| Safe Haskell | None |
|---|
Biobase.SElab.HMM
- data HMM
- data Alphabet
- newtype NegLogProb = NLP Double
- data Node = Node {
- _nid :: Int
- _matchE :: [NegLogProb]
- _insertE :: [NegLogProb]
- _trans :: [NegLogProb]
- trans :: Lens' Node [NegLogProb]
- nid :: Lens' Node Int
- matchE :: Lens' Node [NegLogProb]
- insertE :: Lens' Node [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 (ByteString, ByteString)
- transHeaders :: Lens' HMM3 [ByteString]
- symAlph :: Lens' HMM3 [ByteString]
- rf :: Lens' HMM3 Bool
- nodes :: Lens' HMM3 [Node]
- leng :: Lens' HMM3 Int
- idd :: Lens' HMM3 (Identification HMM)
- description :: Lens' HMM3 (Maybe ByteString)
- date :: Lens' HMM3 ByteString
- cs :: Lens' HMM3 Bool
- compo :: Lens' HMM3 [NegLogProb]
- alph :: Lens' HMM3 Alphabet
- alignMap :: Lens' HMM3 Bool
- acc :: Lens' HMM3 (Maybe (Accession HMM))
Documentation
newtype NegLogProb Source
Negated natural logarithm of probability.
TODO put into types stuff
Instances
The nodes in an HMM. Starting with Node 0 for BEGIN.
Constructors
| Node | |
Fields
| |
trans :: Lens' Node [NegLogProb]Source
matchE :: Lens' Node [NegLogProb]Source
insertE :: Lens' Node [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?
Constructors
| HMM3 | |
Fields
| |
symAlph :: Lens' HMM3 [ByteString]Source
compo :: Lens' HMM3 [NegLogProb]Source