StochHMM
v0.34
Flexible Hidden Markov Model C++ Library and Application
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#include <hmm.h>
Public Member Functions | |
model () | |
Create a model. | |
std::string & | getName () |
Get the Name of the Model. | |
std::string & | getDescription () |
Get Description of model. | |
std::string & | getDate () |
Get Date of model. | |
std::string & | getCommand () |
Get Creation Command of model. | |
std::string & | getAuthor () |
Get Author of model. | |
size_t | state_size () |
Get the number of states that are defined in the model. | |
std::string & | getStateName (size_t iter) |
std::string & | getStateLabel (size_t iter) |
std::string & | getStateGFF (size_t iter) |
state * | getState (size_t iter) |
state * | getState (const std::string &) |
state * | operator[] (size_t iter) |
Get state by using iterator value. | |
std::bitset< STATE_MAX > * | getStateXTo (size_t iter) |
Get vector of states that state at index transitions to. | |
std::bitset< STATE_MAX > * | getInitialTo () |
Get vector of states that the initial state transitions to. | |
std::bitset< STATE_MAX > * | getStateXFrom (size_t iter) |
Get vector of states that transfer to the state at index. | |
std::bitset< STATE_MAX > * | getEndingFrom () |
Get list of states that transition to the ending state. | |
stateInfo * | getStateInfo () |
state * | getInitial () |
Get pointer to the initial state. | |
state * | getEnding () |
Get pointer to the ending state. | |
weight * | getScalingFactor (std::string &) |
double | getDistanceToAttrib (double) |
Get Distance from the model attrib values to user defined value. | |
size_t | track_size () |
Get the number of tracks defined in the model. | |
track * | getTrack (size_t iter) |
track * | getTrack (const std::string &) |
size_t | getTrackIter (const std::string &txt) |
tracks * | getTracks () |
bool | isBasic () |
void | print () |
Print model by std::cout. | |
std::string | stringify () |
bool | import (std::string &, StateFuncs *) |
bool | import (std::string &) |
bool | import (std::string &, StateFuncs *, templates *, weights *) |
bool | importFromString (std::string &) |
bool | importFromString (std::string &, StateFuncs *) |
Import and parse the model from std::string. | |
bool | importFromString (std::string &, StateFuncs *, templates *, weights *) |
Import and parse the model from std::string. | |
bool | parse (const std::string &, StateFuncs *, templates *, weights *) |
bool | parse (std::string &, std::string &) |
Parse the model from std::string. | |
void | setName (std::string &txt) |
Set the name of the model. | |
void | setDesc (std::string &txt) |
Set the model desc. | |
void | setDate (std::string &txt) |
Set the model creation date. | |
void | setCommand (std::string &txt) |
Set the model creation command. | |
void | setAuthor (std::string &txt) |
Set the model author. | |
void | setNumericalAttrib (float value) |
void | setUpperRange (float &value) |
Set the upper range of the attribute. | |
void | setLowerRange (float &value) |
Set the lower range of the attribute. | |
void | addTrack (track *trk) |
Add track to the model. | |
void | addState (state *) |
void | setInit (state *st) |
void | setEnd (state *st) |
Set teh ending state pointer. | |
void | finalize () |
bool | checkTopology () |
std::vector< bool > * | get_explicit () |
bool | hasComplexEmission () |
Private Member Functions | |
bool | _parseHeader (std::string &) |
States that have functions associated with emissions. | |
bool | _parseTracks (std::string &) |
Function to parse header of the model from text file. | |
bool | _parseAmbiguous (std::string &) |
Parse Tracks definitions from text file. | |
bool | _parseScaling (std::string &) |
Parse Ambiguous definitions from text file. | |
bool | _parseTemplates (std::string &) |
Parse Scaling definitions from text file. | |
bool | _parseStates (std::string &, StateFuncs *) |
Parse Templated States definitions from text file. | |
bool | _splitStates (std::string &, stringList &) |
Parse state from text file. | |
bool | _getOrderedStateNames (stringList &, stringList &) |
Split the state definitions into individual states from text file. | |
bool | _processTemplateState (std::string &, stringList &) |
Gets list of states names from model. | |
std::string | _stringifyHeader () |
Adds templated states to using template. | |
std::string | _stringifyTracks () |
Converts Header information from model to string representation found in text file. | |
std::string | _stringifyAmbig () |
Converts Tracks information from model to string representation found in text file. | |
std::string | _stringifyScaling () |
Converts Ambiguous Character information from model to text string. | |
std::string | _stringifyStates () |
Converts Scaling definitions from model to text string. | |
void | _addStateToFromTransition (state *) |
Converts States definitions from model to text string. | |
void | checkBasicModel () |
in banding the trellis decoding functions | |
void | checkExplicitDurationStates () |
Checks to see if the model has basic transitions and emissions(no addtl functions) | |
void | _checkTopology (state *st, std::vector< uint16_t > &visited) |
Checks to see which states are explicit duration states. |
Private Attributes | |
bool | finalized |
bool | basicModel |
std::string | name |
std::string | desc |
Model Name. | |
std::string | date |
Model Description. | |
std::string | command |
Model Creation Date. | |
std::string | author |
Model Creation Command. | |
float | range [2] |
Model Author. | |
bool | attribTwo |
Model Attrib Values. | |
tracks | trcks |
Two attrib Values. | |
std::vector< state * > | states |
Tracks defined by model (Contains alphabet and ambiguous character definitions. | |
std::map< std::string, state * > | stateByName |
All the states contained in the model. | |
stateInfo | info |
state * | initial |
state * | ending |
Initial state q0. | |
weights * | scaling |
Ending state. | |
templates * | templatedStates |
Weights or scaling fractors associated with the model. | |
std::vector< bool > * | explicit_duration_states |
Templated states. | |
std::vector< bool > * | complex_transition_states |
States that are explicit duration states. | |
std::vector< bool > * | complex_emission_states |
States that have functions associated with transitions. |
Hidden Markov Model Class model class combines the States, and model information together in a single unit. This includes the states(emissions, transitions), initial and ending states, track information(alphabet and ambiguous character definitions).
Provides functions to import the model from a text file
Model is used by trellis class to evaluates sequences.
StochHMM::model::model | ( | ) |
Create a model.
Definition at line 156 of file hmm.cpp.
References attribTwo, basicModel, complex_emission_states, complex_transition_states, ending, explicit_duration_states, finalized, initial, range, scaling, and templatedStates.
Referenced by stringify().
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Converts States definitions from model to text string.
Definition at line 1021 of file hmm.cpp.
References StochHMM::state::addFromState(), StochHMM::state::addToState(), StochHMM::state::endi, ending, getName(), getState(), StochHMM::state::getTransitions(), and initial.
Referenced by finalize().
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Checks to see which states are explicit duration states.
Definition at line 1283 of file hmm.cpp.
References StochHMM::state::transi.
Referenced by checkTopology().
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Split the state definitions into individual states from text file.
Definition at line 850 of file hmm.cpp.
References StochHMM::clear_whitespace(), StochHMM::stringList::containsExact(), name, StochHMM::stringList::push_back(), and StochHMM::stringList::size().
Referenced by _parseStates().
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Parse Tracks definitions from text file.
Definition at line 611 of file hmm.cpp.
References getTrack(), info, StochHMM::track::parseAmbiguous(), StochHMM::stringList::size(), and StochHMM::stringList::splitString().
Referenced by parse().
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States that have functions associated with emissions.
Definition at line 441 of file hmm.cpp.
References attribTwo, author, command, StochHMM::stringList::contains(), date, desc, StochHMM::stringList::fromTxt(), StochHMM::stringList::indexOf(), name, range, StochHMM::stringList::size(), and StochHMM::stringToDouble().
Referenced by parse().
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Parse Ambiguous definitions from text file.
Definition at line 636 of file hmm.cpp.
References StochHMM::weights::addWeight(), StochHMM::weight::parse(), scaling, StochHMM::stringList::size(), and StochHMM::stringList::splitND().
Referenced by parse().
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Parse Templated States definitions from text file.
Definition at line 688 of file hmm.cpp.
References _getOrderedStateNames(), _splitStates(), finalize(), StochHMM::state::getName(), initial, StochHMM::state::parse(), scaling, StochHMM::stringList::size(), stateByName, states, and trcks.
Referenced by parse().
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Parse Scaling definitions from text file.
Definition at line 670 of file hmm.cpp.
References StochHMM::templates::parse(), and templatedStates.
Referenced by parse().
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Function to parse header of the model from text file.
Definition at line 581 of file hmm.cpp.
References info, StochHMM::track::parse(), StochHMM::tracks::push_back(), StochHMM::track::setIndex(), StochHMM::stringList::size(), StochHMM::tracks::size(), StochHMM::stringList::splitString(), and trcks.
Referenced by parse().
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Gets list of states names from model.
Definition at line 778 of file hmm.cpp.
References _splitStates(), StochHMM::clear_whitespace(), StochHMM::stringList::contains(), StochHMM::getKeyValue(), StochHMM::templates::getTemplate(), StochHMM::stringList::indexOf(), StochHMM::stringList::print(), StochHMM::stringList::size(), StochHMM::stringList::splitString(), StochHMM::stringList::stringify(), and templatedStates.
Referenced by _splitStates().
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Parse state from text file.
Get templated states using the defined parameters
Definition at line 743 of file hmm.cpp.
References _processTemplateState(), StochHMM::clear_whitespace(), StochHMM::stringList::push_back(), and StochHMM::stringList::size().
Referenced by _parseStates(), and _processTemplateState().
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Converts Tracks information from model to string representation found in text file.
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Adds templated states to using template.
Definition at line 1067 of file hmm.cpp.
References attribTwo, author, command, date, desc, StochHMM::double_to_string(), name, and range.
Referenced by stringify().
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Converts Ambiguous Character information from model to text string.
Definition at line 1097 of file hmm.cpp.
References scaling, and StochHMM::weights::stringify().
Referenced by stringify().
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Converts Scaling definitions from model to text string.
Definition at line 1107 of file hmm.cpp.
References initial, states, and StochHMM::state::stringify().
Referenced by stringify().
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Converts Header information from model to string representation found in text file.
Definition at line 1090 of file hmm.cpp.
References StochHMM::tracks::stringify(), and trcks.
Referenced by stringify().
void StochHMM::model::addState | ( | state * | st | ) |
Add state to model
st | Pointer to state |
Definition at line 735 of file hmm.cpp.
References StochHMM::state::getName(), stateByName, and states.
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in banding the trellis decoding functions
Processes each statea and defines definitions to state and from state for use
Definition at line 975 of file hmm.cpp.
References basicModel, complex_emission_states, complex_transition_states, state_size(), and states.
Referenced by finalize().
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Checks to see if the model has basic transitions and emissions(no addtl functions)
Definition at line 998 of file hmm.cpp.
References StochHMM::DURATION, explicit_duration_states, state_size(), and states.
Referenced by finalize().
bool StochHMM::model::checkTopology | ( | ) |
Check model topology *Iterates through all states to check to see if there are any:
Definition at line 1218 of file hmm.cpp.
References _checkTopology(), getEnding(), initial, and states.
Referenced by finalize().
void StochHMM::model::finalize | ( | ) |
Finalizes model references from and to states *Each model must be finalized before being used to decode *Check the Functions and Labels of the States
Finalize the model before performing decoding *Sets transitions, checks labels, Determines if model is basic or requires intermittent tracebacks
Definition at line 884 of file hmm.cpp.
References _addStateToFromTransition(), StochHMM::state::_finalizeTransitions(), checkBasicModel(), checkExplicitDurationStates(), checkTopology(), explicit_duration_states, finalized, getName(), info, initial, name, stateByName, StochHMM::stateInfo::stateIterByGff, StochHMM::stateInfo::stateIterByLabel, StochHMM::stateInfo::stateIterByName, and states.
Referenced by _parseStates().
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Definition at line 359 of file hmm.h.
References explicit_duration_states.
Referenced by StochHMM::trellis::fast_complex_viterbi(), and StochHMM::trellis::sparse_complex_viterbi().
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double StochHMM::model::getDistanceToAttrib | ( | double | val | ) |
Get Distance from the model attrib values to user defined value.
Get distance to value *This is used when from selecting multiple models *User can set an attribute value. Then when evaluating *an attribute of sequence they can see which model is closest *and choose that model
Definition at line 1207 of file hmm.cpp.
References attribTwo, and range.
Referenced by StochHMM::seqTracks::getNext().
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Get pointer to the ending state.
Definition at line 189 of file hmm.h.
References ending.
Referenced by checkTopology().
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Get list of states that transition to the ending state.
Definition at line 179 of file hmm.h.
References ending, and StochHMM::state::from.
Referenced by StochHMM::trellis::simple_backward(), and StochHMM::trellis::simple_posterior().
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Get pointer to the initial state.
Definition at line 186 of file hmm.h.
References initial.
Referenced by StochHMM::trellis::fast_complex_viterbi(), StochHMM::trellis::naive_backward(), StochHMM::trellis::naive_forward(), StochHMM::trellis::naive_nth_viterbi(), StochHMM::trellis::naive_stochastic_forward(), StochHMM::trellis::naive_stochastic_viterbi(), StochHMM::trellis::naive_viterbi(), StochHMM::trellis::simple_backward(), 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(), and StochHMM::trellis::sparse_complex_viterbi().
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Get vector of states that the initial state transitions to.
Definition at line 168 of file hmm.h.
References initial, and StochHMM::state::to.
Referenced by StochHMM::trellis::fast_complex_viterbi(), 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(), and StochHMM::trellis::sparse_complex_viterbi().
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Get the Name of the Model.
Definition at line 82 of file hmm.h.
References name.
Referenced by _addStateToFromTransition(), finalize(), StochHMM::traceback_path::gff(), print_limited_posterior(), and print_posterior().
weight * StochHMM::model::getScalingFactor | ( | std::string & | name | ) |
Get Scaling factor defined in model by name
std::string | Name of Scaling or Weight defined in model |
Create graphvis file for the state of the model
filepath | complete path to use for graphviz file |
q0 | TRUE will draw the initial state Get pointer to weight by name of weight |
name | Name of weight |
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Get pointer to the state at index
iter | Index of state |
Definition at line 138 of file hmm.h.
References states.
Referenced by _addStateToFromTransition(), StochHMM::trellis::get_explicit_duration_length(), StochHMM::traceback_path::gff(), StochHMM::traceback_path::label(), StochHMM::trellis::naive_backward(), StochHMM::trellis::naive_baum_welch(), StochHMM::trellis::naive_forward(), StochHMM::trellis::naive_nth_viterbi(), StochHMM::trellis::naive_stochastic_forward(), StochHMM::trellis::naive_stochastic_viterbi(), StochHMM::trellis::naive_viterbi(), StochHMM::traceback_path::name(), StochHMM::traceback_path::print_gff(), StochHMM::traceback_path::print_label(), and StochHMM::trellis::transitionFuncTraceback().
state * StochHMM::model::getState | ( | const std::string & | txt | ) |
Get pointer to state by the name
const | std::string Name of state |
Get pointer to state by state name
txt | String name of state |
Definition at line 872 of file hmm.cpp.
References stateByName.
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Get the GFF Tag of the state at index
iter | Index of state |
Definition at line 127 of file hmm.h.
References states.
Referenced by print_limited_posterior().
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Definition at line 181 of file hmm.h.
References info.
Referenced by StochHMM::seqTracks::loadSeqs().
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Get the name of the state at index
iter | Index of state |
Definition at line 107 of file hmm.h.
References states.
Referenced by StochHMM::multiTraceback::print_hits(), print_posterior(), and StochHMM::trellis::update_transitions().
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Get pointer to track at the index
iter | Index of track to get |
Definition at line 217 of file hmm.h.
References StochHMM::tracks::size(), and trcks.
Referenced by StochHMM::seqTracks::_initImportTrackInfo(), and _parseAmbiguous().
track * StochHMM::model::getTrack | ( | const std::string & | name | ) |
Get pointer to track based on Name associated with the track
const | std::string Name associated with Track |
Get pointer to track by track name
name | track name |
Definition at line 1048 of file hmm.cpp.
References StochHMM::tracks::getTrack(), and trcks.
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Get index iterator of the track with a particular name
txt | Name of track to get index for |
Definition at line 233 of file hmm.h.
References StochHMM::tracks::indexOf(), and trcks.
Referenced by StochHMM::seqTracks::_initImportTrackInfo().
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Get pointer to the tracks of the model
Definition at line 237 of file hmm.h.
References trcks.
Referenced by StochHMM::seqTracks::_initImportTrackInfo().
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Definition at line 361 of file hmm.h.
References complex_emission_states.
bool StochHMM::model::import | ( | std::string & | modelFile, |
StateFuncs * | funcs | ||
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Write a simple GraphViz graph Formatting is very basic and function may disappear. Import and Parse the model from text file
std::string | Filename |
StateFuncs | ptr Pointer to StateFuncts, if no State Functions are (Univariate, Multivariate, Emission Functs, Transition Functions) described then you can use NULL |
Import the model file and parse it
modelFile | Model filename |
funcs | Pointer to State functions defined by programmer |
Definition at line 201 of file hmm.cpp.
References parse(), and StochHMM::slurpFile().
Referenced by import_model().
bool StochHMM::model::import | ( | std::string & | modelFile | ) |
bool StochHMM::model::import | ( | std::string & | modelFile, |
StateFuncs * | funcs, | ||
templates * | tmpls, | ||
weights * | scl | ||
) |
Import and Parse the model from text file
std::string | Filename |
StateFuncs | ptr Pointer to StateFunctions |
templates | ptr Pointer to Templated State template |
weight | ptr Pointer to weighting factors |
Definition at line 207 of file hmm.cpp.
References parse(), and StochHMM::slurpFile().
bool StochHMM::model::importFromString | ( | std::string & | modelString | ) |
Import and parse the model from std::string
Definition at line 228 of file hmm.cpp.
References parse().
bool StochHMM::model::importFromString | ( | std::string & | modelString, |
StateFuncs * | funcs | ||
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bool StochHMM::model::importFromString | ( | std::string & | modelString, |
StateFuncs * | funcs, | ||
templates * | tmpls, | ||
weights * | scl | ||
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Check to see if model is a basic HMM
Definition at line 241 of file hmm.h.
References basicModel.
Referenced by StochHMM::trellis::fast_complex_viterbi(), StochHMM::trellis::simple_nth_viterbi(), StochHMM::trellis::simple_posterior(), StochHMM::trellis::simple_viterbi(), StochHMM::trellis::sparse_complex_viterbi(), StochHMM::trellis::stochastic_viterbi(), and StochHMM::trellis::viterbi().
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bool StochHMM::model::parse | ( | const std::string & | model, |
StateFuncs * | funcs, | ||
templates * | tmpls, | ||
weights * | scl | ||
) |
Parse the model from std::string *This is used by import functions to parse the model
Parses text model file *Splits the model into sections that are then parsed by the individiual classes *parse() functions.
Definition at line 235 of file hmm.cpp.
References _parseAmbiguous(), _parseHeader(), _parseScaling(), _parseStates(), _parseTemplates(), _parseTracks(), scaling, and templatedStates.
Referenced by import(), and importFromString().
bool StochHMM::model::parse | ( | std::string & | , |
std::string & | |||
) |
Parse the model from std::string.
void StochHMM::model::print | ( | ) |
Print model by std::cout.
Print the string representation to stdout.
Definition at line 1130 of file hmm.cpp.
References stringify().
Referenced by import_model(), and StochHMM::seqJob::printModel().
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Get the number of states that are defined in the model.
Definition at line 103 of file hmm.h.
References states.
Referenced by StochHMM::trellis::backward(), checkBasicModel(), checkExplicitDurationStates(), StochHMM::trellis::forward(), StochHMM::multiTraceback::get_hit_table(), StochHMM::trellis::naive_stochastic_viterbi(), StochHMM::trellis::naive_viterbi(), StochHMM::trellis::posterior(), StochHMM::multiTraceback::print_hits(), print_limited_posterior(), print_posterior(), StochHMM::trellis::simple_backward(), StochHMM::trellis::simple_forward(), StochHMM::trellis::simple_posterior(), StochHMM::trellis::simple_simple_stochastic_viterbi(), StochHMM::trellis::simple_stochastic_viterbi(), StochHMM::trellis::simple_viterbi(), StochHMM::trellis::stochastic_forward(), StochHMM::trellis::stochastic_viterbi(), StochHMM::trellis::trellis(), and StochHMM::trellis::viterbi().
std::string StochHMM::model::stringify | ( | ) |
Get text representation of the model
Get string representation of model
Definition at line 1055 of file hmm.cpp.
References _stringifyHeader(), _stringifyScaling(), _stringifyStates(), _stringifyTracks(), and model().
Referenced by print().
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Get the number of tracks defined in the model.
Definition at line 211 of file hmm.h.
References StochHMM::tracks::size(), and trcks.
Referenced by StochHMM::seqTracks::_initImportTrackInfo().
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Model Attrib Values.
Definition at line 384 of file hmm.h.
Referenced by _parseHeader(), _stringifyHeader(), getDistanceToAttrib(), model(), setLowerRange(), setNumericalAttrib(), and setUpperRange().
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Model Creation Command.
Definition at line 382 of file hmm.h.
Referenced by _parseHeader(), _stringifyHeader(), getAuthor(), and setAuthor().
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Flag for whether model contains anything other than simple transitions and emissions *If False then the model either contains additional function or emissions
Definition at line 376 of file hmm.h.
Referenced by checkBasicModel(), isBasic(), and model().
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Model Creation Date.
Definition at line 381 of file hmm.h.
Referenced by _parseHeader(), _stringifyHeader(), getCommand(), and setCommand().
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States that have functions associated with transitions.
Definition at line 405 of file hmm.h.
Referenced by checkBasicModel(), hasComplexEmission(), and model().
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States that are explicit duration states.
Definition at line 404 of file hmm.h.
Referenced by checkBasicModel(), and model().
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Model Description.
Definition at line 380 of file hmm.h.
Referenced by _parseHeader(), _stringifyHeader(), getDate(), and setDate().
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Model Name.
Definition at line 379 of file hmm.h.
Referenced by _parseHeader(), _stringifyHeader(), getDescription(), and setDesc().
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Initial state q0.
Definition at line 395 of file hmm.h.
Referenced by _addStateToFromTransition(), getEnding(), getEndingFrom(), model(), and setEnd().
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Templated states.
Definition at line 402 of file hmm.h.
Referenced by checkExplicitDurationStates(), finalize(), get_explicit(), and model().
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Flag set to tell whether the transitions bitsets have been set foreach *state. Model is also checked for correct order of states
Definition at line 371 of file hmm.h.
Referenced by finalize(), and model().
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Definition at line 391 of file hmm.h.
Referenced by _parseAmbiguous(), _parseTracks(), finalize(), and getStateInfo().
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Definition at line 394 of file hmm.h.
Referenced by _addStateToFromTransition(), _parseStates(), _stringifyStates(), checkTopology(), finalize(), getInitial(), getInitialTo(), model(), and setInit().
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Definition at line 378 of file hmm.h.
Referenced by _getOrderedStateNames(), _parseHeader(), _stringifyHeader(), finalize(), getName(), getScalingFactor(), and setName().
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Model Author.
Definition at line 383 of file hmm.h.
Referenced by _parseHeader(), _stringifyHeader(), getDistanceToAttrib(), model(), setLowerRange(), setNumericalAttrib(), and setUpperRange().
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Ending state.
Definition at line 397 of file hmm.h.
Referenced by _parseScaling(), _parseStates(), _stringifyScaling(), getScalingFactor(), model(), and parse().
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All the states contained in the model.
Definition at line 390 of file hmm.h.
Referenced by _parseStates(), addState(), finalize(), and getState().
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Tracks defined by model (Contains alphabet and ambiguous character definitions.
Definition at line 388 of file hmm.h.
Referenced by _parseStates(), _stringifyStates(), addState(), checkBasicModel(), checkExplicitDurationStates(), checkTopology(), finalize(), getState(), getStateGFF(), getStateLabel(), getStateName(), getStateXFrom(), getStateXTo(), operator[](), and state_size().
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Weights or scaling fractors associated with the model.
Definition at line 400 of file hmm.h.
Referenced by _parseTemplates(), _processTemplateState(), model(), and parse().
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Two attrib Values.
Definition at line 386 of file hmm.h.
Referenced by _parseStates(), _parseTracks(), _stringifyTracks(), addTrack(), getTrack(), getTrackIter(), getTracks(), and track_size().