Safe Haskell | None |
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- data HMM
- data Alphabet
- newtype NegLogProb = NLP Double
- data Node = Node {
- _nid :: Int
- _matchE :: [NegLogProb]
- _insertE :: [NegLogProb]
- _trans :: [NegLogProb]
- trans :: Lens Node Node [NegLogProb] [NegLogProb]
- nid :: Lens Node Node Int Int
- matchE :: Lens Node Node [NegLogProb] [NegLogProb]
- insertE :: Lens Node Node [NegLogProb] [NegLogProb]
- data HMM3 = HMM3 {
- _version :: (ByteString, ByteString)
- _idd :: Identification HMM
- _acc :: Maybe (Accession HMM)
- _description :: Maybe ByteString
- _leng :: Int
- _alph :: Alphabet
- _rf :: Bool
- _cs :: Bool
- _alignMap :: Bool
- _date :: ByteString
- _symAlph :: [ByteString]
- _transHeaders :: [ByteString]
- _compo :: [NegLogProb]
- _nodes :: [Node]
- version :: Lens HMM3 HMM3 (ByteString, ByteString) (ByteString, ByteString)
- transHeaders :: Lens HMM3 HMM3 [ByteString] [ByteString]
- symAlph :: Lens HMM3 HMM3 [ByteString] [ByteString]
- rf :: Lens HMM3 HMM3 Bool Bool
- nodes :: Lens HMM3 HMM3 [Node] [Node]
- leng :: Lens HMM3 HMM3 Int Int
- idd :: Lens HMM3 HMM3 (Identification HMM) (Identification HMM)
- description :: Lens HMM3 HMM3 (Maybe ByteString) (Maybe ByteString)
- date :: Lens HMM3 HMM3 ByteString ByteString
- cs :: Lens HMM3 HMM3 Bool Bool
- compo :: Lens HMM3 HMM3 [NegLogProb] [NegLogProb]
- alph :: Lens HMM3 HMM3 Alphabet Alphabet
- alignMap :: Lens HMM3 HMM3 Bool Bool
- acc :: Lens HMM3 HMM3 (Maybe (Accession HMM)) (Maybe (Accession HMM))
Documentation
newtype NegLogProb Source
Negated natural logarithm of probability.
TODO put into types stuff
The nodes in an HMM. Starting with Node 0 for BEGIN.
Node | |
|
trans :: Lens Node Node [NegLogProb] [NegLogProb]Source
matchE :: Lens Node Node [NegLogProb] [NegLogProb]Source
insertE :: Lens Node Node [NegLogProb] [NegLogProb]Source
The HMM3 data structure in ``slow mode''.
TODO shouldn't this be Identification Pfam ?
TODO maybe redo the whole idd idea and just keep the string?
HMM3 | |
|
symAlph :: Lens HMM3 HMM3 [ByteString] [ByteString]Source
idd :: Lens HMM3 HMM3 (Identification HMM) (Identification HMM)Source
compo :: Lens HMM3 HMM3 [NegLogProb] [NegLogProb]Source