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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
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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 | |
EmissionState |
FullHmmerProfileHMM.jState()
Gets the J loop state |
EmissionState |
FullHmmerProfileHMM.cState()
Gets the c loop state |
EmissionState |
FullHmmerProfileHMM.nState()
Gets the n loop state |
protected EmissionState |
HmmerProfileHMM.makeNewInsertState(java.lang.String str,
Annotation ann,
int[] adv,
Distribution dis)
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protected EmissionState |
HmmerProfileHMM.makeNewMatchState(java.lang.String str,
Annotation ann,
int[] adv,
Distribution dis)
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