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A state in a markov process that has an emission spectrum.
These states have an associated Distribution. Within an HMM, these are the states that actualy make your observed sequence. They also must supply training behaviour to set the emission spectrum up.
Nested Class Summary |
Nested classes inherited from class org.biojava.bio.Annotatable |
Annotatable.AnnotationForwarder |
Field Summary | |
static ChangeType |
ADVANCE
This signals that the advance array has been altered. |
static ChangeType |
DISTRIBUTION
This signals that the distribution associate with an EmissionState has been altered. |
Fields inherited from interface org.biojava.bio.Annotatable |
ANNOTATION |
Method Summary | |
int[] |
getAdvance()
Determine the number of symbols this state advances along one or more symbol lists. |
Distribution |
getDistribution()
Get the Distribution associated with this state. |
void |
setAdvance(int[] advance)
Set the advance array. |
void |
setDistribution(Distribution dis)
Set the Distribution associated with this state. |
Methods inherited from interface org.biojava.bio.symbol.BasisSymbol |
getSymbols |
Methods inherited from interface org.biojava.bio.symbol.Symbol |
getMatches, getName |
Methods inherited from interface org.biojava.bio.Annotatable |
getAnnotation |
Methods inherited from interface org.biojava.utils.Changeable |
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener |
Methods inherited from interface org.biojava.bio.dp.Trainable |
registerWithTrainer |
Field Detail |
public static final ChangeType DISTRIBUTION
This signals that the distribution associate with an EmissionState has been altered.
If the distribution has changed its weights, then the event'e getChainedEvent method will return the event fired by the distribution. If one distribution has been replaced by another, then the new and old Distributions will be in current and previous, respectively.
public static final ChangeType ADVANCE
This signals that the advance array has been altered.
current and previous should hold the current and previous advances, respectively.
Method Detail |
public int[] getAdvance()
public void setAdvance(int[] advance) throws ChangeVetoException
advance
- an array of ints, specifying how many symbols are consumed
from each sequence
ChangeVetoException
- if the implementation doesn't support setting
advance, or if the change is vetoedpublic Distribution getDistribution()
Get the Distribution associated with this state.
If the state is to be added to an HMM, then the state's emission spectrum must be compatible with the HMM - that is, their emission alphabets must match.
public void setDistribution(Distribution dis) throws ChangeVetoException
dis
- the new Distribution to use
ChangeVetoException
- if the implementation doesn't support setting
the distribution, or if the change is vetoed
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