RNAlien-1.1.0: Unsupervized construction of RNA family models

Safe HaskellNone
LanguageHaskell98

Bio.RNAlienData

Description

This module contains data structures for RNAlien

Synopsis

Documentation

data StaticOptions Source

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
 
cpuThreads :: Int
 
blastDatabase :: Maybe String
 
taxRestriction :: Maybe String
 
verbositySwitch :: Bool
 

Instances

data ModelConstruction Source

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 :: [String]
 
potentialMembers :: [SearchResult]
 

Instances

data TaxonomyRecord Source

Constructors

TaxonomyRecord 

Fields

recordTaxonomyId :: Int
 
sequenceRecords :: [SequenceRecord]
 

Instances

data SequenceRecord Source

Constructors

SequenceRecord 

Fields

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

Instances

data CMsearch Source

Constructors

CMsearch 

Fields

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

Instances

data CMsearchHit Source

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

data SearchResult Source

Constructors

SearchResult 

Fields

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

Instances

data CMstat Source

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