Safe Haskell	None
Language	Haskell2010

Biobase.RNAlien.Types

Description

This module contains data structures for RNAlien

Synopsis

data StaticOptions = StaticOptions {
- 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
- offline :: Bool
}
data ModelConstruction = ModelConstruction {
- iterationNumber :: Int
- inputFasta :: [Fasta () ()]
- taxRecords :: [TaxonomyRecord]
- upperTaxonomyLimit :: Maybe Int
- taxonomicContext :: Maybe Taxon
- evalueThreshold :: Double
- alignmentModeInfernal :: Bool
- selectedQueries :: [Fasta () ()]
- potentialMembers :: [SearchResult]
- genomeFastas :: [Fasta () ()]
}
data TaxonomyRecord = TaxonomyRecord {
- recordTaxonomyId :: Int
- sequenceRecords :: [SequenceRecord]
}
data SequenceRecord = SequenceRecord {
- nucleotideSequence :: Fasta () ()
- aligned :: Int
- recordDescription :: ByteString
}
data CMsearch = CMsearch {
- queryCMfile :: String
- targetSequenceDatabase :: String
- numberOfWorkerThreads :: String
- cmsearchHits :: [CMsearchHit]
}
data CMsearchHit = CMsearchHit {
- 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
}
data SearchResult = SearchResult {
- candidates :: [(Fasta () (), Int, ByteString)]
- blastDatabaseSize :: Maybe Double
}
data CMstat = CMstat {
- statIndex :: Int
- statName :: String
- statAccession :: String
- statSequenceNumber :: Int
- statEffectiveSequences :: Double
- statConsensusLength :: Int
- statW :: Int
- statBasepairs :: Int
- statBifurcations :: Int
- statModel :: String
- relativeEntropyCM :: Double
- relativeEntropyHMM :: Double
}

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

Instances

Show StaticOptions Source #
Instance details Defined in Biobase.RNAlien.Types Methods showsPrec :: Int -> StaticOptions -> ShowS # show :: StaticOptions -> String # showList :: [StaticOptions] -> ShowS #

data ModelConstruction Source #

Keeps track of model construction

Constructors

ModelConstruction
Fields iterationNumber :: Int inputFasta :: [Fasta () ()] taxRecords :: [TaxonomyRecord] upperTaxonomyLimit :: Maybe Int taxonomicContext :: Maybe Taxon evalueThreshold :: Double alignmentModeInfernal :: Bool selectedQueries :: [Fasta () ()] potentialMembers :: [SearchResult] genomeFastas :: [Fasta () ()]

Instances

Show ModelConstruction Source #
Instance details Defined in Biobase.RNAlien.Types Methods showsPrec :: Int -> ModelConstruction -> ShowS # show :: ModelConstruction -> String # showList :: [ModelConstruction] -> ShowS #

data TaxonomyRecord Source #

Constructors

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

Instances

Show TaxonomyRecord Source #
Instance details Defined in Biobase.RNAlien.Types Methods showsPrec :: Int -> TaxonomyRecord -> ShowS # show :: TaxonomyRecord -> String # showList :: [TaxonomyRecord] -> ShowS #

data SequenceRecord Source #

Constructors

SequenceRecord
Fields nucleotideSequence :: Fasta () () aligned :: Int recordDescription :: ByteString

Instances

Show SequenceRecord Source #
Instance details Defined in Biobase.RNAlien.Types Methods showsPrec :: Int -> SequenceRecord -> ShowS # show :: SequenceRecord -> String # showList :: [SequenceRecord] -> ShowS #

data CMsearch Source #

Constructors

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

Instances

Eq CMsearch Source #
Instance details Defined in Biobase.RNAlien.Types Methods (==) :: CMsearch -> CMsearch -> Bool # (/=) :: CMsearch -> CMsearch -> Bool #
Read CMsearch Source #
Instance details Defined in Biobase.RNAlien.Types Methods readsPrec :: Int -> ReadS CMsearch # readList :: ReadS [CMsearch] # readPrec :: ReadPrec CMsearch # readListPrec :: ReadPrec [CMsearch] #
Show CMsearch Source #
Instance details Defined in Biobase.RNAlien.Types Methods showsPrec :: Int -> CMsearch -> ShowS # show :: CMsearch -> String # showList :: [CMsearch] -> ShowS #

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

Eq CMsearchHit Source #
Instance details Defined in Biobase.RNAlien.Types Methods (==) :: CMsearchHit -> CMsearchHit -> Bool # (/=) :: CMsearchHit -> CMsearchHit -> Bool #
Read CMsearchHit Source #
Instance details Defined in Biobase.RNAlien.Types Methods readsPrec :: Int -> ReadS CMsearchHit # readList :: ReadS [CMsearchHit] # readPrec :: ReadPrec CMsearchHit # readListPrec :: ReadPrec [CMsearchHit] #
Show CMsearchHit Source #
Instance details Defined in Biobase.RNAlien.Types Methods showsPrec :: Int -> CMsearchHit -> ShowS # show :: CMsearchHit -> String # showList :: [CMsearchHit] -> ShowS #

data SearchResult Source #

Constructors

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

Instances

Show SearchResult Source #
Instance details Defined in Biobase.RNAlien.Types Methods showsPrec :: Int -> SearchResult -> ShowS # show :: SearchResult -> String # showList :: [SearchResult] -> ShowS #

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

Eq CMstat Source #
Instance details Defined in Biobase.RNAlien.Types Methods (==) :: CMstat -> CMstat -> Bool # (/=) :: CMstat -> CMstat -> Bool #
Read CMstat Source #
Instance details Defined in Biobase.RNAlien.Types Methods readsPrec :: Int -> ReadS CMstat # readList :: ReadS [CMstat] # readPrec :: ReadPrec CMstat # readListPrec :: ReadPrec [CMstat] #
Show CMstat Source #
Instance details Defined in Biobase.RNAlien.Types Methods showsPrec :: Int -> CMstat -> ShowS # show :: CMstat -> String # showList :: [CMstat] -> ShowS #