Bio.RNAlienData

This module contains data structures for RNAlien

Documentation

data StaticOptions

Static construction options

Constructors

StaticOptions

Fields

• tempDirPath :: String
• sessionID :: String
• nSCICutoff :: Double
• userTaxId :: Maybe Int
• singleHitperTaxToggle :: Bool
• querySelectionMethod :: String
• queryNumber :: Int
• lengthFilterToggle :: Bool
• coverageFilterToggle :: Bool
• blastSoftmaskingToggle :: Bool
• cpuThreads :: Int
• blastDatabase :: Maybe String
• taxRestriction :: Maybe String
• verbositySwitch :: Bool

Instances

Show StaticOptions

Methods

showsPrec :: Int -> StaticOptions -> ShowS

show :: StaticOptions -> String

showList :: [StaticOptions] -> ShowS

data ModelConstruction

Keeps track of model construction

Constructors

ModelConstruction

Fields

• iterationNumber :: Int
• inputFasta :: Sequence
• taxRecords :: [TaxonomyRecord]
• upperTaxonomyLimit :: Maybe Int
• taxonomicContext :: Maybe Taxon
• evalueThreshold :: Double
• alignmentModeInfernal :: Bool
• selectedQueries :: [Sequence]
• potentialMembers :: [SearchResult]

Instances

Show ModelConstruction

Methods

showsPrec :: Int -> ModelConstruction -> ShowS

show :: ModelConstruction -> String

showList :: [ModelConstruction] -> ShowS

data TaxonomyRecord

Constructors

TaxonomyRecord

Fields

• recordTaxonomyId :: Int
• sequenceRecords :: [SequenceRecord]

Instances

Show TaxonomyRecord

Methods

showsPrec :: Int -> TaxonomyRecord -> ShowS

show :: TaxonomyRecord -> String

showList :: [TaxonomyRecord] -> ShowS

data SequenceRecord

Constructors

SequenceRecord

Fields

• nucleotideSequence :: Sequence
• aligned :: Int
• recordDescription :: ByteString

Instances

Show SequenceRecord

Methods

showsPrec :: Int -> SequenceRecord -> ShowS

show :: SequenceRecord -> String

showList :: [SequenceRecord] -> ShowS

data CMsearch

Constructors

CMsearch

Fields

• queryCMfile :: String
• targetSequenceDatabase :: String
• numberOfWorkerThreads :: String
• cmsearchHits :: [CMsearchHit]

Instances

Eq CMsearch

Methods

(==) :: CMsearch -> CMsearch -> Bool

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

Read CMsearch

Methods

readsPrec :: Int -> ReadS CMsearch

readList :: ReadS [CMsearch]

readPrec :: ReadPrec CMsearch

readListPrec :: ReadPrec [CMsearch]

Show CMsearch

Methods

showsPrec :: Int -> CMsearch -> ShowS

show :: CMsearch -> String

showList :: [CMsearch] -> ShowS

data CMsearchHit

Constructors

CMsearchHit

Fields

• hitRank :: Int
• hitSignificance :: Char
• hitEvalue :: Double
• hitScore :: Double
• hitBias :: Double
• hitSequenceHeader :: ByteString
• hitStart :: Int
• hitEnd :: Int
• hitStrand :: Char
• hitModel :: ByteString
• hitTruncation :: ByteString
• hitGCContent :: Double
• hitDescription :: ByteString

Instances

Eq CMsearchHit

Methods

(==) :: CMsearchHit -> CMsearchHit -> Bool

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

Read CMsearchHit

Methods

readsPrec :: Int -> ReadS CMsearchHit

readList :: ReadS [CMsearchHit]

readPrec :: ReadPrec CMsearchHit

readListPrec :: ReadPrec [CMsearchHit]

Show CMsearchHit

Methods

showsPrec :: Int -> CMsearchHit -> ShowS

show :: CMsearchHit -> String

showList :: [CMsearchHit] -> ShowS

data SearchResult

Constructors

SearchResult

Fields

• candidates :: [(Sequence, Int, ByteString)]
• blastDatabaseSize :: Maybe Double

Instances

Show SearchResult

Methods

showsPrec :: Int -> SearchResult -> ShowS

show :: SearchResult -> String

showList :: [SearchResult] -> ShowS

data CMstat

Constructors

CMstat

Fields

• statIndex :: Int
• statName :: String
• statAccession :: String
• statSequenceNumber :: Int
• statEffectiveSequences :: Double
• statConsensusLength :: Int
• statW :: Int
• statBasepairs :: Int
• statBifurcations :: Int
• statModel :: String
• relativeEntropyCM :: Double
• relativeEntropyHMM :: Double

Instances

Eq CMstat

Methods

(==) :: CMstat -> CMstat -> Bool

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

Read CMstat

Methods

readsPrec :: Int -> ReadS CMstat

readList :: ReadS [CMstat]

readPrec :: ReadPrec CMstat

readListPrec :: ReadPrec [CMstat]

Show CMstat

Methods

showsPrec :: Int -> CMstat -> ShowS

show :: CMstat -> String

showList :: [CMstat] -> ShowS