Uses of Interface
org.biojava.bio.dp.EmissionState

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 and Description
class	MagicalState Start/end state for HMMs.
class	SimpleEmissionState

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

Modifier and Type	Method and 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 and Description
class	ProfileEmissionState A state in a HMMer model.

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

Modifier and Type	Method and 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