Safe Haskell	None
Language	Haskell98

Bio.RNAlienData

Description

This module contains data structures for RNAlien

Synopsis

Documentation

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 Source #
Methods showsPrec :: Int -> StaticOptions -> ShowS # show :: StaticOptions -> String # showList :: [StaticOptions] -> ShowS #

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 Source #
Methods showsPrec :: Int -> ModelConstruction -> ShowS # show :: ModelConstruction -> String # showList :: [ModelConstruction] -> ShowS #

Constructors

TaxonomyRecord
Fields recordTaxonomyId :: Int sequenceRecords :: [SequenceRecord]

Instances

Show TaxonomyRecord Source #
Methods showsPrec :: Int -> TaxonomyRecord -> ShowS # show :: TaxonomyRecord -> String # showList :: [TaxonomyRecord] -> ShowS #

Constructors

SequenceRecord
Fields nucleotideSequence :: Sequence aligned :: Int recordDescription :: ByteString

Instances

Show SequenceRecord Source #
Methods showsPrec :: Int -> SequenceRecord -> ShowS # show :: SequenceRecord -> String # showList :: [SequenceRecord] -> ShowS #

Constructors

CMsearch
Fields queryCMfile :: String targetSequenceDatabase :: String numberOfWorkerThreads :: String cmsearchHits :: [CMsearchHit]

Instances

Eq CMsearch Source #
Methods (==) :: CMsearch -> CMsearch -> Bool # (/=) :: CMsearch -> CMsearch -> Bool #
Read CMsearch Source #
Methods readsPrec :: Int -> ReadS CMsearch # readList :: ReadS [CMsearch] # readPrec :: ReadPrec CMsearch # readListPrec :: ReadPrec [CMsearch] #
Show CMsearch Source #
Methods showsPrec :: Int -> CMsearch -> ShowS # show :: CMsearch -> String # showList :: [CMsearch] -> ShowS #

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 Source #
Methods (==) :: CMsearchHit -> CMsearchHit -> Bool # (/=) :: CMsearchHit -> CMsearchHit -> Bool #
Read CMsearchHit Source #
Methods readsPrec :: Int -> ReadS CMsearchHit # readList :: ReadS [CMsearchHit] # readPrec :: ReadPrec CMsearchHit # readListPrec :: ReadPrec [CMsearchHit] #
Show CMsearchHit Source #
Methods showsPrec :: Int -> CMsearchHit -> ShowS # show :: CMsearchHit -> String # showList :: [CMsearchHit] -> ShowS #

Constructors

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

Instances

Show SearchResult Source #
Methods showsPrec :: Int -> SearchResult -> ShowS # show :: SearchResult -> String # showList :: [SearchResult] -> ShowS #

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 Source #
Methods (==) :: CMstat -> CMstat -> Bool # (/=) :: CMstat -> CMstat -> Bool #
Read CMstat Source #
Methods readsPrec :: Int -> ReadS CMstat # readList :: ReadS [CMstat] # readPrec :: ReadPrec CMstat # readListPrec :: ReadPrec [CMstat] #
Show CMstat Source #
Methods showsPrec :: Int -> CMstat -> ShowS # show :: CMstat -> String # showList :: [CMstat] -> ShowS #