cobot-io-0.1.3.8: Biological data file formats and IO

Safe HaskellNone
LanguageHaskell2010

Bio.GB.Type

Synopsis

Documentation

data GenBankSequence Source #

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

Constructors

GenBankSequence 

Fields

data Meta Source #

Meta-information about sequence.

Constructors

Meta 

Fields

Instances
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 #

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
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 #

data Locus Source #

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

Constructors

Locus 

Fields

Instances
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 #

data Version Source #

Id of sequence in GenBank database.

Constructors

Version 

Fields

Instances
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

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
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

data Reference Source #

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

Constructors

Reference 

Fields

Instances
Eq Reference Source # 
Instance details

Defined in Bio.GB.Type

Show Reference Source # 
Instance details

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data Feature Source #

One single feature.

Constructors

Feature 

Fields

  • fName :: Text

    main information about feature

  • fStrand53 :: Bool

    set to True if sequence is contained on 5'-3' strand. Set to False otherwise

  • fProps :: [(Text, Text)]

    properties of feature (such as "label", "gene", "note" etc.)

Instances
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

Show Feature Source # 
Instance details

Defined in Bio.GB.Type

IsMarking Feature Source # 
Instance details

Defined in Bio.GB.Type