Biobase.Infernal.CM

Contents

Synopsis

Data types for Covariance Models

A complete covariance model. Each node and each state can be tagged with additional data. Typically, say after parsing, the tag will be ().

Constructors

CM
Fields nodes :: Array Int (Node n) states :: Array Int (State s) header :: [(String, String)] localBegin :: Array Int Double localEnd :: Array Int Double cmType :: CMType nullModel :: Array Nucleotide Double

Instances

(Show n, Show s) => Show (CM n s)

data Node n Source

Describes one node

Constructors

Node
Fields nid :: Int ntype :: NodeType nparents :: [Int] nchildren :: [Int] nstates :: [Int] ntag :: n

Instances

Show n => Show (Node n)

data State s Source

One state

Constructors

State
Fields sid :: Int stype :: StateType snode :: Int sparents :: [Int] schildren :: [Transition] semission :: [Emission] stag :: s

Instances

Show s => Show (State s)

data CMType Source

CMType is important if we want to set localBegin / localEnd!

Constructors

CMProb
CMScore

Instances

Eq CMType
Show CMType

data Emission Source

can emit either one nucleotide or a pair

Constructors

EmitS
Fields eNuc :: Nucleotide escore :: Double
EmitP
Fields eNucL :: Nucleotide eNucR :: Nucleotide escore :: Double

Instances

Show Emission

data Transition Source

branches are transition without attached probability becaue both branches are always taken

Constructors

Branch
Fields tchild :: Int
Transition
Fields tchild :: Int tscore :: Double

Instances

Show Transition

data NodeType Source

the different node types

Constructors

MATP
MATL
MATR
BIF
ROOT
BEGL
BEGR
END

Instances

Bounded NodeType
Enum NodeType
Eq NodeType
Ord NodeType
Read NodeType
Show NodeType

data StateType Source

the different state types

Constructors

MP
IL
IR
D
ML
MR
B
S
E

Instances

Bounded StateType
Enum StateType
Eq StateType
Ord StateType
Read StateType
Show StateType

make a local model out of a global one

cmMakeLocal :: Double -> Double -> CM n s -> CM n sSource

generate a local model with local begin prob and local end prob

cmMakeLocalBegin :: Double -> CM n s -> CM n sSource

cmMakeLocalEnd :: Double -> CM n s -> CM n sSource

Transform between score and probability mode

cmScore2Prob :: CM n s -> CM n sSource

given a CM in score mode, change it to probability mode

cmProb2Score :: CM n s -> CM n sSource

Given a CM in prob mode, change to score mode

cmNormalizeProbabilities :: CM n s -> CM n sSource

normalize all PROBabilities in a CM

statesScore2Prob :: CM n s -> Array Int (State s) -> Array Int (State s)Source

localBeginScore2Prob :: Array Int Double -> Array Int Double Source

localEndScore2Prob :: Array Int Double -> Array Int Double Source

statesProb2Score :: CM n s -> Array Int (State s) -> Array Int (State s)Source

localBeginProb2Score :: Array Int Double -> Array Int Double Source

localEndProb2Score :: Array Int Double -> Array Int Double Source

Helper Functions

nodeMainState :: CM n s -> Node n -> State sSource

extract the main state for each node (eg MP state for MATP node)

localBeginPossible :: CM n s -> Node n -> Bool Source

Checks for each node, if it can be target of a local begin.

localEndPossible :: CM n s -> Node n -> Bool Source

Checks for each node if it can lead to a local end.

stateScore2Prob :: CM n s -> State s -> State sSource

transform scores into probabilities, given a nullmodel for x

back into scores

Transform a state, setting probabilities instead of scores. Requires CM knowledge for background model.

stateProb2Score :: CM n s -> State s -> State sSource

Transform a state, setting scores instead of probabilities.

transitionTargets :: [Transition] -> [Int]Source

nodeMainStateAssocs :: [(NodeType, StateType)]Source