PrefixI 'False) (U1 :: Type -> Type)))) :+: ((C1 ('MetaCons "Mod_GC" 'PrefixI 'False) (U1 :: Type -> Type) :+: (C1 ('MetaCons "Mod_GT" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Mod_AT" 'PrefixI 'False) (U1 :: Type -> Type))) :+: (C1 ('MetaCons "Mod_TG" 'PrefixI 'False) (U1 :: Type -> Type) :+: (C1 ('MetaCons "Mod_AC" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Mod_CC" 'PrefixI 'False) (U1 :: Type -> Type))))) :+: (((C1 ('MetaCons "Mod_AA" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Mod_TC" 'PrefixI 'False) (U1 :: Type -> Type)) :+: (C1 ('MetaCons "Mod_TT" 'PrefixI 'False) (U1 :: Type -> Type) :+: (C1 ('MetaCons "Mod_CG" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Mod_GG" 'PrefixI 'False) (U1 :: Type -> Type)))) :+: ((C1 ('MetaCons "Mod_AG" 'PrefixI 'False) (U1 :: Type -> Type) :+: (C1 ('MetaCons "Mod_GA" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Mod_CA" 'PrefixI 'False) (U1 :: Type -> Type))) :+: (C1 ('MetaCons "Mod_CT" 'PrefixI 'False) (U1 :: Type -> Type) :+: (C1 ('MetaCons "Mod_TA" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Mod_AAA" 'PrefixI 'False) (U1 :: Type -> Type)))))) :+: ((((C1 ('MetaCons "Mod_AAC" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Mod_ACT" 'PrefixI 'False) (U1 :: Type -> Type)) :+: (C1 ('MetaCons "Mod_ATC" 'PrefixI 'False) (U1 :: Type -> Type) :+: (C1 ('MetaCons "Mod_ATG" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Mod_CAG" 'PrefixI 'False) (U1 :: Type -> Type)))) :+: ((C1 ('MetaCons "Mod_AGA" 'PrefixI 'False) (U1 :: Type -> Type) :+: (C1 ('MetaCons "Mod_CAT" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Mod_CCG" 'PrefixI 'False) (U1 :: Type -> Type))) :+: (C1 ('MetaCons "Mod_CGT" 'PrefixI 'False) (U1 :: Type -> Type) :+: (C1 ('MetaCons "Mod_CTG" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Mod_GAA" 'PrefixI 'False) (U1 :: Type -> Type))))) :+: (((C1 ('MetaCons "Mod_GAC" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Mod_GCT" 'PrefixI 'False) (U1 :: Type -> Type)) :+: (C1 ('MetaCons "Mod_GGT" 'PrefixI 'False) (U1 :: Type -> Type) :+: (C1 ('MetaCons "Mod_GTT" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Mod_TAC" 'PrefixI 'False) (U1 :: Type -> Type)))) :+: ((C1 ('MetaCons "Mod_TCT" 'PrefixI 'False) (U1 :: Type -> Type) :+: (C1 ('MetaCons "Mod_TGC" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Mod_TGG" 'PrefixI 'False) (U1 :: Type -> Type))) :+: (C1 ('MetaCons "Mod_TTC" 'PrefixI 'False) (U1 :: Type -> Type) :+: (C1 ('MetaCons "Mod_TTT" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Unknown" 'PrefixI 'False) (S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 String)))))))))

data ModItem Source #

Constructors

Mod Modification
Letter Char

Instances

Instances details

Eq ModItem Source #
Instance details Defined in Bio.FASTA.Type Methods (==) :: ModItem -> ModItem -> Bool # (/=) :: ModItem -> ModItem -> Bool #
Show ModItem Source #
Instance details Defined in Bio.FASTA.Type Methods showsPrec :: Int -> ModItem -> ShowS # show :: ModItem -> String # showList :: [ModItem] -> ShowS #
Generic ModItem Source #
Instance details Defined in Bio.FASTA.Type Associated Types type Rep ModItem :: Type -> Type # Methods from :: ModItem -> Rep ModItem x # to :: Rep ModItem x -> ModItem #
ParsableFastaToken ModItem Source #
Instance details Defined in Bio.FASTA.Parser Methods parseToken :: (Char -> Bool) -> Parser ModItem Source #
WritableFastaToken ModItem Source #
Instance details Defined in Bio.FASTA.Writer Methods tokenToString :: ModItem -> String Source #
type Rep ModItem Source #
Instance details Defined in Bio.FASTA.Type type Rep ModItem = D1 ('MetaData "ModItem" "Bio.FASTA.Type" "cobot-io-0.1.4.3-FtR1iZLExqtGkRGhoXEUKM" 'False) (C1 ('MetaCons "Mod" 'PrefixI 'False) (S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Modification)) :+: C1 ('MetaCons "Letter" 'PrefixI 'False) (S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Char)))

modificationToString :: Modification -> String Source #