Here is a list of all class members with links to the classes they belong to:

- s -

• same_length : StochHMM::sequences
• scaling : StochHMM::model , StochHMM::models
• score : StochHMM::cell , StochHMM::PWM , StochHMM::gff_feature , StochHMM::traceback_path , StochHMM::nthScore
• score_tb : StochHMM::nthScore
• scores : StochHMM::cell , StochHMM::emm
• scoreSimple() : StochHMM::PWM
• scoreTable : StochHMM::transition
• scoreUndefSpacer() : StochHMM::PWM
• scoreVariableSpacer() : StochHMM::PWM
• scoring_current : StochHMM::trellis
• scoring_previous : StochHMM::trellis
• seq : StochHMM::sequence , StochHMM::sequences , trainingSeq
• seq_length : StochHMM::alt_simple_stochTable
• seq_size : StochHMM::trellis
• seqFilename : StochHMM::seqJob
• seqFilenames : StochHMM::seqTracks
• seqFiles : trainingSeqs
• seqFormat : StochHMM::seqTracks
• seqJob() : StochHMM::seqJob
• seqLength : StochHMM::Counter
• seqname : StochHMM::gff_feature
• seqs : trainingSeqs , StochHMM::trellis
• seqTracks : StochHMM::seqJob , trainingEmission , StochHMM::seqTracks
• seqtrk : StochHMM::Counter , StochHMM::sequence
• sequence() : StochHMM::sequence , trainingSeq
• sequences : StochHMM::ExDefSequence , StochHMM::sequence , StochHMM::sequences
• sequencesCounted : StochHMM::Counter
• sequenceStream : StochHMM::sequence , StochHMM::sequenceStream
• seqValue() : StochHMM::sequence , StochHMM::sequences
• set : StochHMM::opt_data , StochHMM::seqJob , 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
• setDefinition : StochHMM::ambigCharacter
• 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::transition , StochHMM::weight , StochHMM::model , StochHMM::state , StochHMM::track
• 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 : StochHMM::PWM
• 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 >
• simpleThreshold : StochHMM::PWM
• size() : StochHMM::dynamic_bitset , StochHMM::models , StochHMM::seqTracks , StochHMM::seqJob , StochHMM::sequence , StochHMM::sequences , StochHMM::simpleTable< T > , StochHMM::sparseArray< T > , StochHMM::traceback_path , StochHMM::multiTraceback , StochHMM::tracks , StochHMM::weight , trainingSeq , StochHMM::stringList , StochHMM::Index
• sopt() : StochHMM::options
• source : StochHMM::gff_feature
• 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
• st_tb : StochHMM::nthScore
• start : StochHMM::gff_feature
• start_position : StochHMM::alignment
• state : StochHMM::transition , StochHMM::state , StochHMM::track , StochHMM::emm , StochHMM::state
• state_id : StochHMM::stochTable::stoch_value
• state_prev : StochHMM::stochTable::stoch_value
• state_size() : StochHMM::model , StochHMM::trellis
• state_val : StochHMM::stochTable
• stateByName : StochHMM::model
• stateEmm : trainingSeqs
• StateFuncs() : StochHMM::StateFuncs
• stateIterator : StochHMM::state
• stateIterByGff : StochHMM::stateInfo
• stateIterByLabel : StochHMM::stateInfo
• stateIterByName : StochHMM::stateInfo
• stateMask : trainingSeqs
• stateName : StochHMM::transition
• states : StochHMM::stencil , StochHMM::model , StochHMM::alt_simple_stochTable
• stencil() : StochHMM::stencil
• stoch_val() : StochHMM::alt_simple_stochTable::stoch_val
• stoch_value() : StochHMM::stochTable::stoch_value
• stochastic_forward() : StochHMM::trellis
• stochastic_table : StochHMM::trellis
• stochastic_traceback() : StochHMM::trellis
• stochastic_viterbi() : StochHMM::trellis
• stochasticTraceback() : StochHMM::alignment
• stochTable() : StochHMM::stochTable
• store() : StochHMM::trellis
• store_values : StochHMM::trellis
• str : StochHMM::opt_data
• strand : StochHMM::gff_feature
• stringify() : StochHMM::ExDefSequence , StochHMM::emm , StochHMM::ExDef , StochHMM::weightDef , StochHMM::stencil , StochHMM::weights , StochHMM::weight , StochHMM::track , StochHMM::dynamic_bitset , StochHMM::model , StochHMM::PWM , StochHMM::trellis , StochHMM::matrixPosition , StochHMM::tracks , StochHMM::state , StochHMM::templates , StochHMM::emissionFuncParam , StochHMM::transitionFuncParam , StochHMM::sequence , StochHMM::lexicalTable , StochHMM::sequences , StochHMM::transition , StochHMM::stochTable , StochHMM::alt_simple_stochTable , StochHMM::stringList
• stringify_all() : StochHMM::dynamic_bitset
• stringifyAmbig() : StochHMM::lexicalTable , StochHMM::track
• stringList() : StochHMM::stringList
• subarray_length : StochHMM::simpleTable< T >
• subarray_position : StochHMM::lexicalTable
• subarray_sequence : StochHMM::lexicalTable
• subarray_value : StochHMM::lexicalTable
• swap_ptr : StochHMM::trellis
• swap_ptr_duration : StochHMM::trellis
• symbol : StochHMM::ambigCharacter
• symbolIndex() : StochHMM::track
• symbolIndices : StochHMM::track