Biobase.BLAST.Types

Encoding of tabular NCBI BLAST+ output

Documentation

jsonLower :: Value -> Value

Turn all keys in a JSON object to lowercase.

newtype BlastJSON2

Constructors

BlastJSON2

Fields

• _blastoutput2 :: BlastOutput2

Instances

Eq BlastJSON2

Defined in Biobase.BLAST.Types

Methods

(==) :: BlastJSON2 -> BlastJSON2 -> Bool

(/=) :: BlastJSON2 -> BlastJSON2 -> Bool

Show BlastJSON2

Defined in Biobase.BLAST.Types

Methods

showsPrec :: Int -> BlastJSON2 -> ShowS

show :: BlastJSON2 -> String

showList :: [BlastJSON2] -> ShowS

Generic BlastJSON2

Defined in Biobase.BLAST.Types

Associated Types

type Rep BlastJSON2 :: Type -> Type

Methods

from :: BlastJSON2 -> Rep BlastJSON2 x

to :: Rep BlastJSON2 x -> BlastJSON2

ToJSON BlastJSON2

Defined in Biobase.BLAST.Types

Methods

toJSON :: BlastJSON2 -> Value

toEncoding :: BlastJSON2 -> Encoding

toJSONList :: [BlastJSON2] -> Value

toEncodingList :: [BlastJSON2] -> Encoding

FromJSON BlastJSON2

Defined in Biobase.BLAST.Types

Methods

parseJSON :: Value -> Parser BlastJSON2

parseJSONList :: Value -> Parser [BlastJSON2]

type Rep BlastJSON2

Defined in Biobase.BLAST.Types

type Rep BlastJSON2 = D1 ('MetaData "BlastJSON2" "Biobase.BLAST.Types" "BiobaseBlast-0.3.3.0-8blL5vmeO2AKrfnTtE3loe" 'True) (C1 ('MetaCons "BlastJSON2" 'PrefixI 'True) (S1 ('MetaSel ('Just "_blastoutput2") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 BlastOutput2)))

newtype BlastCmdJSON2

Constructors

BlastCmdJSON2

Fields

• _blastcmdoutput2 :: [BlastOutput2]

Instances

Eq BlastCmdJSON2

Defined in Biobase.BLAST.Types

Methods

(==) :: BlastCmdJSON2 -> BlastCmdJSON2 -> Bool

(/=) :: BlastCmdJSON2 -> BlastCmdJSON2 -> Bool

Show BlastCmdJSON2

Defined in Biobase.BLAST.Types

Methods

showsPrec :: Int -> BlastCmdJSON2 -> ShowS

show :: BlastCmdJSON2 -> String

showList :: [BlastCmdJSON2] -> ShowS

Generic BlastCmdJSON2

Defined in Biobase.BLAST.Types

Associated Types

type Rep BlastCmdJSON2 :: Type -> Type

Methods

from :: BlastCmdJSON2 -> Rep BlastCmdJSON2 x

to :: Rep BlastCmdJSON2 x -> BlastCmdJSON2

ToJSON BlastCmdJSON2

Defined in Biobase.BLAST.Types

Methods

toJSON :: BlastCmdJSON2 -> Value

toEncoding :: BlastCmdJSON2 -> Encoding

toJSONList :: [BlastCmdJSON2] -> Value

toEncodingList :: [BlastCmdJSON2] -> Encoding

FromJSON BlastCmdJSON2

Defined in Biobase.BLAST.Types

Methods

parseJSON :: Value -> Parser BlastCmdJSON2

parseJSONList :: Value -> Parser [BlastCmdJSON2]

type Rep BlastCmdJSON2

Defined in Biobase.BLAST.Types

type Rep BlastCmdJSON2 = D1 ('MetaData "BlastCmdJSON2" "Biobase.BLAST.Types" "BiobaseBlast-0.3.3.0-8blL5vmeO2AKrfnTtE3loe" 'True) (C1 ('MetaCons "BlastCmdJSON2" 'PrefixI 'True) (S1 ('MetaSel ('Just "_blastcmdoutput2") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 [BlastOutput2])))

newtype BlastOutput2

Constructors

BlastOutput2

Fields

• _report :: BlastReport

Instances

Eq BlastOutput2

Defined in Biobase.BLAST.Types

Methods

(==) :: BlastOutput2 -> BlastOutput2 -> Bool

(/=) :: BlastOutput2 -> BlastOutput2 -> Bool

Show BlastOutput2

Defined in Biobase.BLAST.Types

Methods

showsPrec :: Int -> BlastOutput2 -> ShowS

show :: BlastOutput2 -> String

showList :: [BlastOutput2] -> ShowS

Generic BlastOutput2

Defined in Biobase.BLAST.Types

Associated Types

type Rep BlastOutput2 :: Type -> Type

Methods

from :: BlastOutput2 -> Rep BlastOutput2 x

to :: Rep BlastOutput2 x -> BlastOutput2

ToJSON BlastOutput2

Defined in Biobase.BLAST.Types

Methods

toJSON :: BlastOutput2 -> Value

toEncoding :: BlastOutput2 -> Encoding

toJSONList :: [BlastOutput2] -> Value

toEncodingList :: [BlastOutput2] -> Encoding

FromJSON BlastOutput2

Defined in Biobase.BLAST.Types

Methods

parseJSON :: Value -> Parser BlastOutput2

parseJSONList :: Value -> Parser [BlastOutput2]

type Rep BlastOutput2

Defined in Biobase.BLAST.Types

type Rep BlastOutput2 = D1 ('MetaData "BlastOutput2" "Biobase.BLAST.Types" "BiobaseBlast-0.3.3.0-8blL5vmeO2AKrfnTtE3loe" 'True) (C1 ('MetaCons "BlastOutput2" 'PrefixI 'True) (S1 ('MetaSel ('Just "_report") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 BlastReport)))

data BlastReport

Constructors

BlastReport

Fields

• _program :: !Text
• _version :: !Text
• _reference :: !Text
• _search_target :: !SearchTarget
• _params :: !Params
• _results :: !BlastJSONResult

Instances

Eq BlastReport

Defined in Biobase.BLAST.Types

Methods

(==) :: BlastReport -> BlastReport -> Bool

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

Show BlastReport

Defined in Biobase.BLAST.Types

Methods

showsPrec :: Int -> BlastReport -> ShowS

show :: BlastReport -> String

showList :: [BlastReport] -> ShowS

Generic BlastReport

Defined in Biobase.BLAST.Types

Associated Types

type Rep BlastReport :: Type -> Type

Methods

from :: BlastReport -> Rep BlastReport x

to :: Rep BlastReport x -> BlastReport

ToJSON BlastReport

Defined in Biobase.BLAST.Types

Methods

toJSON :: BlastReport -> Value

toEncoding :: BlastReport -> Encoding

toJSONList :: [BlastReport] -> Value

toEncodingList :: [BlastReport] -> Encoding

FromJSON BlastReport

Defined in Biobase.BLAST.Types

Methods

parseJSON :: Value -> Parser BlastReport

parseJSONList :: Value -> Parser [BlastReport]

type Rep BlastReport

Defined in Biobase.BLAST.Types

type Rep BlastReport = D1 ('MetaData "BlastReport" "Biobase.BLAST.Types" "BiobaseBlast-0.3.3.0-8blL5vmeO2AKrfnTtE3loe" 'False) (C1 ('MetaCons "BlastReport" 'PrefixI 'True) ((S1 ('MetaSel ('Just "_program") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Text) :*: (S1 ('MetaSel ('Just "_version") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Text) :*: S1 ('MetaSel ('Just "_reference") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Text))) :*: (S1 ('MetaSel ('Just "_search_target") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 SearchTarget) :*: (S1 ('MetaSel ('Just "_params") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Params) :*: S1 ('MetaSel ('Just "_results") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 BlastJSONResult)))))

newtype SearchTarget

Constructors

SearchTarget

Fields

• _db :: Text

Instances

Eq SearchTarget

Defined in Biobase.BLAST.Types

Methods

(==) :: SearchTarget -> SearchTarget -> Bool

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

Show SearchTarget

Defined in Biobase.BLAST.Types

Methods

showsPrec :: Int -> SearchTarget -> ShowS

show :: SearchTarget -> String

showList :: [SearchTarget] -> ShowS

Generic SearchTarget

Defined in Biobase.BLAST.Types

Associated Types

type Rep SearchTarget :: Type -> Type

Methods

from :: SearchTarget -> Rep SearchTarget x

to :: Rep SearchTarget x -> SearchTarget

ToJSON SearchTarget

Defined in Biobase.BLAST.Types

Methods

toJSON :: SearchTarget -> Value

toEncoding :: SearchTarget -> Encoding

toJSONList :: [SearchTarget] -> Value

toEncodingList :: [SearchTarget] -> Encoding

FromJSON SearchTarget

Defined in Biobase.BLAST.Types

Methods

parseJSON :: Value -> Parser SearchTarget

parseJSONList :: Value -> Parser [SearchTarget]

type Rep SearchTarget

Defined in Biobase.BLAST.Types

type Rep SearchTarget = D1 ('MetaData "SearchTarget" "Biobase.BLAST.Types" "BiobaseBlast-0.3.3.0-8blL5vmeO2AKrfnTtE3loe" 'True) (C1 ('MetaCons "SearchTarget" 'PrefixI 'True) (S1 ('MetaSel ('Just "_db") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Text)))

data Params

Constructors

Params

Fields

• _expect :: !Double
• _sc_match :: !Int
• _sc_mismatch :: !Int
• _gap_open :: !Int
• _gap_extend :: !Int
• _filter :: !Text

Instances

Eq Params

Defined in Biobase.BLAST.Types

Methods

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

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

Show Params

Defined in Biobase.BLAST.Types

Methods

showsPrec :: Int -> Params -> ShowS

show :: Params -> String

showList :: [Params] -> ShowS

Generic Params

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

Defined in Biobase.BLAST.Types

Methods

toJSON :: Params -> Value

toEncoding :: Params -> Encoding

toJSONList :: [Params] -> Value

toEncodingList :: [Params] -> Encoding

FromJSON Params

Defined in Biobase.BLAST.Types

Methods

parseJSON :: Value -> Parser Params

parseJSONList :: Value -> Parser [Params]

type Rep Params

Defined in Biobase.BLAST.Types

type Rep Params = D1 ('MetaData "Params" "Biobase.BLAST.Types" "BiobaseBlast-0.3.3.0-8blL5vmeO2AKrfnTtE3loe" 'False) (C1 ('MetaCons "Params" 'PrefixI 'True) ((S1 ('MetaSel ('Just "_expect") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Double) :*: (S1 ('MetaSel ('Just "_sc_match") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Int) :*: S1 ('MetaSel ('Just "_sc_mismatch") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Int))) :*: (S1 ('MetaSel ('Just "_gap_open") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Int) :*: (S1 ('MetaSel ('Just "_gap_extend") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Int) :*: S1 ('MetaSel ('Just "_filter") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Text)))))

data BlastJSONResult

Constructors

BlastJSONResult

Fields

• _search :: !Search

Instances

Eq BlastJSONResult

Defined in Biobase.BLAST.Types

Methods

(==) :: BlastJSONResult -> BlastJSONResult -> Bool

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

Show BlastJSONResult

Defined in Biobase.BLAST.Types

Methods

showsPrec :: Int -> BlastJSONResult -> ShowS

show :: BlastJSONResult -> String

showList :: [BlastJSONResult] -> ShowS

Generic BlastJSONResult

Defined in Biobase.BLAST.Types

Associated Types

type Rep BlastJSONResult :: Type -> Type

Methods

from :: BlastJSONResult -> Rep BlastJSONResult x

to :: Rep BlastJSONResult x -> BlastJSONResult

ToJSON BlastJSONResult

Defined in Biobase.BLAST.Types

Methods

toJSON :: BlastJSONResult -> Value

toEncoding :: BlastJSONResult -> Encoding

toJSONList :: [BlastJSONResult] -> Value

toEncodingList :: [BlastJSONResult] -> Encoding

FromJSON BlastJSONResult

Defined in Biobase.BLAST.Types

Methods

parseJSON :: Value -> Parser BlastJSONResult

parseJSONList :: Value -> Parser [BlastJSONResult]

type Rep BlastJSONResult

Defined in Biobase.BLAST.Types

type Rep BlastJSONResult = D1 ('MetaData "BlastJSONResult" "Biobase.BLAST.Types" "BiobaseBlast-0.3.3.0-8blL5vmeO2AKrfnTtE3loe" 'False) (C1 ('MetaCons "BlastJSONResult" 'PrefixI 'True) (S1 ('MetaSel ('Just "_search") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Search)))

data Search

Constructors

Search

Fields

• _query_id :: !Text
• _query_title :: !Text
• _query_len :: !Int
• _hits :: Seq Hit
• _stat :: !SearchStat

Instances

Eq Search

Defined in Biobase.BLAST.Types

Methods

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

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

Show Search

Defined in Biobase.BLAST.Types

Methods

showsPrec :: Int -> Search -> ShowS

show :: Search -> String

showList :: [Search] -> ShowS

Generic Search

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

Defined in Biobase.BLAST.Types

Methods

toJSON :: Search -> Value

toEncoding :: Search -> Encoding

toJSONList :: [Search] -> Value

toEncodingList :: [Search] -> Encoding

FromJSON Search

Defined in Biobase.BLAST.Types

Methods

parseJSON :: Value -> Parser Search

parseJSONList :: Value -> Parser [Search]

type Rep Search

Defined in Biobase.BLAST.Types

type Rep Search = D1 ('MetaData "Search" "Biobase.BLAST.Types" "BiobaseBlast-0.3.3.0-8blL5vmeO2AKrfnTtE3loe" 'False) (C1 ('MetaCons "Search" 'PrefixI 'True) ((S1 ('MetaSel ('Just "_query_id") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Text) :*: S1 ('MetaSel ('Just "_query_title") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Text)) :*: (S1 ('MetaSel ('Just "_query_len") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Int) :*: (S1 ('MetaSel ('Just "_hits") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Seq Hit)) :*: S1 ('MetaSel ('Just "_stat") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 SearchStat)))))

data Hit

Constructors

Hit

Fields

• _num :: !Int
• _description :: ![HitDescription]
• _len :: !Int
• _hsps :: ![Hsp]

Instances

Eq Hit

Defined in Biobase.BLAST.Types

Methods

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

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

Show Hit

Defined in Biobase.BLAST.Types

Methods

showsPrec :: Int -> Hit -> ShowS

show :: Hit -> String

showList :: [Hit] -> ShowS

Generic Hit

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

Defined in Biobase.BLAST.Types

Methods

toJSON :: Hit -> Value

toEncoding :: Hit -> Encoding

toJSONList :: [Hit] -> Value

toEncodingList :: [Hit] -> Encoding

FromJSON Hit

Defined in Biobase.BLAST.Types

Methods

parseJSON :: Value -> Parser Hit

parseJSONList :: Value -> Parser [Hit]

type Rep Hit

Defined in Biobase.BLAST.Types

type Rep Hit = D1 ('MetaData "Hit" "Biobase.BLAST.Types" "BiobaseBlast-0.3.3.0-8blL5vmeO2AKrfnTtE3loe" 'False) (C1 ('MetaCons "Hit" 'PrefixI 'True) ((S1 ('MetaSel ('Just "_num") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Int) :*: S1 ('MetaSel ('Just "_description") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 [HitDescription])) :*: (S1 ('MetaSel ('Just "_len") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Int) :*: S1 ('MetaSel ('Just "_hsps") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 [Hsp]))))

data Hsp

Constructors

Hsp

Fields

• _hsp_num :: !Int
• _bit_score :: !Double
• _score :: !Int
• _evalue :: !Double
• _identity :: !Int
• _query_from :: !Int
• _query_to :: !Int
• _query_strand :: !Text
• _hit_from :: !Int
• _hit_to :: !Int
• _hit_strand :: !Text
• _align_len :: !Int
• _gaps :: !Int
• _qseq :: !Text
• _hseq :: !Text
• _midline :: !Text

Instances

Eq Hsp

Defined in Biobase.BLAST.Types

Methods

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

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

Show Hsp

Defined in Biobase.BLAST.Types

Methods

showsPrec :: Int -> Hsp -> ShowS

show :: Hsp -> String

showList :: [Hsp] -> ShowS

Generic Hsp

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

Defined in Biobase.BLAST.Types

Methods

toJSON :: Hsp -> Value

toEncoding :: Hsp -> Encoding

toJSONList :: [Hsp] -> Value

toEncodingList :: [Hsp] -> Encoding

FromJSON Hsp

Defined in Biobase.BLAST.Types

Methods

parseJSON :: Value -> Parser Hsp

parseJSONList :: Value -> Parser [Hsp]

type Rep Hsp

Defined in Biobase.BLAST.Types

type Rep Hsp = D1 ('MetaData "Hsp" "Biobase.BLAST.Types" "BiobaseBlast-0.3.3.0-8blL5vmeO2AKrfnTtE3loe" '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

Constructors

HitDescription

Fields

• _id :: !Text
• _accession :: !Text
• _title :: !Text
• _taxid :: Maybe Int

Instances

Eq HitDescription

Defined in Biobase.BLAST.Types

Methods

(==) :: HitDescription -> HitDescription -> Bool

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

Show HitDescription

Defined in Biobase.BLAST.Types

Methods

showsPrec :: Int -> HitDescription -> ShowS

show :: HitDescription -> String

showList :: [HitDescription] -> ShowS

Generic HitDescription

Defined in Biobase.BLAST.Types

Associated Types

type Rep HitDescription :: Type -> Type

Methods

from :: HitDescription -> Rep HitDescription x

to :: Rep HitDescription x -> HitDescription

ToJSON HitDescription

Defined in Biobase.BLAST.Types

Methods

toJSON :: HitDescription -> Value

toEncoding :: HitDescription -> Encoding

toJSONList :: [HitDescription] -> Value

toEncodingList :: [HitDescription] -> Encoding

FromJSON HitDescription

Defined in Biobase.BLAST.Types

Methods

parseJSON :: Value -> Parser HitDescription

parseJSONList :: Value -> Parser [HitDescription]

type Rep HitDescription

Defined in Biobase.BLAST.Types

type Rep HitDescription = D1 ('MetaData "HitDescription" "Biobase.BLAST.Types" "BiobaseBlast-0.3.3.0-8blL5vmeO2AKrfnTtE3loe" '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

Constructors

SearchStat

Fields

• _db_num :: !Int
• _db_len :: !Int
• _hsp_len :: !Int
• _eff_space :: !Int
• _kappa :: !Double
• _lambda :: !Double
• _entropy :: !Double

Instances

Eq SearchStat

Defined in Biobase.BLAST.Types

Methods

(==) :: SearchStat -> SearchStat -> Bool

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

Show SearchStat

Defined in Biobase.BLAST.Types

Methods

showsPrec :: Int -> SearchStat -> ShowS

show :: SearchStat -> String

showList :: [SearchStat] -> ShowS

Generic SearchStat

Defined in Biobase.BLAST.Types

Associated Types

type Rep SearchStat :: Type -> Type

Methods

from :: SearchStat -> Rep SearchStat x

to :: Rep SearchStat x -> SearchStat

ToJSON SearchStat

Defined in Biobase.BLAST.Types

Methods

toJSON :: SearchStat -> Value

toEncoding :: SearchStat -> Encoding

toJSONList :: [SearchStat] -> Value

toEncodingList :: [SearchStat] -> Encoding

FromJSON SearchStat

Defined in Biobase.BLAST.Types

Methods

parseJSON :: Value -> Parser SearchStat

parseJSONList :: Value -> Parser [SearchStat]

type Rep SearchStat

Defined in Biobase.BLAST.Types

type Rep SearchStat = D1 ('MetaData "SearchStat" "Biobase.BLAST.Types" "BiobaseBlast-0.3.3.0-8blL5vmeO2AKrfnTtE3loe" 'False) (C1 ('MetaCons "SearchStat" 'PrefixI 'True) ((S1 ('MetaSel ('Just "_db_num") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Int) :*: (S1 ('MetaSel ('Just "_db_len") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Int) :*: S1 ('MetaSel ('Just "_hsp_len") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Int))) :*: ((S1 ('MetaSel ('Just "_eff_space") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Int) :*: S1 ('MetaSel ('Just "_kappa") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Double)) :*: (S1 ('MetaSel ('Just "_lambda") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Double) :*: S1 ('MetaSel ('Just "_entropy") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Double)))))

data BlastTabularResult

Constructors

BlastTabularResult

Fields

• _blastProgram :: !BlastProgram
• _blastQueryId :: !ByteString
• _blastDatabase :: !ByteString
• _blastHitNumber :: !Int
• _hitLines :: !(Vector BlastTabularHit)

Instances

Eq BlastTabularResult

Defined in Biobase.BLAST.Types

Methods

(==) :: BlastTabularResult -> BlastTabularResult -> Bool

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

Show BlastTabularResult

Defined in Biobase.BLAST.Types

Methods

showsPrec :: Int -> BlastTabularResult -> ShowS

show :: BlastTabularResult -> String

showList :: [BlastTabularResult] -> ShowS

data BlastTabularHit

Constructors

BlastTabularHit

Fields

• _queryId :: !ByteString
• _subjectId :: !ByteString
• _seqIdentity :: !Double
• _alignmentLength :: !Int
• _misMatches :: !Int
• _gapOpenScore :: !Int
• _queryStart :: !Int
• _queryEnd :: !Int
• _hitSeqStart :: !Int
• _hitSeqEnd :: !Int
• _eValue :: !Double
• _bitScore :: !Double
• _subjectFrame :: !Int
• _querySeq :: !ByteString
• _subjectSeq :: !ByteString

Instances

Eq BlastTabularHit

Defined in Biobase.BLAST.Types

Methods

(==) :: BlastTabularHit -> BlastTabularHit -> Bool

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

Show BlastTabularHit

Defined in Biobase.BLAST.Types

Methods

showsPrec :: Int -> BlastTabularHit -> ShowS

show :: BlastTabularHit -> String

showList :: [BlastTabularHit] -> ShowS

data BlastProgram

Constructors

BlastX

BlastP

BlastN

Instances

Eq BlastProgram

Defined in Biobase.BLAST.Types

Methods

(==) :: BlastProgram -> BlastProgram -> Bool

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

Show BlastProgram

Defined in Biobase.BLAST.Types

Methods

showsPrec :: Int -> BlastProgram -> ShowS

show :: BlastProgram -> String

showList :: [BlastProgram] -> ShowS

ToJSON BlastProgram

Defined in Biobase.BLAST.Types

Methods

toJSON :: BlastProgram -> Value

toEncoding :: BlastProgram -> Encoding

toJSONList :: [BlastProgram] -> Value

toEncodingList :: [BlastProgram] -> Encoding

FromJSON BlastProgram

Defined in Biobase.BLAST.Types

Methods

parseJSON :: Value -> Parser BlastProgram

parseJSONList :: Value -> Parser [BlastProgram]

hitLines :: Lens' BlastTabularResult (Vector BlastTabularHit)

blastQueryId :: Lens' BlastTabularResult ByteString

blastProgram :: Lens' BlastTabularResult BlastProgram

blastHitNumber :: Lens' BlastTabularResult Int

blastDatabase :: Lens' BlastTabularResult ByteString

subjectSeq :: Lens' BlastTabularHit ByteString

subjectId :: Lens' BlastTabularHit ByteString

subjectFrame :: Lens' BlastTabularHit Int

seqIdentity :: Lens' BlastTabularHit Double

queryStart :: Lens' BlastTabularHit Int

querySeq :: Lens' BlastTabularHit ByteString

queryId :: Lens' BlastTabularHit ByteString

queryEnd :: Lens' BlastTabularHit Int

misMatches :: Lens' BlastTabularHit Int

hitSeqStart :: Lens' BlastTabularHit Int

hitSeqEnd :: Lens' BlastTabularHit Int

gapOpenScore :: Lens' BlastTabularHit Int

eValue :: Lens' BlastTabularHit Double

bitScore :: Lens' BlastTabularHit Double

alignmentLength :: Lens' BlastTabularHit Int

db :: Iso' SearchTarget Text

lambda :: Lens' SearchStat Double

kappa :: Lens' SearchStat Double

hsp_len :: Lens' SearchStat Int

entropy :: Lens' SearchStat Double

eff_space :: Lens' SearchStat Int

db_num :: Lens' SearchStat Int

db_len :: Lens' SearchStat Int

title :: Lens' HitDescription Text

taxid :: Lens' HitDescription (Maybe Int)

id :: Lens' HitDescription Text

accession :: Lens' HitDescription Text

num :: Lens' Hit Int

len :: Lens' Hit Int

hsps :: Lens' Hit [Hsp]

description :: Lens' Hit [HitDescription]

score :: Lens' Hsp Int

query_to :: Lens' Hsp Int

query_strand :: Lens' Hsp Text

query_from :: Lens' Hsp Int

qseq :: Lens' Hsp Text

midline :: Lens' Hsp Text

identity :: Lens' Hsp Int

hsp_num :: Lens' Hsp Int

hseq :: Lens' Hsp Text

hit_to :: Lens' Hsp Int

hit_strand :: Lens' Hsp Text

hit_from :: Lens' Hsp Int

gaps :: Lens' Hsp Int

evalue :: Lens' Hsp Double

bit_score :: Lens' Hsp Double

align_len :: Lens' Hsp Int

stat :: Lens' Search SearchStat

query_title :: Lens' Search Text

query_len :: Lens' Search Int

query_id :: Lens' Search Text

hits :: Lens' Search (Seq Hit)

search :: Iso' BlastJSONResult Search

sc_mismatch :: Lens' Params Int

sc_match :: Lens' Params Int

gap_open :: Lens' Params Int

gap_extend :: Lens' Params Int

filter :: Lens' Params Text

expect :: Lens' Params Double

version :: Lens' BlastReport Text

search_target :: Lens' BlastReport SearchTarget

results :: Lens' BlastReport BlastJSONResult

reference :: Lens' BlastReport Text

program :: Lens' BlastReport Text

params :: Lens' BlastReport Params

report :: Iso' BlastOutput2 BlastReport

blastcmdoutput2 :: Iso' BlastCmdJSON2 [BlastOutput2]

blastoutput2 :: Iso' BlastJSON2 BlastOutput2