Safe Haskell	None
Language	Haskell2010

Biobase.BLAST.Types

Description

Encoding of tabular NCBI BLAST+ output

Synopsis

jsonLower :: Value -> Value
newtype BlastJSON2 = BlastJSON2 {
- _blastoutput2 :: BlastOutput2
}
newtype BlastCmdJSON2 = BlastCmdJSON2 {
- _blastcmdoutput2 :: [BlastOutput2]
}
newtype BlastOutput2 = BlastOutput2 {
- _report :: BlastReport
}
data BlastReport = BlastReport {
- _program :: !Text
- _version :: !Text
- _reference :: !Text
- _search_target :: !SearchTarget
- _params :: !Params
- _results :: !BlastJSONResult
}
newtype SearchTarget = SearchTarget {
- _db :: Text
}
data Params = Params {
- _expect :: !Double
- _sc_match :: !Int
- _sc_mismatch :: !Int
- _gap_open :: !Int
- _gap_extend :: !Int
- _filter :: !Text
}
data BlastJSONResult = BlastJSONResult {
- _search :: !Search
}
data Search = Search {
- _query_id :: !Text
- _query_title :: !Text
- _query_len :: !Int
- _hits :: Seq Hit
- _stat :: !SearchStat
}
data Hit = Hit {
- _num :: !Int
- _description :: ![HitDescription]
- _len :: !Int
- _hsps :: ![Hsp]
}
data Hsp = Hsp {
- _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
}
data HitDescription = HitDescription {
- _id :: !Text
- _accession :: !Text
- _title :: !Text
- _taxid :: Maybe Int
}
data SearchStat = SearchStat {
- _db_num :: !Int
- _db_len :: !Int
- _hsp_len :: !Int
- _eff_space :: !Int
- _kappa :: !Double
- _lambda :: !Double
- _entropy :: !Double
}
data BlastTabularResult = BlastTabularResult {
- _blastProgram :: !BlastProgram
- _blastQueryId :: !ByteString
- _blastDatabase :: !ByteString
- _blastHitNumber :: !Int
- _hitLines :: !(Vector BlastTabularHit)
}
data BlastTabularHit = BlastTabularHit {
- _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
}
data BlastProgram
- = BlastX
- | BlastP
- | BlastN
blastcmdoutput2 :: Iso' BlastCmdJSON2 [BlastOutput2]
blastoutput2 :: Iso' BlastJSON2 BlastOutput2
report :: Iso' BlastOutput2 BlastReport
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
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
search :: Iso' BlastJSONResult Search
stat :: Lens' Search SearchStat
query_title :: Lens' Search Text
query_len :: Lens' Search Int
query_id :: Lens' Search Text
hits :: Lens' Search (Seq Hit)
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
title :: Lens' HitDescription Text
taxid :: Lens' HitDescription (Maybe Int)
id :: Lens' HitDescription Text
accession :: Lens' HitDescription 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
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

Documentation

jsonLower :: Value -> Value Source #

Turn all keys in a JSON object to lowercase.

newtype BlastJSON2 Source #

Constructors

BlastJSON2
Fields _blastoutput2 :: BlastOutput2

Instances

Eq BlastJSON2 Source #
Instance details Defined in Biobase.BLAST.Types Methods (==) :: BlastJSON2 -> BlastJSON2 -> Bool # (/=) :: BlastJSON2 -> BlastJSON2 -> Bool #
Show BlastJSON2 Source #
Instance details Defined in Biobase.BLAST.Types Methods showsPrec :: Int -> BlastJSON2 -> ShowS # show :: BlastJSON2 -> String # showList :: [BlastJSON2] -> ShowS #
Generic BlastJSON2 Source #
Instance details 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 Source #
Instance details Defined in Biobase.BLAST.Types Methods toJSON :: BlastJSON2 -> Value # toEncoding :: BlastJSON2 -> Encoding # toJSONList :: [BlastJSON2] -> Value # toEncodingList :: [BlastJSON2] -> Encoding #
FromJSON BlastJSON2 Source #
Instance details Defined in Biobase.BLAST.Types Methods parseJSON :: Value -> Parser BlastJSON2 # parseJSONList :: Value -> Parser [BlastJSON2] #
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
Fields _blastcmdoutput2 :: [BlastOutput2]

Instances

Eq BlastCmdJSON2 Source #
Instance details Defined in Biobase.BLAST.Types Methods (==) :: BlastCmdJSON2 -> BlastCmdJSON2 -> Bool # (/=) :: BlastCmdJSON2 -> BlastCmdJSON2 -> Bool #
Show BlastCmdJSON2 Source #
Instance details Defined in Biobase.BLAST.Types Methods showsPrec :: Int -> BlastCmdJSON2 -> ShowS # show :: BlastCmdJSON2 -> String # showList :: [BlastCmdJSON2] -> ShowS #
Generic BlastCmdJSON2 Source #
Instance details 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 Source #
Instance details Defined in Biobase.BLAST.Types Methods toJSON :: BlastCmdJSON2 -> Value # toEncoding :: BlastCmdJSON2 -> Encoding # toJSONList :: [BlastCmdJSON2] -> Value # toEncodingList :: [BlastCmdJSON2] -> Encoding #
FromJSON BlastCmdJSON2 Source #
Instance details Defined in Biobase.BLAST.Types Methods parseJSON :: Value -> Parser BlastCmdJSON2 # parseJSONList :: Value -> Parser [BlastCmdJSON2] #
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 _report :: BlastReport

Instances

Eq BlastOutput2 Source #
Instance details Defined in Biobase.BLAST.Types Methods (==) :: BlastOutput2 -> BlastOutput2 -> Bool # (/=) :: BlastOutput2 -> BlastOutput2 -> Bool #
Show BlastOutput2 Source #
Instance details Defined in Biobase.BLAST.Types Methods showsPrec :: Int -> BlastOutput2 -> ShowS # show :: BlastOutput2 -> String # showList :: [BlastOutput2] -> ShowS #
Generic BlastOutput2 Source #
Instance details 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 Source #
Instance details Defined in Biobase.BLAST.Types Methods toJSON :: BlastOutput2 -> Value # toEncoding :: BlastOutput2 -> Encoding # toJSONList :: [BlastOutput2] -> Value # toEncodingList :: [BlastOutput2] -> Encoding #
FromJSON BlastOutput2 Source #
Instance details Defined in Biobase.BLAST.Types Methods parseJSON :: Value -> Parser BlastOutput2 # parseJSONList :: Value -> Parser [BlastOutput2] #
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 #

Constructors

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

Instances

Eq BlastReport Source #
Instance details Defined in Biobase.BLAST.Types Methods (==) :: BlastReport -> BlastReport -> Bool # (/=) :: BlastReport -> BlastReport -> Bool #
Show BlastReport Source #
Instance details Defined in Biobase.BLAST.Types Methods showsPrec :: Int -> BlastReport -> ShowS # show :: BlastReport -> String # showList :: [BlastReport] -> ShowS #
Generic BlastReport Source #
Instance details 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 Source #
Instance details Defined in Biobase.BLAST.Types Methods toJSON :: BlastReport -> Value # toEncoding :: BlastReport -> Encoding # toJSONList :: [BlastReport] -> Value # toEncodingList :: [BlastReport] -> Encoding #
FromJSON BlastReport Source #
Instance details Defined in Biobase.BLAST.Types Methods parseJSON :: Value -> Parser BlastReport # parseJSONList :: Value -> Parser [BlastReport] #
type Rep BlastReport Source #
Instance details Defined in Biobase.BLAST.Types type Rep BlastReport = D1 (MetaData "BlastReport" "Biobase.BLAST.Types" "BiobaseBlast-0.3.1.0-ExXGKuwRYfO3NhZPO3sW8q" 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 Source #

Constructors

SearchTarget
Fields _db :: Text

Instances

Eq SearchTarget Source #
Instance details Defined in Biobase.BLAST.Types Methods (==) :: SearchTarget -> SearchTarget -> Bool # (/=) :: SearchTarget -> SearchTarget -> Bool #
Show SearchTarget Source #
Instance details Defined in Biobase.BLAST.Types Methods showsPrec :: Int -> SearchTarget -> ShowS # show :: SearchTarget -> String # showList :: [SearchTarget] -> ShowS #
Generic SearchTarget Source #
Instance details 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 Source #
Instance details Defined in Biobase.BLAST.Types Methods toJSON :: SearchTarget -> Value # toEncoding :: SearchTarget -> Encoding # toJSONList :: [SearchTarget] -> Value # toEncodingList :: [SearchTarget] -> Encoding #
FromJSON SearchTarget Source #
Instance details Defined in Biobase.BLAST.Types Methods parseJSON :: Value -> Parser SearchTarget # parseJSONList :: Value -> Parser [SearchTarget] #
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
Fields _expect :: !Double _sc_match :: !Int _sc_mismatch :: !Int _gap_open :: !Int _gap_extend :: !Int _filter :: !Text

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 Methods showsPrec :: Int -> Params -> ShowS # show :: Params -> String # showList :: [Params] -> ShowS #
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 Methods toJSON :: Params -> Value # toEncoding :: Params -> Encoding # toJSONList :: [Params] -> Value # toEncodingList :: [Params] -> Encoding #
FromJSON Params Source #
Instance details Defined in Biobase.BLAST.Types Methods parseJSON :: Value -> Parser Params # parseJSONList :: Value -> Parser [Params] #
type Rep Params Source #
Instance details Defined in Biobase.BLAST.Types type Rep Params = D1 (MetaData "Params" "Biobase.BLAST.Types" "BiobaseBlast-0.3.1.0-ExXGKuwRYfO3NhZPO3sW8q" 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 Source #

Constructors

BlastJSONResult
Fields _search :: !Search

Instances

Eq BlastJSONResult Source #
Instance details Defined in Biobase.BLAST.Types Methods (==) :: BlastJSONResult -> BlastJSONResult -> Bool # (/=) :: BlastJSONResult -> BlastJSONResult -> Bool #
Show BlastJSONResult Source #
Instance details Defined in Biobase.BLAST.Types Methods showsPrec :: Int -> BlastJSONResult -> ShowS # show :: BlastJSONResult -> String # showList :: [BlastJSONResult] -> ShowS #
Generic BlastJSONResult Source #
Instance details 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 Source #
Instance details Defined in Biobase.BLAST.Types Methods toJSON :: BlastJSONResult -> Value # toEncoding :: BlastJSONResult -> Encoding # toJSONList :: [BlastJSONResult] -> Value # toEncodingList :: [BlastJSONResult] -> Encoding #
FromJSON BlastJSONResult Source #
Instance details Defined in Biobase.BLAST.Types Methods parseJSON :: Value -> Parser BlastJSONResult # parseJSONList :: Value -> Parser [BlastJSONResult] #
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
Fields _query_id :: !Text _query_title :: !Text _query_len :: !Int _hits :: Seq Hit _stat :: !SearchStat

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 Methods showsPrec :: Int -> Search -> ShowS # show :: Search -> String # showList :: [Search] -> ShowS #
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 Methods toJSON :: Search -> Value # toEncoding :: Search -> Encoding # toJSONList :: [Search] -> Value # toEncodingList :: [Search] -> Encoding #
FromJSON Search Source #
Instance details Defined in Biobase.BLAST.Types Methods parseJSON :: Value -> Parser Search # parseJSONList :: Value -> Parser [Search] #
type Rep Search Source #
Instance details Defined in Biobase.BLAST.Types type Rep Search = D1 (MetaData "Search" "Biobase.BLAST.Types" "BiobaseBlast-0.3.1.0-ExXGKuwRYfO3NhZPO3sW8q" 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 Source #

Constructors

Hit
Fields _num :: !Int _description :: ![HitDescription] _len :: !Int _hsps :: ![Hsp]

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 Methods toJSON :: Hit -> Value # toEncoding :: Hit -> Encoding # toJSONList :: [Hit] -> Value # toEncodingList :: [Hit] -> Encoding #
FromJSON Hit Source #
Instance details Defined in Biobase.BLAST.Types Methods parseJSON :: Value -> Parser Hit # parseJSONList :: Value -> Parser [Hit] #
type Rep Hit Source #
Instance details Defined in Biobase.BLAST.Types type Rep Hit = D1 (MetaData "Hit" "Biobase.BLAST.Types" "BiobaseBlast-0.3.1.0-ExXGKuwRYfO3NhZPO3sW8q" 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 Source #

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 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 Methods toJSON :: Hsp -> Value # toEncoding :: Hsp -> Encoding # toJSONList :: [Hsp] -> Value # toEncodingList :: [Hsp] -> Encoding #
FromJSON Hsp Source #
Instance details Defined in Biobase.BLAST.Types Methods parseJSON :: Value -> Parser Hsp # parseJSONList :: Value -> Parser [Hsp] #
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 _id :: !Text _accession :: !Text _title :: !Text _taxid :: Maybe Int

Instances

Eq HitDescription Source #
Instance details Defined in Biobase.BLAST.Types Methods (==) :: HitDescription -> HitDescription -> Bool # (/=) :: HitDescription -> HitDescription -> Bool #
Show HitDescription Source #
Instance details Defined in Biobase.BLAST.Types Methods showsPrec :: Int -> HitDescription -> ShowS # show :: HitDescription -> String # showList :: [HitDescription] -> ShowS #
Generic HitDescription Source #
Instance details 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 Source #
Instance details Defined in Biobase.BLAST.Types Methods toJSON :: HitDescription -> Value # toEncoding :: HitDescription -> Encoding # toJSONList :: [HitDescription] -> Value # toEncodingList :: [HitDescription] -> Encoding #
FromJSON HitDescription Source #
Instance details Defined in Biobase.BLAST.Types Methods parseJSON :: Value -> Parser HitDescription # parseJSONList :: Value -> Parser [HitDescription] #
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
Fields _db_num :: !Int _db_len :: !Int _hsp_len :: !Int _eff_space :: !Int _kappa :: !Double _lambda :: !Double _entropy :: !Double

Instances

Eq SearchStat Source #
Instance details Defined in Biobase.BLAST.Types Methods (==) :: SearchStat -> SearchStat -> Bool # (/=) :: SearchStat -> SearchStat -> Bool #
Show SearchStat Source #
Instance details Defined in Biobase.BLAST.Types Methods showsPrec :: Int -> SearchStat -> ShowS # show :: SearchStat -> String # showList :: [SearchStat] -> ShowS #
Generic SearchStat Source #
Instance details 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 Source #
Instance details Defined in Biobase.BLAST.Types Methods toJSON :: SearchStat -> Value # toEncoding :: SearchStat -> Encoding # toJSONList :: [SearchStat] -> Value # toEncodingList :: [SearchStat] -> Encoding #
FromJSON SearchStat Source #
Instance details Defined in Biobase.BLAST.Types Methods parseJSON :: Value -> Parser SearchStat # parseJSONList :: Value -> Parser [SearchStat] #
type Rep SearchStat Source #
Instance details Defined in Biobase.BLAST.Types type Rep SearchStat = D1 (MetaData "SearchStat" "Biobase.BLAST.Types" "BiobaseBlast-0.3.1.0-ExXGKuwRYfO3NhZPO3sW8q" 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 Source #

Constructors

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

Instances

Eq BlastTabularResult Source #
Instance details Defined in Biobase.BLAST.Types Methods (==) :: BlastTabularResult -> BlastTabularResult -> Bool # (/=) :: BlastTabularResult -> BlastTabularResult -> Bool #
Show BlastTabularResult Source #
Instance details Defined in Biobase.BLAST.Types Methods showsPrec :: Int -> BlastTabularResult -> ShowS # show :: BlastTabularResult -> String # showList :: [BlastTabularResult] -> ShowS #

data BlastTabularHit Source #

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 Source #
Instance details Defined in Biobase.BLAST.Types Methods (==) :: BlastTabularHit -> BlastTabularHit -> Bool # (/=) :: BlastTabularHit -> BlastTabularHit -> Bool #
Show BlastTabularHit Source #
Instance details Defined in Biobase.BLAST.Types Methods showsPrec :: Int -> BlastTabularHit -> ShowS # show :: BlastTabularHit -> String # showList :: [BlastTabularHit] -> ShowS #

data BlastProgram Source #

Constructors

BlastX
BlastP
BlastN

Instances

Eq BlastProgram Source #
Instance details Defined in Biobase.BLAST.Types Methods (==) :: BlastProgram -> BlastProgram -> Bool # (/=) :: BlastProgram -> BlastProgram -> Bool #
Show BlastProgram Source #
Instance details Defined in Biobase.BLAST.Types Methods showsPrec :: Int -> BlastProgram -> ShowS # show :: BlastProgram -> String # showList :: [BlastProgram] -> ShowS #
ToJSON BlastProgram Source #
Instance details Defined in Biobase.BLAST.Types Methods toJSON :: BlastProgram -> Value # toEncoding :: BlastProgram -> Encoding # toJSONList :: [BlastProgram] -> Value # toEncodingList :: [BlastProgram] -> Encoding #
FromJSON BlastProgram Source #
Instance details Defined in Biobase.BLAST.Types Methods parseJSON :: Value -> Parser BlastProgram # parseJSONList :: Value -> Parser [BlastProgram] #