BiobaseBlast-0.3.1.0: BLAST-related tools

Safe HaskellNone
LanguageHaskell2010

Biobase.BLAST.Types

Description

Encoding of tabular NCBI BLAST+ output

Synopsis

Documentation

jsonLower :: Value -> Value Source #

Turn all keys in a JSON object to lowercase.

newtype BlastJSON2 Source #

Constructors

BlastJSON2 
Instances
Eq BlastJSON2 Source # 
Instance details

Defined in Biobase.BLAST.Types

Show BlastJSON2 Source # 
Instance details

Defined in Biobase.BLAST.Types

Generic BlastJSON2 Source # 
Instance details

Defined in Biobase.BLAST.Types

Associated Types

type Rep BlastJSON2 :: Type -> Type #

ToJSON BlastJSON2 Source # 
Instance details

Defined in Biobase.BLAST.Types

FromJSON BlastJSON2 Source # 
Instance details

Defined in Biobase.BLAST.Types

type Rep BlastJSON2 Source # 
Instance details

Defined in Biobase.BLAST.Types

type Rep BlastJSON2 = D1 (MetaData "BlastJSON2" "Biobase.BLAST.Types" "BiobaseBlast-0.3.1.0-ExXGKuwRYfO3NhZPO3sW8q" True) (C1 (MetaCons "BlastJSON2" PrefixI True) (S1 (MetaSel (Just "_blastoutput2") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 BlastOutput2)))

newtype BlastCmdJSON2 Source #

Constructors

BlastCmdJSON2 
Instances
Eq BlastCmdJSON2 Source # 
Instance details

Defined in Biobase.BLAST.Types

Show BlastCmdJSON2 Source # 
Instance details

Defined in Biobase.BLAST.Types

Generic BlastCmdJSON2 Source # 
Instance details

Defined in Biobase.BLAST.Types

Associated Types

type Rep BlastCmdJSON2 :: Type -> Type #

ToJSON BlastCmdJSON2 Source # 
Instance details

Defined in Biobase.BLAST.Types

FromJSON BlastCmdJSON2 Source # 
Instance details

Defined in Biobase.BLAST.Types

type Rep BlastCmdJSON2 Source # 
Instance details

Defined in Biobase.BLAST.Types

type Rep BlastCmdJSON2 = D1 (MetaData "BlastCmdJSON2" "Biobase.BLAST.Types" "BiobaseBlast-0.3.1.0-ExXGKuwRYfO3NhZPO3sW8q" True) (C1 (MetaCons "BlastCmdJSON2" PrefixI True) (S1 (MetaSel (Just "_blastcmdoutput2") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 [BlastOutput2])))

newtype BlastOutput2 Source #

Constructors

BlastOutput2 

Fields

Instances
Eq BlastOutput2 Source # 
Instance details

Defined in Biobase.BLAST.Types

Show BlastOutput2 Source # 
Instance details

Defined in Biobase.BLAST.Types

Generic BlastOutput2 Source # 
Instance details

Defined in Biobase.BLAST.Types

Associated Types

type Rep BlastOutput2 :: Type -> Type #

ToJSON BlastOutput2 Source # 
Instance details

Defined in Biobase.BLAST.Types

FromJSON BlastOutput2 Source # 
Instance details

Defined in Biobase.BLAST.Types

type Rep BlastOutput2 Source # 
Instance details

Defined in Biobase.BLAST.Types

type Rep BlastOutput2 = D1 (MetaData "BlastOutput2" "Biobase.BLAST.Types" "BiobaseBlast-0.3.1.0-ExXGKuwRYfO3NhZPO3sW8q" True) (C1 (MetaCons "BlastOutput2" PrefixI True) (S1 (MetaSel (Just "_report") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 BlastReport)))

data BlastReport Source #

Instances
Eq BlastReport Source # 
Instance details

Defined in Biobase.BLAST.Types

Show BlastReport Source # 
Instance details

Defined in Biobase.BLAST.Types

Generic BlastReport Source # 
Instance details

Defined in Biobase.BLAST.Types

Associated Types

type Rep BlastReport :: Type -> Type #

ToJSON BlastReport Source # 
Instance details

Defined in Biobase.BLAST.Types

FromJSON BlastReport Source # 
Instance details

Defined in Biobase.BLAST.Types

type Rep BlastReport Source # 
Instance details

Defined in Biobase.BLAST.Types

newtype SearchTarget Source #

Constructors

SearchTarget 

Fields

Instances
Eq SearchTarget Source # 
Instance details

Defined in Biobase.BLAST.Types

Show SearchTarget Source # 
Instance details

Defined in Biobase.BLAST.Types

Generic SearchTarget Source # 
Instance details

Defined in Biobase.BLAST.Types

Associated Types

type Rep SearchTarget :: Type -> Type #

ToJSON SearchTarget Source # 
Instance details

Defined in Biobase.BLAST.Types

FromJSON SearchTarget Source # 
Instance details

Defined in Biobase.BLAST.Types

type Rep SearchTarget Source # 
Instance details

Defined in Biobase.BLAST.Types

type Rep SearchTarget = D1 (MetaData "SearchTarget" "Biobase.BLAST.Types" "BiobaseBlast-0.3.1.0-ExXGKuwRYfO3NhZPO3sW8q" True) (C1 (MetaCons "SearchTarget" PrefixI True) (S1 (MetaSel (Just "_db") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Text)))

data Params Source #

Constructors

Params 
Instances
Eq Params Source # 
Instance details

Defined in Biobase.BLAST.Types

Methods

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

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

Show Params Source # 
Instance details

Defined in Biobase.BLAST.Types

Generic Params Source # 
Instance details

Defined in Biobase.BLAST.Types

Associated Types

type Rep Params :: Type -> Type #

Methods

from :: Params -> Rep Params x #

to :: Rep Params x -> Params #

ToJSON Params Source # 
Instance details

Defined in Biobase.BLAST.Types

FromJSON Params Source # 
Instance details

Defined in Biobase.BLAST.Types

type Rep Params Source # 
Instance details

Defined in Biobase.BLAST.Types

data BlastJSONResult Source #

Constructors

BlastJSONResult 

Fields

Instances
Eq BlastJSONResult Source # 
Instance details

Defined in Biobase.BLAST.Types

Show BlastJSONResult Source # 
Instance details

Defined in Biobase.BLAST.Types

Generic BlastJSONResult Source # 
Instance details

Defined in Biobase.BLAST.Types

Associated Types

type Rep BlastJSONResult :: Type -> Type #

ToJSON BlastJSONResult Source # 
Instance details

Defined in Biobase.BLAST.Types

FromJSON BlastJSONResult Source # 
Instance details

Defined in Biobase.BLAST.Types

type Rep BlastJSONResult Source # 
Instance details

Defined in Biobase.BLAST.Types

type Rep BlastJSONResult = D1 (MetaData "BlastJSONResult" "Biobase.BLAST.Types" "BiobaseBlast-0.3.1.0-ExXGKuwRYfO3NhZPO3sW8q" False) (C1 (MetaCons "BlastJSONResult" PrefixI True) (S1 (MetaSel (Just "_search") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 Search)))

data Search Source #

Constructors

Search 
Instances
Eq Search Source # 
Instance details

Defined in Biobase.BLAST.Types

Methods

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

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

Show Search Source # 
Instance details

Defined in Biobase.BLAST.Types

Generic Search Source # 
Instance details

Defined in Biobase.BLAST.Types

Associated Types

type Rep Search :: Type -> Type #

Methods

from :: Search -> Rep Search x #

to :: Rep Search x -> Search #

ToJSON Search Source # 
Instance details

Defined in Biobase.BLAST.Types

FromJSON Search Source # 
Instance details

Defined in Biobase.BLAST.Types

type Rep Search Source # 
Instance details

Defined in Biobase.BLAST.Types

data Hit Source #

Constructors

Hit 

Fields

Instances
Eq Hit Source # 
Instance details

Defined in Biobase.BLAST.Types

Methods

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

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

Show Hit Source # 
Instance details

Defined in Biobase.BLAST.Types

Methods

showsPrec :: Int -> Hit -> ShowS #

show :: Hit -> String #

showList :: [Hit] -> ShowS #

Generic Hit Source # 
Instance details

Defined in Biobase.BLAST.Types

Associated Types

type Rep Hit :: Type -> Type #

Methods

from :: Hit -> Rep Hit x #

to :: Rep Hit x -> Hit #

ToJSON Hit Source # 
Instance details

Defined in Biobase.BLAST.Types

FromJSON Hit Source # 
Instance details

Defined in Biobase.BLAST.Types

type Rep Hit Source # 
Instance details

Defined in Biobase.BLAST.Types

data Hsp Source #

Constructors

Hsp 
Instances
Eq Hsp Source # 
Instance details

Defined in Biobase.BLAST.Types

Methods

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

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

Show Hsp Source # 
Instance details

Defined in Biobase.BLAST.Types

Methods

showsPrec :: Int -> Hsp -> ShowS #

show :: Hsp -> String #

showList :: [Hsp] -> ShowS #

Generic Hsp Source # 
Instance details

Defined in Biobase.BLAST.Types

Associated Types

type Rep Hsp :: Type -> Type #

Methods

from :: Hsp -> Rep Hsp x #

to :: Rep Hsp x -> Hsp #

ToJSON Hsp Source # 
Instance details

Defined in Biobase.BLAST.Types

FromJSON Hsp Source # 
Instance details

Defined in Biobase.BLAST.Types

type Rep Hsp Source # 
Instance details

Defined in Biobase.BLAST.Types

type Rep Hsp = D1 (MetaData "Hsp" "Biobase.BLAST.Types" "BiobaseBlast-0.3.1.0-ExXGKuwRYfO3NhZPO3sW8q" False) (C1 (MetaCons "Hsp" PrefixI True) ((((S1 (MetaSel (Just "_hsp_num") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 Int) :*: S1 (MetaSel (Just "_bit_score") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 Double)) :*: (S1 (MetaSel (Just "_score") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 Int) :*: S1 (MetaSel (Just "_evalue") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 Double))) :*: ((S1 (MetaSel (Just "_identity") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 Int) :*: S1 (MetaSel (Just "_query_from") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 Int)) :*: (S1 (MetaSel (Just "_query_to") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 Int) :*: S1 (MetaSel (Just "_query_strand") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 Text)))) :*: (((S1 (MetaSel (Just "_hit_from") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 Int) :*: S1 (MetaSel (Just "_hit_to") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 Int)) :*: (S1 (MetaSel (Just "_hit_strand") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 Text) :*: S1 (MetaSel (Just "_align_len") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 Int))) :*: ((S1 (MetaSel (Just "_gaps") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 Int) :*: S1 (MetaSel (Just "_qseq") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 Text)) :*: (S1 (MetaSel (Just "_hseq") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 Text) :*: S1 (MetaSel (Just "_midline") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 Text))))))

data HitDescription Source #

Constructors

HitDescription 

Fields

Instances
Eq HitDescription Source # 
Instance details

Defined in Biobase.BLAST.Types

Show HitDescription Source # 
Instance details

Defined in Biobase.BLAST.Types

Generic HitDescription Source # 
Instance details

Defined in Biobase.BLAST.Types

Associated Types

type Rep HitDescription :: Type -> Type #

ToJSON HitDescription Source # 
Instance details

Defined in Biobase.BLAST.Types

FromJSON HitDescription Source # 
Instance details

Defined in Biobase.BLAST.Types

type Rep HitDescription Source # 
Instance details

Defined in Biobase.BLAST.Types

type Rep HitDescription = D1 (MetaData "HitDescription" "Biobase.BLAST.Types" "BiobaseBlast-0.3.1.0-ExXGKuwRYfO3NhZPO3sW8q" False) (C1 (MetaCons "HitDescription" PrefixI True) ((S1 (MetaSel (Just "_id") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 Text) :*: S1 (MetaSel (Just "_accession") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 Text)) :*: (S1 (MetaSel (Just "_title") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 Text) :*: S1 (MetaSel (Just "_taxid") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 (Maybe Int)))))

data SearchStat Source #

Constructors

SearchStat 
Instances
Eq SearchStat Source # 
Instance details

Defined in Biobase.BLAST.Types

Show SearchStat Source # 
Instance details

Defined in Biobase.BLAST.Types

Generic SearchStat Source # 
Instance details

Defined in Biobase.BLAST.Types

Associated Types

type Rep SearchStat :: Type -> Type #

ToJSON SearchStat Source # 
Instance details

Defined in Biobase.BLAST.Types

FromJSON SearchStat Source # 
Instance details

Defined in Biobase.BLAST.Types

type Rep SearchStat Source # 
Instance details

Defined in Biobase.BLAST.Types