Uses of Interface org.biojava.bio.dp.EmissionState (biojava-legacy 1.9.7 API)

Packages that use EmissionState

Package

Description

org.biojava.bio.dp

HMM and Dynamic Programming Algorithms.

org.biojava.bio.program.hmmer

Tools for working with profile Hidden Markov Models from the HMMer package.

Uses of EmissionState in org.biojava.bio.dp

Classes in org.biojava.bio.dp that implement EmissionState

Modifier and Type

Class

Description

final class

MagicalState

Start/end state for HMMs.

class

SimpleEmissionState

Methods in org.biojava.bio.dp that return EmissionState

Modifier and Type

Method

Description

EmissionState

ProfileHMM.getInsert(int indx)

Retrieves the insert state at column indx.

EmissionState

ProfileHMM.getMatch(int indx)

Retrieve the match state at column indx.
Uses of EmissionState in org.biojava.bio.program.hmmer

Classes in org.biojava.bio.program.hmmer that implement EmissionState

Modifier and Type

Class

Description

class

ProfileEmissionState

A state in a HMMer model.

Methods in org.biojava.bio.program.hmmer that return EmissionState

Modifier and Type

Method

Description

EmissionState

FullHmmerProfileHMM.cState()

Gets the c loop state

EmissionState

FullHmmerProfileHMM.jState()

Gets the J loop state

protected EmissionState

HmmerProfileHMM.makeNewInsertState(String str, Annotation ann, int[] adv, Distribution dis)

protected EmissionState

HmmerProfileHMM.makeNewMatchState(String str, Annotation ann, int[] adv, Distribution dis)

EmissionState

FullHmmerProfileHMM.nState()

Gets the n loop state