Interface StatePath
- All Superinterfaces:
Alignment
,Changeable
,SymbolList
- All Known Implementing Classes:
SimpleStatePath
A state path should have the following structure:
SCORES -> list of step-wise scores for each state (transition + emission)
SEQUENCE -> sequence emitted by the machine
SEQUENCE
-> Gapped view (gap inserted for every position aligned with a dot-state
-> Sequence emitted by emission states as Alignment
label_n = input_SymbolList_n
-> gapped view of SymbolList_n
I think that this scheme keeps the emitted alignment as close as possible to a sensible path through the sequence coordinate space, while making this gappable adapts this to the same co-ordinate system as the HMM state-path space.
- Author:
- Matthew Pocock
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Nested Class Summary
Nested classes/interfaces inherited from interface org.biojava.bio.alignment.Alignment
Alignment.SymbolListIterator
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final Object
Alignment label for the likelyhood at each step.static final Object
Alignment label for the emitted sequence.static final Object
Alignment label for the state path.Fields inherited from interface org.biojava.bio.symbol.SymbolList
EDIT, EMPTY_LIST
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Method Summary
Modifier and TypeMethodDescriptiondouble
getScore()
Return the overall score for this state-path and it's emissions.Methods inherited from interface org.biojava.bio.alignment.Alignment
getLabels, subAlignment, symbolAt, symbolListForLabel, symbolListIterator
Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
Methods inherited from interface org.biojava.bio.symbol.SymbolList
edit, getAlphabet, iterator, length, seqString, subList, subStr, symbolAt, toList
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Field Details
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SEQUENCE
Alignment label for the emitted sequence. -
STATES
Alignment label for the state path. -
SCORES
Alignment label for the likelyhood at each step.
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Method Details
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getScore
double getScore()Return the overall score for this state-path and it's emissions.- Returns:
- the score
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