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.getMatch(int indx)
          Retrieve the match state at column indx.
 EmissionState ProfileHMM.getInsert(int indx)
          Retrieves the insert 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
protected  EmissionState HmmerProfileHMM.makeNewInsertState(java.lang.String str, Annotation ann, int[] adv, Distribution dis)
           
protected  EmissionState HmmerProfileHMM.makeNewMatchState(java.lang.String str, Annotation ann, int[] adv, Distribution dis)
           
 EmissionState FullHmmerProfileHMM.jState()
          Gets the J loop state
 EmissionState FullHmmerProfileHMM.cState()
          Gets the c loop state
 EmissionState FullHmmerProfileHMM.nState()
          Gets the n loop state