Safe Haskell	None
Language	Haskell2010

Bio.GB.Type

Synopsis

data GenBankSequence = GenBankSequence {
- meta :: Meta
- gbSeq :: MarkedSequence Feature Char
}
data Meta = Meta {
- locus :: Locus
- definition :: Maybe Text
- accession :: Maybe Text
- version :: Maybe Version
- keywords :: Maybe Text
- source :: Maybe Source
- references :: [Reference]
- comments :: [Text]
}
data Form
- = Linear
- | Circular
data Locus = Locus {
- name :: Text
- len :: Int
- molType :: Text
- form :: Maybe Form
- gbDivision :: Maybe Text
- modificationDate :: Text
}
data Version = Version {
- versionT :: Text
- gbId :: Maybe Text
}
data Source = Source {
- sourceT :: Text
- organism :: Maybe Text
}
data Reference = Reference {
- referenceT :: Text
- authors :: Maybe Text
- title :: Maybe Text
- journal :: Maybe Text
- pubmed :: Maybe Text
}
data Feature = Feature {
- fName :: Text
- fProps :: [(Text, Text)]
}
type Parser = Parsec Void Text

Documentation

data GenBankSequence Source #

Type that represents contents of .gb file that is used to store information about genetic constructions.

Constructors

GenBankSequence
Fields meta :: Meta meta-information about the sequence gbSeq :: MarkedSequence Feature Char sequence that is marked by `Feature`s

Instances

Instances details

Eq GenBankSequence Source #
Instance details Defined in Bio.GB.Type Methods (==) :: GenBankSequence -> GenBankSequence -> Bool # (/=) :: GenBankSequence -> GenBankSequence -> Bool #
Show GenBankSequence Source #
Instance details Defined in Bio.GB.Type Methods showsPrec :: Int -> GenBankSequence -> ShowS # show :: GenBankSequence -> String # showList :: [GenBankSequence] -> ShowS #
Generic GenBankSequence Source #
Instance details Defined in Bio.GB.Type Associated Types type Rep GenBankSequence :: Type -> Type # Methods from :: GenBankSequence -> Rep GenBankSequence x # to :: Rep GenBankSequence x -> GenBankSequence #
NFData GenBankSequence Source #
Instance details Defined in Bio.GB.Type Methods rnf :: GenBankSequence -> () #
type Rep GenBankSequence Source #
Instance details Defined in Bio.GB.Type type Rep GenBankSequence = D1 ('MetaData "GenBankSequence" "Bio.GB.Type" "cobot-io-0.1.4.3-FtR1iZLExqtGkRGhoXEUKM" 'False) (C1 ('MetaCons "GenBankSequence" 'PrefixI 'True) (S1 ('MetaSel ('Just "meta") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Meta) :*: S1 ('MetaSel ('Just "gbSeq") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (MarkedSequence Feature Char))))

data Meta Source #

Meta-information about sequence.

Constructors

Instances

Instances details

Eq Meta Source #
Instance details Defined in Bio.GB.Type Methods (==) :: Meta -> Meta -> Bool # (/=) :: Meta -> Meta -> Bool #
Show Meta Source #
Instance details Defined in Bio.GB.Type Methods showsPrec :: Int -> Meta -> ShowS # show :: Meta -> String # showList :: [Meta] -> ShowS #
Generic Meta Source #
Instance details Defined in Bio.GB.Type Associated Types type Rep Meta :: Type -> Type # Methods from :: Meta -> Rep Meta x # to :: Rep Meta x -> Meta #
NFData Meta Source #
Instance details Defined in Bio.GB.Type Methods rnf :: Meta -> () #
type Rep Meta Source #
Instance details Defined in Bio.GB.Type type Rep Meta = D1 ('MetaData "Meta" "Bio.GB.Type" "cobot-io-0.1.4.3-FtR1iZLExqtGkRGhoXEUKM" 'False) (C1 ('MetaCons "Meta" 'PrefixI 'True) (((S1 ('MetaSel ('Just "locus") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Locus) :: S1 ('MetaSel ('Just "definition") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe Text))) :: (S1 ('MetaSel ('Just "accession") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe Text)) :: S1 ('MetaSel ('Just "version") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe Version)))) :: ((S1 ('MetaSel ('Just "keywords") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe Text)) :: S1 ('MetaSel ('Just "source") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe Source))) :: (S1 ('MetaSel ('Just "references") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 [Reference]) :*: S1 ('MetaSel ('Just "comments") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 [Text])))))

data Form Source #

At this moment there are two known (to me) forms of seuqences that can be present in .gb file.

Constructors

Linear
Circular

Instances

Instances details

Eq Form Source #
Instance details Defined in Bio.GB.Type Methods (==) :: Form -> Form -> Bool # (/=) :: Form -> Form -> Bool #
Show Form Source #
Instance details Defined in Bio.GB.Type Methods showsPrec :: Int -> Form -> ShowS # show :: Form -> String # showList :: [Form] -> ShowS #
Generic Form Source #
Instance details Defined in Bio.GB.Type Associated Types type Rep Form :: Type -> Type # Methods from :: Form -> Rep Form x # to :: Rep Form x -> Form #
NFData Form Source #
Instance details Defined in Bio.GB.Type Methods rnf :: Form -> () #
type Rep Form Source #
Instance details Defined in Bio.GB.Type type Rep Form = D1 ('MetaData "Form" "Bio.GB.Type" "cobot-io-0.1.4.3-FtR1iZLExqtGkRGhoXEUKM" 'False) (C1 ('MetaCons "Linear" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Circular" 'PrefixI 'False) (U1 :: Type -> Type))

data Locus Source #

First line that should be present in every .gb file. Contains general info about sequence.

Constructors

Locus
Fields name :: Text name of sequence len :: Int length of sequence molType :: Text type of molecule that is sequenced form :: Maybe Form form of sequence gbDivision :: Maybe Text GenBank division to which a record belongs modificationDate :: Text date of last modification of sequence

Instances

Instances details

Eq Locus Source #
Instance details Defined in Bio.GB.Type Methods (==) :: Locus -> Locus -> Bool # (/=) :: Locus -> Locus -> Bool #
Show Locus Source #
Instance details Defined in Bio.GB.Type Methods showsPrec :: Int -> Locus -> ShowS # show :: Locus -> String # showList :: [Locus] -> ShowS #
Generic Locus Source #
Instance details Defined in Bio.GB.Type Associated Types type Rep Locus :: Type -> Type # Methods from :: Locus -> Rep Locus x # to :: Rep Locus x -> Locus #
NFData Locus Source #
Instance details Defined in Bio.GB.Type Methods rnf :: Locus -> () #
type Rep Locus Source #
Instance details Defined in Bio.GB.Type type Rep Locus = D1 ('MetaData "Locus" "Bio.GB.Type" "cobot-io-0.1.4.3-FtR1iZLExqtGkRGhoXEUKM" 'False) (C1 ('MetaCons "Locus" 'PrefixI 'True) ((S1 ('MetaSel ('Just "name") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Text) :: (S1 ('MetaSel ('Just "len") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Int) :: S1 ('MetaSel ('Just "molType") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Text))) :: (S1 ('MetaSel ('Just "form") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe Form)) :: (S1 ('MetaSel ('Just "gbDivision") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe Text)) :*: S1 ('MetaSel ('Just "modificationDate") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Text)))))

data Version Source #

Id of sequence in GenBank database.

Constructors

Version
Fields versionT :: Text id itself gbId :: Maybe Text GenInfo Identifier that is assigned when sequence changes

Instances

Instances details

Eq Version Source #
Instance details Defined in Bio.GB.Type Methods (==) :: Version -> Version -> Bool # (/=) :: Version -> Version -> Bool #
Show Version Source #
Instance details Defined in Bio.GB.Type Methods showsPrec :: Int -> Version -> ShowS # show :: Version -> String # showList :: [Version] -> ShowS #
Generic Version Source #
Instance details Defined in Bio.GB.Type Associated Types type Rep Version :: Type -> Type # Methods from :: Version -> Rep Version x # to :: Rep Version x -> Version #
NFData Version Source #
Instance details Defined in Bio.GB.Type Methods rnf :: Version -> () #
type Rep Version Source #
Instance details Defined in Bio.GB.Type type Rep Version = D1 ('MetaData "Version" "Bio.GB.Type" "cobot-io-0.1.4.3-FtR1iZLExqtGkRGhoXEUKM" 'False) (C1 ('MetaCons "Version" 'PrefixI 'True) (S1 ('MetaSel ('Just "versionT") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Text) :*: S1 ('MetaSel ('Just "gbId") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe Text))))

data Source Source #

Information about source of this sequence.

Constructors

Source
Fields sourceT :: Text free-format (as if all this format is not too much "free format") information including an abbreviated form of the organism name, sometimes followed by a molecule type organism :: Maybe Text the formal scientific name for the source organism

Instances

Instances details

Eq Source Source #
Instance details Defined in Bio.GB.Type Methods (==) :: Source -> Source -> Bool # (/=) :: Source -> Source -> Bool #
Show Source Source #
Instance details Defined in Bio.GB.Type Methods showsPrec :: Int -> Source -> ShowS # show :: Source -> String # showList :: [Source] -> ShowS #
Generic Source Source #
Instance details Defined in Bio.GB.Type Associated Types type Rep Source :: Type -> Type # Methods from :: Source -> Rep Source x # to :: Rep Source x -> Source #
NFData Source Source #
Instance details Defined in Bio.GB.Type Methods rnf :: Source -> () #
type Rep Source Source #
Instance details Defined in Bio.GB.Type type Rep Source = D1 ('MetaData "Source" "Bio.GB.Type" "cobot-io-0.1.4.3-FtR1iZLExqtGkRGhoXEUKM" 'False) (C1 ('MetaCons "Source" 'PrefixI 'True) (S1 ('MetaSel ('Just "sourceT") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Text) :*: S1 ('MetaSel ('Just "organism") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe Text))))

data Reference Source #

Publications by the authors of the sequence that discuss the data reported in the record.

Constructors

Reference
Fields referenceT :: Text reference itself authors :: Maybe Text list of authors in the order in which they appear in the cited article title :: Maybe Text title of the published work journal :: Maybe Text MEDLINE abbreviation of the journal name pubmed :: Maybe Text PubMed Identifier

Instances

Instances details

Eq Reference Source #
Instance details Defined in Bio.GB.Type Methods (==) :: Reference -> Reference -> Bool # (/=) :: Reference -> Reference -> Bool #
Show Reference Source #
Instance details Defined in Bio.GB.Type Methods showsPrec :: Int -> Reference -> ShowS # show :: Reference -> String # showList :: [Reference] -> ShowS #
Generic Reference Source #
Instance details Defined in Bio.GB.Type Associated Types type Rep Reference :: Type -> Type # Methods from :: Reference -> Rep Reference x # to :: Rep Reference x -> Reference #
NFData Reference Source #
Instance details Defined in Bio.GB.Type Methods rnf :: Reference -> () #
type Rep Reference Source #
Instance details Defined in Bio.GB.Type type Rep Reference = D1 ('MetaData "Reference" "Bio.GB.Type" "cobot-io-0.1.4.3-FtR1iZLExqtGkRGhoXEUKM" 'False) (C1 ('MetaCons "Reference" 'PrefixI 'True) ((S1 ('MetaSel ('Just "referenceT") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Text) :: S1 ('MetaSel ('Just "authors") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe Text))) :: (S1 ('MetaSel ('Just "title") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe Text)) :: (S1 ('MetaSel ('Just "journal") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe Text)) :: S1 ('MetaSel ('Just "pubmed") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe Text))))))

data Feature Source #

One single feature.

Constructors

Feature
Fields fName :: Text main information about feature fProps :: [(Text, Text)] properties of feature (such as "label", "gene", "note" etc.)

Instances

Instances details

Eq Feature Source #
Instance details Defined in Bio.GB.Type Methods (==) :: Feature -> Feature -> Bool # (/=) :: Feature -> Feature -> Bool #
Ord Feature Source #
Instance details Defined in Bio.GB.Type Methods compare :: Feature -> Feature -> Ordering # (<) :: Feature -> Feature -> Bool # (<=) :: Feature -> Feature -> Bool # (>) :: Feature -> Feature -> Bool # (>=) :: Feature -> Feature -> Bool # max :: Feature -> Feature -> Feature # min :: Feature -> Feature -> Feature #
Show Feature Source #
Instance details Defined in Bio.GB.Type Methods showsPrec :: Int -> Feature -> ShowS # show :: Feature -> String # showList :: [Feature] -> ShowS #
Generic Feature Source #
Instance details Defined in Bio.GB.Type Associated Types type Rep Feature :: Type -> Type # Methods from :: Feature -> Rep Feature x # to :: Rep Feature x -> Feature #
NFData Feature Source #
Instance details Defined in Bio.GB.Type Methods rnf :: Feature -> () #
IsMarking Feature Source #
Instance details Defined in Bio.GB.Type
type Rep Feature Source #
Instance details Defined in Bio.GB.Type type Rep Feature = D1 ('MetaData "Feature" "Bio.GB.Type" "cobot-io-0.1.4.3-FtR1iZLExqtGkRGhoXEUKM" 'False) (C1 ('MetaCons "Feature" 'PrefixI 'True) (S1 ('MetaSel ('Just "fName") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Text) :*: S1 ('MetaSel ('Just "fProps") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 [(Text, Text)])))

type Parser = Parsec Void Text Source #