Biobase.Infernal.CM

Data types for Covariance Models

data CM n s

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

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

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

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

Constructors

CMProb

CMScore

Instances

Eq CMType

Show CMType

data Emission

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

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

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

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 s

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

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

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

Transform between score and probability mode

cmScore2Prob :: CM n s -> CM n s

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

cmProb2Score :: CM n s -> CM n s

Given a CM in prob mode, change to score mode

cmNormalizeProbabilities :: CM n s -> CM n s

normalize all PROBabilities in a CM

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

localBeginScore2Prob :: Array Int Double -> Array Int Double

localEndScore2Prob :: Array Int Double -> Array Int Double

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

localBeginProb2Score :: Array Int Double -> Array Int Double

localEndProb2Score :: Array Int Double -> Array Int Double

Helper Functions

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

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

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

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

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

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

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

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 s

Transform a state, setting scores instead of probabilities.

transitionTargets :: [Transition] -> [Int]

nodeMainStateAssocs :: [(NodeType, StateType)]