Biobase.Fasta.Types

Documentation

data Fasta

Constructors

Fasta

Fields

• fastaHeader :: ByteString
• fastaSequence :: ByteString

Instances

Eq Fasta

Defined in Biobase.Fasta.Types

Methods

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

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

Show Fasta

Defined in Biobase.Fasta.Export

Methods

showsPrec :: Int -> Fasta -> ShowS

show :: Fasta -> String

showList :: [Fasta] -> ShowS

newtype RawFastaEntry

Constructors

RawFastaEntry

Fields

• _rawFastaEntry :: ByteString

Instances

Eq RawFastaEntry

Defined in Biobase.Fasta.Types

Methods

(==) :: RawFastaEntry -> RawFastaEntry -> Bool

(/=) :: RawFastaEntry -> RawFastaEntry -> Bool

Ord RawFastaEntry

Defined in Biobase.Fasta.Types

Methods

compare :: RawFastaEntry -> RawFastaEntry -> Ordering

(<) :: RawFastaEntry -> RawFastaEntry -> Bool

(<=) :: RawFastaEntry -> RawFastaEntry -> Bool

(>) :: RawFastaEntry -> RawFastaEntry -> Bool

(>=) :: RawFastaEntry -> RawFastaEntry -> Bool

max :: RawFastaEntry -> RawFastaEntry -> RawFastaEntry

min :: RawFastaEntry -> RawFastaEntry -> RawFastaEntry

Show RawFastaEntry

Defined in Biobase.Fasta.Types

Methods

showsPrec :: Int -> RawFastaEntry -> ShowS

show :: RawFastaEntry -> String

showList :: [RawFastaEntry] -> ShowS

data StreamEvent

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.

Fields

• streamHeader :: !ByteString
• streamLines :: !LineInfo

StreamFasta

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

Fields

• streamFasta :: !ByteString
• prevStreamFasta :: !ByteString
• streamLines :: !LineInfo
• streamHeader :: !ByteString

Instances

Eq StreamEvent

Defined in Biobase.Fasta.Types

Methods

(==) :: StreamEvent -> StreamEvent -> Bool

(/=) :: StreamEvent -> StreamEvent -> Bool

Ord StreamEvent

Defined in Biobase.Fasta.Types

Methods

compare :: StreamEvent -> StreamEvent -> Ordering

(<) :: StreamEvent -> StreamEvent -> Bool

(<=) :: StreamEvent -> StreamEvent -> Bool

(>) :: StreamEvent -> StreamEvent -> Bool

(>=) :: StreamEvent -> StreamEvent -> Bool

max :: StreamEvent -> StreamEvent -> StreamEvent

min :: StreamEvent -> StreamEvent -> StreamEvent

Show StreamEvent

Defined in Biobase.Fasta.Types

Methods

showsPrec :: Int -> StreamEvent -> ShowS

show :: StreamEvent -> String

showList :: [StreamEvent] -> ShowS

Generic StreamEvent

Defined in Biobase.Fasta.Types

Associated Types

type Rep StreamEvent :: Type -> Type

Methods

from :: StreamEvent -> Rep StreamEvent x

to :: Rep StreamEvent x -> StreamEvent

NFData StreamEvent

Defined in Biobase.Fasta.Types

Methods

rnf :: StreamEvent -> ()

type Rep StreamEvent

Defined in Biobase.Fasta.Types

type Rep StreamEvent = D1 (MetaData "StreamEvent" "Biobase.Fasta.Types" "BiobaseFasta-0.2.0.0-IddPn5hBiRV7T2edw2bY5f" False) (C1 (MetaCons "StreamHeader" PrefixI True) (S1 (MetaSel (Just "streamHeader") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 ByteString) :*: S1 (MetaSel (Just "streamLines") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 LineInfo)) :+: C1 (MetaCons "StreamFasta" PrefixI True) ((S1 (MetaSel (Just "streamFasta") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 ByteString) :*: S1 (MetaSel (Just "prevStreamFasta") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 ByteString)) :*: (S1 (MetaSel (Just "streamLines") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 LineInfo) :*: S1 (MetaSel (Just "streamHeader") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 ByteString))))

data LineInfo

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

Defined in Biobase.Fasta.Types

Methods

(==) :: LineInfo -> LineInfo -> Bool

(/=) :: LineInfo -> LineInfo -> Bool

Ord LineInfo

Defined in Biobase.Fasta.Types

Methods

compare :: LineInfo -> LineInfo -> Ordering

(<) :: LineInfo -> LineInfo -> Bool

(<=) :: LineInfo -> LineInfo -> Bool

(>) :: LineInfo -> LineInfo -> Bool

(>=) :: LineInfo -> LineInfo -> Bool

max :: LineInfo -> LineInfo -> LineInfo

min :: LineInfo -> LineInfo -> LineInfo

Show LineInfo

Defined in Biobase.Fasta.Types

Methods

showsPrec :: Int -> LineInfo -> ShowS

show :: LineInfo -> String

showList :: [LineInfo] -> ShowS

Generic LineInfo

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

Defined in Biobase.Fasta.Types

Methods

rnf :: LineInfo -> ()

type Rep LineInfo

Defined in Biobase.Fasta.Types

type Rep LineInfo = D1 (MetaData "LineInfo" "Biobase.Fasta.Types" "BiobaseFasta-0.2.0.0-IddPn5hBiRV7T2edw2bY5f" False) (C1 (MetaCons "LineInfo" PrefixI True) ((S1 (MetaSel (Just "firstLine") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 Int) :*: S1 (MetaSel (Just "firstCol") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 Int)) :*: (S1 (MetaSel (Just "lastLine") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 Int) :*: (S1 (MetaSel (Just "lastCol") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 Int) :*: S1 (MetaSel (Just "firstIndex") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 Int)))))