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

- p -

• parity() : StochHMM::dynamic_bitset
• parse() : StochHMM::emm , StochHMM::transitionFuncParam , StochHMM::model , StochHMM::transition , StochHMM::weight , StochHMM::stencil , StochHMM::emissionFuncParam , StochHMM::templates , StochHMM::PWM , StochHMM::emm , StochHMM::ExDefSequence , StochHMM::matrixPosition , StochHMM::state , StochHMM::model , StochHMM::track , StochHMM::transition
• parse_commandline() : StochHMM::options
• parseAmbiguous() : StochHMM::track
• pass_values : StochHMM::emm
• path : StochHMM::seqJob , StochHMM::traceback_path , StochHMM::multiTraceback
• pathAccess : StochHMM::multiTraceback
• paths : StochHMM::multiTraceback
• pdf : StochHMM::emm
• pdfFunctions : StochHMM::StateFuncs
• pdfName : StochHMM::emm
• period : StochHMM::Counter
• pop_back() : StochHMM::sparseArray< T >
• pop_ith() : StochHMM::stringList
• pos : StochHMM::dynamic_bitset::bit_ref
• position : StochHMM::stochTable
• positionMatrix : StochHMM::matrixPosition
• positionNames : StochHMM::PWM
• posterior() : StochHMM::trellis
• posterior_score : StochHMM::trellis
• postprocessTracks : StochHMM::seqTracks
• preset : StochHMM::opt_parameters
• prev_cell : StochHMM::stochTable::stoch_value
• previous_state : StochHMM::alt_simple_stochTable::stoch_val
• previousSeq : StochHMM::sequenceStream
• print() : StochHMM::weight , StochHMM::weights , StochHMM::trellis , StochHMM::stringList , StochHMM::ExDefSequence , StochHMM::sequences , StochHMM::emm , StochHMM::transitionFuncParam , StochHMM::emissionFuncParam , StochHMM::model , StochHMM::lexicalTable , StochHMM::stencil , StochHMM::templates , StochHMM::PWM , StochHMM::seqTracks , StochHMM::sequence , StochHMM::state , StochHMM::stochTable , StochHMM::alt_simple_stochTable , StochHMM::track , StochHMM::tracks , StochHMM::transition
• print_gff() : StochHMM::traceback_path , StochHMM::multiTraceback
• print_hits() : StochHMM::multiTraceback
• print_label() : StochHMM::traceback_path , StochHMM::multiTraceback
• print_path() : StochHMM::traceback_path , StochHMM::multiTraceback
• printAlignment() : StochHMM::alignment
• printFilenames() : StochHMM::seqJob
• printModel() : StochHMM::seqJob
• printSeq() : StochHMM::seqJob
• printTable() : StochHMM::Counter
• printTrellis() : StochHMM::alignment
• prob : StochHMM::stochTable::stoch_value , StochHMM::lexicalTable , StochHMM::alt_simple_stochTable::stoch_val
• processString() : StochHMM::stringList
• pseudoCount : StochHMM::Counter
• push() : StochHMM::alt_simple_stochTable , StochHMM::stochTable
• push_back() : StochHMM::traceback_path , StochHMM::dynamic_bitset , StochHMM::stringList , StochHMM::tracks , StochHMM::sparseArray< T >
• push_ending() : StochHMM::alt_simple_stochTable
• PWM() : StochHMM::PWM