BiobaseInfernal-0.7.0.1: Infernal data structures and tools

Safe HaskellNone

Biobase.SElab.Types

Contents

Description

Infernal Stockholm files and covariance models, and other related files use a bunch of different identifiers. We provide newtypes for more type safety.

TODO Use (Bio.Core.Sequence.Offset) instead of Int for sequence info

TODO move BitScores, null models, probabilities into its own library.

Synopsis

Accession and string Identifier with phantom types.

newtype Accession t Source

Accession number, in the format of RFxxxxx, PFxxxxx, or CLxxxxx. We keep only the Int-part. A phantom type specifies which kind of accession number this is. For Species, we just have an index, it seems.

Constructors

ACC 

Fields

unACC :: Int
 

Instances

newtype Identification t Source

One word name for the family or clan. Phantom-typed with the correct type of model. Can be a longer name for species.

Constructors

IDD 

Fields

unIDD :: ByteString
 

data Clan Source

Tag as being a clan.

data Pfam Source

Tag as being a Pfam model.

data Rfam Source

Tag as being an Rfam model. Used for Stockholm and CM files.

data Species Source

Species have an accession number, too.

newtype BitScore Source

Infernal bit score. Behaves like a double (deriving Num).

Infernal users guide, p.42: log-odds score in log_2 (aka bits).

S = log_2 (P(seq|CM) / P(seq|null))

Constructors

BitScore 

Fields

unBitScore :: Double
 

prob2Score :: Double -> Double -> BitScoreSource

Given a null model and a probability, calculate the corresponding BitScore.

score2Prob :: Double -> BitScore -> DoubleSource

Given a null model and a BitScore return the corresponding probability.

newtype Classification Source

Classification names (taxonomic classification)