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• get() : StochHMM::simpleTable< T > , StochHMM::nthTrace
• get_dbl_posterior() : StochHMM::trellis
• get_emission() : StochHMM::emm
• get_emission_prob() : StochHMM::state
• get_explicit() : StochHMM::model
• get_explicit_duration_length() : StochHMM::trellis
• get_hit_table() : StochHMM::multiTraceback
• get_index() : StochHMM::sequence
• get_intersection() : StochHMM::dynamic_bitset
• get_model() : StochHMM::trellis
• get_naive_backward_scores() : StochHMM::trellis
• get_naive_forward_scores() : StochHMM::trellis
• get_naive_viterbi_scores() : StochHMM::trellis
• get_reduced_order() : StochHMM::transition
• get_state_position() : StochHMM::stochTable
• get_transition_prob() : StochHMM::state
• get_union() : StochHMM::dynamic_bitset
• get_unique() : StochHMM::dynamic_bitset
• getAbsolute() : StochHMM::weight
• getAbsState() : StochHMM::ExDefSequence
• getAlignment() : StochHMM::alignment
• getAlignmentSize() : StochHMM::alignment
• getAlpha() : StochHMM::track
• getAlphaMax() : StochHMM::track
• getAlphaSize() : StochHMM::lexicalTable , StochHMM::track
• getAlphaType() : StochHMM::track
• getAmbDefinedScore() : StochHMM::lexicalTable
• getAmbiguousCharacter() : StochHMM::track
• getAmbiguousScore() : StochHMM::lexicalTable
• getAmbiguousSet() : StochHMM::track
• getAmbiguousSize() : StochHMM::track
• getAmbScoringType() : StochHMM::lexicalTable
• getAttrib() : StochHMM::sequence , StochHMM::sequences
• getAuthor() : StochHMM::model
• getBackwardProbability() : StochHMM::trellis
• getBackwardTable() : StochHMM::trellis
• getCombineName() : StochHMM::transitionFuncParam
• getCombineType() : StochHMM::transitionFuncParam
• getCommand() : StochHMM::model
• getComment() : StochHMM::stringList
• getComplementIndex() : StochHMM::track
• getComplementSymbol() : StochHMM::track
• getCountsTable() : StochHMM::lexicalTable
• getDate() : StochHMM::model
• getDef() : StochHMM::ambigCharacter
• getDescription() : StochHMM::model , StochHMM::track
• getDigitalSeq() : StochHMM::sequence
• getDistanceToAttrib() : StochHMM::model
• getDNA() : trainingSeq
• getEmission() : StochHMM::matrixPosition , StochHMM::state
• getEmissionFunction() : StochHMM::StateFuncs
• getEmissionValue() : StochHMM::matrixPosition
• getEnding() : StochHMM::model , StochHMM::state
• getEndingFrom() : StochHMM::model
• getEndingTransition() : StochHMM::trellis
• getEndTrans() : StochHMM::state
• getExDef() : StochHMM::seqTracks , StochHMM::sequence
• getExtFunction() : StochHMM::emm , StochHMM::transition
• getFasta() : StochHMM::seqTracks , StochHMM::sequence , StochHMM::sequenceStream
• getFastas() : StochHMM::sequences
• getFastq() : StochHMM::seqTracks , StochHMM::sequence
• getForwardProbability() : StochHMM::trellis
• getForwardTable() : StochHMM::trellis
• getFrom() : StochHMM::state
• getFunction() : StochHMM::TrackFuncs
• getGFF() : StochHMM::state
• getHeader() : StochHMM::seqJob , StochHMM::sequence , StochHMM::sequences , trainingSeq
• getHighScore() : StochHMM::alignment
• getIndex() : StochHMM::track
• getInformation() : StochHMM::seqTracks
• getInitial() : StochHMM::model
• getInitialTo() : StochHMM::model
• getIterator() : StochHMM::state
• getJob() : StochHMM::seqTracks
• getLabel() : StochHMM::state
• getLength() : StochHMM::sequence , StochHMM::sequences
• getLexicalFunctionName() : StochHMM::transition
• getLine() : StochHMM::stringList
• getLogEmm() : StochHMM::lexicalTable
• getLogProbabilityTable() : StochHMM::lexicalTable
• getMask() : StochHMM::sequence , trainingSeq
• getMaskedFasta() : StochHMM::sequence
• getMaxAmbiguous() : StochHMM::track
• getMaxMask() : StochHMM::sequence
• getMaxUnambiguous() : StochHMM::track
• getModel() : StochHMM::models , StochHMM::seqJob , StochHMM::traceback_path , StochHMM::trellis
• getMultivariatePdfFunction() : StochHMM::StateFuncs
• getName() : StochHMM::weight , StochHMM::model , StochHMM::emissionFuncParam , StochHMM::state , StochHMM::track , StochHMM::transition
• getNext() : StochHMM::seqTracks
• getNumberOfAlphabets() : StochHMM::lexicalTable
• getopt() : StochHMM::options
• getOrder() : StochHMM::lexicalTable
• getPath() : StochHMM::seqJob
• getPDFFunction() : StochHMM::StateFuncs
• getPosteriorTable() : StochHMM::trellis
• getProbabilityTable() : StochHMM::lexicalTable
• getReal() : StochHMM::sequence , StochHMM::seqTracks
• getReducedOrder() : StochHMM::lexicalTable
• getScalingFactor() : StochHMM::model
• getScore() : StochHMM::traceback_path , StochHMM::cell
• getSeq() : StochHMM::sequences , StochHMM::trellis
• getSeqAttrib() : StochHMM::seqJob
• getSeqFilename() : StochHMM::seqJob
• getSeqs() : StochHMM::seqJob
• getSequence() : trainingSeq
• getState() : StochHMM::model , StochHMM::ExDef , StochHMM::model , StochHMM::transition
• getStateGFF() : StochHMM::model
• getStateInfo() : StochHMM::model
• getStateLabel() : StochHMM::model
• getStateName() : StochHMM::model
• getStateXFrom() : StochHMM::model
• getStateXTo() : StochHMM::model
• getSymbol() : StochHMM::sequence , StochHMM::ambigCharacter
• getTables() : StochHMM::emm
• getTemplate() : StochHMM::stencil , StochHMM::templates
• getThreshold() : StochHMM::matrixPosition
• getThresholdPtr() : StochHMM::matrixPosition
• getTo() : StochHMM::state
• getTotalAlphabetSize() : StochHMM::track
• getTraceback() : StochHMM::cell
• getTracebackIdentifier() : StochHMM::transition
• getTracebackName() : StochHMM::transitionFuncParam
• getTracebackString() : StochHMM::transition
• getTracebackType() : StochHMM::transitionFuncParam
• getTrack() : StochHMM::lexicalTable , StochHMM::model , StochHMM::tracks , StochHMM::transitionFuncParam , StochHMM::emissionFuncParam , StochHMM::PWM , StochHMM::sequence , StochHMM::model
• getTrackCount() : StochHMM::seqTracks
• getTrackFunction() : StochHMM::track
• getTrackIter() : StochHMM::model
• getTrackName() : StochHMM::emissionFuncParam , StochHMM::transitionFuncParam
• getTracks() : StochHMM::model
• getTrackToUse() : StochHMM::track
• getTrans() : StochHMM::state
• getTransition() : StochHMM::transition , StochHMM::trellis
• getTransitionFunction() : StochHMM::StateFuncs
• getTransitionNames() : StochHMM::matrixPosition
• getTransitions() : StochHMM::state
• getTransitionType() : StochHMM::transition
• getUnambiguousSet() : StochHMM::track
• getUndigitized() : StochHMM::sequences , StochHMM::sequence
• getValue() : StochHMM::lexicalTable
• getWeight() : StochHMM::weightDef , StochHMM::sequences , StochHMM::ExDefSequence , StochHMM::ExDef
• getWeightedScore() : StochHMM::weight
• gff() : StochHMM::traceback_path
• good() : trainingSeqs