- s -

• score() : StochHMM::PWM
• scoreSimple() : StochHMM::PWM
• scoreUndefSpacer() : StochHMM::PWM
• scoreVariableSpacer() : StochHMM::PWM
• seqJob() : StochHMM::seqJob
• seqTracks() : StochHMM::seqTracks
• sequence() : StochHMM::sequence , trainingSeq
• sequences() : StochHMM::sequences
• sequenceStream() : StochHMM::sequenceStream
• seqValue() : StochHMM::sequence , StochHMM::sequences
• set() : StochHMM::dynamic_bitset
• set_parameters() : StochHMM::options
• setAbsolute() : StochHMM::weight
• setAlphabet() : trainingSeqs
• setAlphaType() : StochHMM::track
• setAmbiguous() : StochHMM::Index , StochHMM::track
• setAttrib() : StochHMM::sequence
• setAttribFunc() : StochHMM::seqTracks
• setAuthor() : StochHMM::model
• setBackground() : StochHMM::PWM
• setBuffer() : StochHMM::sequenceStream
• setCommand() : StochHMM::model
• setComplement() : StochHMM::emm
• setCurrentThreshold() : StochHMM::PWM
• setDate() : StochHMM::model
• setDelimiters() : StochHMM::stringList
• setDesc() : StochHMM::model
• setDescription() : StochHMM::track
• setDiag() : StochHMM::cell
• setDistribution() : StochHMM::transition
• setEmissionFunc() : StochHMM::emissionFuncParam
• setEnd() : StochHMM::model
• setEndingTransition() : StochHMM::state
• setExDef() : StochHMM::sequences
• setGap() : StochHMM::alignment
• setGapExt() : StochHMM::alignment
• setGFF() : StochHMM::state
• setHeader() : StochHMM::sequence
• setIndex() : StochHMM::track
• setInit() : StochHMM::model
• setIter() : StochHMM::state
• setLabel() : StochHMM::state
• setLeft() : StochHMM::cell
• setLength() : StochHMM::sequences
• setLexicalFunction() : StochHMM::emm
• setLowerRange() : StochHMM::model
• setMasked() : trainingSeq
• setMatch() : StochHMM::alignment
• setMatrix() : StochHMM::alignment
• setMaxWeight() : StochHMM::weight
• setMinWeight() : StochHMM::weight
• setMismatch() : StochHMM::alignment
• setModel() : StochHMM::traceback_path
• setName() : StochHMM::model , StochHMM::state , StochHMM::track , StochHMM::transition , StochHMM::weight
• setNumericalAttrib() : StochHMM::model
• setNumImportJobs() : StochHMM::seqTracks
• setOrder() : StochHMM::Counter
• setPeriod() : StochHMM::Counter
• setPseudoCount() : StochHMM::Counter
• setQuery() : StochHMM::alignment
• setRealNumber() : StochHMM::emm
• setRealSeq() : StochHMM::sequence
• setRemoveWS() : StochHMM::stringList
• setRetain() : StochHMM::sequenceStream
• setScore() : StochHMM::cell , StochHMM::traceback_path
• setSeq() : StochHMM::sequence
• setSeqFilename() : StochHMM::seqJob
• setSimpleThreshold() : StochHMM::PWM
• setState() : StochHMM::ExDef , StochHMM::transition
• setTarget() : StochHMM::alignment
• setTB_Identifier() : StochHMM::transition
• setTB_String() : StochHMM::transition
• setThreshold() : StochHMM::matrixPosition
• setTraceback() : StochHMM::cell
• setTrack() : StochHMM::Counter , StochHMM::PWM , StochHMM::sequence
• setTrackFilename() : StochHMM::seqTracks
• setTrackFunc() : StochHMM::seqTracks
• setTransFunc() : StochHMM::transitionFuncParam
• setTransProb() : StochHMM::transition
• setTransTB() : StochHMM::transitionFuncParam
• setTransType() : StochHMM::transition
• setUnkScore() : StochHMM::lexicalTable
• setUnkScoreType() : StochHMM::lexicalTable
• setUp() : StochHMM::cell
• setUpperRange() : StochHMM::model
• setWeights() : StochHMM::weight
• setWhitespace() : StochHMM::stringList
• shuffle() : StochHMM::sequence
• simple_backward() : StochHMM::trellis
• simple_baum_welch() : StochHMM::trellis
• simple_forward() : StochHMM::trellis
• simple_nth_viterbi() : StochHMM::trellis
• simple_posterior() : StochHMM::trellis
• simple_simple_stochastic_viterbi() : StochHMM::trellis
• simple_stochastic_forward() : StochHMM::trellis
• simple_stochastic_viterbi() : StochHMM::trellis
• simple_viterbi() : StochHMM::trellis
• simpleTable() : StochHMM::simpleTable< T >
• size() : StochHMM::sequence , StochHMM::weight , StochHMM::tracks , StochHMM::simpleTable< T > , StochHMM::sparseArray< T > , StochHMM::Index , StochHMM::seqTracks , StochHMM::seqJob , StochHMM::simpleTable< T > , StochHMM::sequences , StochHMM::stringList , StochHMM::traceback_path , StochHMM::multiTraceback , trainingSeq , StochHMM::dynamic_bitset , StochHMM::models
• sopt() : StochHMM::options
• sparse_complex_backward() : StochHMM::trellis
• sparse_complex_baum_welch() : StochHMM::trellis
• sparse_complex_stochastic_forward() : StochHMM::trellis
• sparse_complex_viterbi() : StochHMM::trellis
• sparseArray() : StochHMM::sparseArray< T >
• splitND() : StochHMM::stringList
• splitString() : StochHMM::stringList
• state() : StochHMM::state
• state_size() : StochHMM::model
• StateFuncs() : StochHMM::StateFuncs
• stencil() : StochHMM::stencil
• stoch_val() : StochHMM::alt_simple_stochTable::stoch_val
• stoch_value() : StochHMM::stochTable::stoch_value
• stochastic_forward() : StochHMM::trellis
• stochastic_traceback() : StochHMM::trellis
• stochastic_viterbi() : StochHMM::trellis
• stochasticTraceback() : StochHMM::alignment
• stochTable() : StochHMM::stochTable
• store() : StochHMM::trellis
• stringify() : StochHMM::templates , StochHMM::state , StochHMM::ExDef , StochHMM::weightDef , StochHMM::stencil , StochHMM::weight , StochHMM::transition , StochHMM::tracks , StochHMM::sequences , StochHMM::transitionFuncParam , StochHMM::stochTable , StochHMM::emissionFuncParam , StochHMM::stringList , StochHMM::PWM , StochHMM::weights , StochHMM::matrixPosition , StochHMM::sequence , StochHMM::dynamic_bitset , StochHMM::track , StochHMM::lexicalTable , StochHMM::emm , StochHMM::ExDefSequence , StochHMM::trellis , StochHMM::alt_simple_stochTable , StochHMM::model
• stringify_all() : StochHMM::dynamic_bitset
• stringifyAmbig() : StochHMM::track , StochHMM::lexicalTable
• stringList() : StochHMM::stringList
• symbolIndex() : StochHMM::track