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

Packages that use EmissionState
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
`class` `MagicalState` Start/end state for HMMs.
`class` `SimpleEmissionState`

Methods in org.biojava.bio.dp that return EmissionState
`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
`class` `ProfileEmissionState` A state in a HMMer model.

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