BiobaseFasta-0.2.0.0: streaming FASTA parser

Safe HaskellNone
LanguageHaskell2010

Biobase.Fasta.Types

Synopsis

Documentation

data Fasta Source #

 
Instances
Eq Fasta Source # 
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Defined in Biobase.Fasta.Types

Methods

(==) :: Fasta -> Fasta -> Bool #

(/=) :: Fasta -> Fasta -> Bool #

Show Fasta Source # 
Instance details

Defined in Biobase.Fasta.Export

Methods

showsPrec :: Int -> Fasta -> ShowS #

show :: Fasta -> String #

showList :: [Fasta] -> ShowS #

data StreamEvent Source #

StreamEvents are chunked pieces of data, where the raw data is a strict ByteString. Each element also retains information on the first and last line and column (via streamLines) that are part of this chunk.

Constructors

StreamHeader

A Header event, multiple header events signal that the header name was longer than the chunk size.

StreamFasta

A data event. We keep a pointer to the previous chunk (which is useful for some algorithms). The chunk is free of newlines!

Instances
Eq StreamEvent Source # 
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Defined in Biobase.Fasta.Types

Ord StreamEvent Source # 
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Show StreamEvent Source # 
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Generic StreamEvent Source # 
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Associated Types

type Rep StreamEvent :: Type -> Type #

NFData StreamEvent Source # 
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Defined in Biobase.Fasta.Types

Methods

rnf :: StreamEvent -> () #

type Rep StreamEvent Source # 
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Defined in Biobase.Fasta.Types

data LineInfo Source #

Complete information on line and column start and end for a chunk.

TODO This is a 1-based format? Lets use the BiobaseTypes facilities!

Constructors

LineInfo 

Fields

  • firstLine :: !Int

    first line for this chunk (lines in complete file!)

  • firstCol :: !Int

    first column in first line for this chunk

  • lastLine :: !Int

    last line for this chunk (lines in complete file!)

  • lastCol :: !Int

    last column in last line for this chunk

  • firstIndex :: !Int

    first index in this fasta block. Counts just the number of symbols in the Fasta payload.

Instances
Eq LineInfo Source # 
Instance details

Defined in Biobase.Fasta.Types

Ord LineInfo Source # 
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Show LineInfo Source # 
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Generic LineInfo Source # 
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Defined in Biobase.Fasta.Types

Associated Types

type Rep LineInfo :: Type -> Type #

Methods

from :: LineInfo -> Rep LineInfo x #

to :: Rep LineInfo x -> LineInfo #

NFData LineInfo Source # 
Instance details

Defined in Biobase.Fasta.Types

Methods

rnf :: LineInfo -> () #

type Rep LineInfo Source # 
Instance details

Defined in Biobase.Fasta.Types