bpp-phyl3
3.0.0
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Collection of Substitution Process, which owns all the necessary objects: Substitution models, frequencies sets, rate distributions and trees. More...
#include <Bpp/Phyl/Likelihood/SubstitutionProcessCollection.h>
Public Member Functions | |
SubstitutionProcessCollection () | |
Create empty collections. More... | |
SubstitutionProcessCollection (const SubstitutionProcessCollection &set) | |
SubstitutionProcessCollection & | operator= (const SubstitutionProcessCollection &set) |
virtual | ~SubstitutionProcessCollection () |
SubstitutionProcessCollection * | clone () const |
void | clear () |
Resets all the information contained in this object. More... | |
void | addParametrizable (std::shared_ptr< Parametrizable > parametrizable, size_t parametrizableIndex, bool withParameters=true) |
Add a new parametrizable to the matching collection with a given number. More... | |
void | replaceParametrizable (std::shared_ptr< Parametrizable > parametrizable, size_t parametrizableIndex, bool withParameters=true) |
void | addModel (std::shared_ptr< BranchModelInterface > model, size_t modelIndex) |
specific methods to add specific objects. More... | |
void | replaceModel (std::shared_ptr< BranchModelInterface > model, size_t modelIndex) |
void | addFrequencies (std::shared_ptr< FrequencySetInterface > frequencies, size_t frequenciesIndex) |
void | replaceFrequencies (std::shared_ptr< FrequencySetInterface > frequencies, size_t frequenciesIndex) |
void | addDistribution (std::shared_ptr< DiscreteDistributionInterface > distribution, size_t distributionIndex) |
void | addTree (std::shared_ptr< ParametrizablePhyloTree > tree, size_t treeIndex) |
void | replaceTree (std::shared_ptr< ParametrizablePhyloTree > tree, size_t treeIndex) |
void | addScenario (std::shared_ptr< ModelScenario > scen, size_t scenIndex) |
BranchModelInterface & | model (size_t modelIndex) |
Get a BranchModel from the collection. More... | |
const BranchModelInterface & | model (size_t modelIndex) const |
std::shared_ptr< BranchModelInterface > | getModel (size_t modelIndex) |
std::shared_ptr< const BranchModelInterface > | getModel (size_t modelIndex) const |
size_t | getModelIndex (std::shared_ptr< BranchModelInterface > model) const |
Return the number of a BranchModel in the collection. More... | |
bool | hasModel (std::shared_ptr< BranchModelInterface > model) const |
Return if a BranchModel is in the collection. More... | |
FrequencySetInterface & | frequencySet (size_t frequenciesIndex) |
Get a FrequencySet from the collection. More... | |
const FrequencySetInterface & | frequencySet (size_t frequenciesIndex) const |
std::shared_ptr< FrequencySetInterface > | getFrequencySet (size_t frequenciesIndex) |
std::shared_ptr< const FrequencySetInterface > | getFrequencySet (size_t frequenciesIndex) const |
std::shared_ptr< DiscreteDistributionInterface > | getRateDistribution (size_t distributionIndex) |
Get a DiscreteDistribution from the collection. More... | |
std::shared_ptr< const DiscreteDistributionInterface > | getRateDistribution (size_t distributionIndex) const |
DiscreteDistributionInterface & | rateDistribution (size_t distributionIndex) |
const DiscreteDistributionInterface & | rateDistribution (size_t distributionIndex) const |
ParametrizablePhyloTree & | tree (size_t treeIndex) |
Get a tree from the set. More... | |
const ParametrizablePhyloTree & | tree (size_t treeIndex) const |
std::shared_ptr< ParametrizablePhyloTree > | getTree (size_t treeIndex) |
std::shared_ptr< const ParametrizablePhyloTree > | getTree (size_t treeIndex) const |
bool | hasModelScenario (size_t numPath) const |
checks if the set has a ModelScenario More... | |
std::shared_ptr< const ModelScenario > | getModelScenario (size_t numPath) const |
Get a ModelScenario from the set. More... | |
std::shared_ptr< ModelScenario > | getModelScenario (size_t numPath) |
std::vector< size_t > | getScenarioNumbers () const |
std::vector< size_t > | getModelNumbers () const |
Get the numbers of the specified objects from the collections. More... | |
std::vector< size_t > | getFrequenciesNumbers () const |
std::vector< size_t > | getRateDistributionNumbers () const |
std::vector< size_t > | getTreeNumbers () const |
std::vector< size_t > | getSubstitutionProcessNumbers () const |
bool | hasModelNumber (size_t n) const |
bool | hasFrequenciesNumber (size_t n) const |
bool | hasDistributionNumber (size_t n) const |
bool | hasTreeNumber (size_t n) const |
bool | hasSubstitutionProcessNumber (size_t n) const |
void | addSubstitutionProcess (size_t nProc, std::map< size_t, std::vector< unsigned int >> mModBr, size_t nTree, size_t nRate, size_t nFreq) |
void | addSubstitutionProcess (size_t nProc, std::map< size_t, std::vector< unsigned int >> mModBr, size_t nTree, size_t nRate) |
void | addOnePerBranchSubstitutionProcess (size_t nProc, size_t nMod, size_t nTree, size_t nRate, size_t nFreq, const std::vector< std::string > &sharedParameterNames) |
void | addOnePerBranchSubstitutionProcess (size_t nProc, size_t nMod, size_t nTree, size_t nRate, const std::vector< std::string > &sharedParameterNames) |
size_t | getNumberOfSubstitutionProcess () const |
Methods to retrieve Substitution Process. More... | |
SubstitutionProcessCollectionMember & | substitutionProcess (size_t i) |
const SubstitutionProcessCollectionMember & | substitutionProcess (size_t i) const |
std::shared_ptr< SubstitutionProcessCollectionMember > | getSubstitutionProcess (size_t i) |
std::shared_ptr< const SubstitutionProcessCollectionMember > | getSubstitutionProcess (size_t i) const |
ParameterList | getBranchLengthParameters (bool independent) const |
Methods to retrieve parameters. More... | |
ParameterList | getBranchLengthParameters (size_t nTree, bool independent) const |
ParameterList | getSubstitutionProcessParameters (size_t nProc, bool independent) const |
Get the parameters associated to substitution process(es). More... | |
ParameterList | getSubstitutionProcessParameters () const |
ParameterList | getSubstitutionModelParameters (size_t nMod, bool independent) const |
Get the parameters associated to substitution model(s). More... | |
ParameterList | getSubstitutionModelParameters (bool independent) const |
ParameterList | getNonDerivableParameters () const |
Get the Non-derivable parameters. More... | |
ParameterList | getRateDistributionParameters (size_t nRate, bool independent) const |
Get the parameters associated to the rate distribution(s). More... | |
ParameterList | getRateDistributionParameters (bool independent) const |
ParameterList | getRootFrequenciesParameters (size_t nFreq, bool independent) const |
Get the parameters associated to the root frequencies(s). More... | |
ParameterList | getRootFrequenciesParameters (bool independent) const |
bool | hasIndependentParameter (const std::string &name) const |
const ParameterList & | getIndependentParameters () const |
size_t | getNumberOfIndependentParameters () const |
ParameterList | getAliasedParameters (const ParameterList &pl) const |
ParameterList | getFromParameters (const ParameterList &pl) const |
virtual std::vector< std::string > | getAlias (const std::string &name) const |
virtual std::map< std::string, std::string > | getAliases () const |
std::string | getFrom (const std::string &name) const |
bool | hasParameter (const std::string &name) const override |
const ParameterList & | getParameters () const override |
const Parameter & | parameter (const std::string &name) const override |
const std::shared_ptr< Parameter > & | getParameter (const std::string &name) const |
double | getParameterValue (const std::string &name) const override |
void | setAllParametersValues (const ParameterList ¶meters) override |
void | setParameterValue (const std::string &name, double value) override |
void | setParametersValues (const ParameterList ¶meters) override |
bool | matchParametersValues (const ParameterList ¶meters) override |
void | removeConstraint (const std::string &name) override |
void | setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint) override |
size_t | getNumberOfParameters () const override |
std::string | getNamespace () const override |
std::string | getParameterNameWithoutNamespace (const std::string &name) const override |
void | fireParameterChanged (const ParameterList ¶meters) |
AbstractParameterAliasable functions, redirected towards the process members. More... | |
void | setNamespace (const std::string &prefix) |
void | aliasParameters (const std::string &p1, const std::string &p2) |
void | unaliasParameters (const std::string &p1, const std::string &p2) |
void | aliasParameters (std::map< std::string, std::string > &unparsedParams, bool verbose) |
Protected Member Functions | |
const std::shared_ptr< Parameter > & | getParameter (size_t i) const |
std::shared_ptr< Parameter > & | getParameter (size_t i) |
void | addParameter_ (Parameter *parameter) |
void | addParameters_ (const ParameterList ¶meters) |
void | shareParameter_ (const std::shared_ptr< Parameter > ¶meter) |
void | shareParameters_ (const ParameterList ¶meters) |
void | includeParameters_ (const ParameterList ¶meters) |
void | deleteParameter_ (size_t index) |
void | deleteParameter_ (std::string &name) |
void | deleteParameters_ (const std::vector< std::string > &names) |
void | resetParameters_ () |
Parameter & | getParameter_ (const std::string &name) |
Parameter & | getParameter_ (size_t index) |
const Parameter & | getParameter_ (size_t index) const |
Parameter & | getParameterWithNamespace_ (const std::string &name) |
const Parameter & | getParameterWithNamespace_ (const std::string &name) const |
ParameterList & | getParameters_ () override |
Private Attributes | |
ParametrizableCollection< BranchModelInterface > | modelColl_ |
std::map< size_t, std::vector< size_t > > | mModelToSubPro_ |
ParametrizableCollection< FrequencySetInterface > | freqColl_ |
std::map< size_t, std::vector< size_t > > | mFreqToSubPro_ |
ParametrizableCollection< DiscreteDistributionInterface > | distColl_ |
std::map< size_t, std::vector< size_t > > | mVConstDist_ |
std::map< size_t, std::vector< size_t > > | mDistToSubPro_ |
ParametrizableCollection< ParametrizablePhyloTree > | treeColl_ |
std::map< size_t, std::vector< size_t > > | mTreeToSubPro_ |
std::map< size_t, std::shared_ptr< ModelScenario > > | mModelScenario_ |
std::map< size_t, std::shared_ptr< SubstitutionProcessCollectionMember > > | mSubProcess_ |
ParameterList | independentParameters_ |
std::map< std::string, std::shared_ptr< AliasParameterListener > > | aliasListenersRegister_ |
ParameterList | parameters_ |
std::string | prefix_ |
Collection of Substitution Process, which owns all the necessary objects: Substitution models, frequencies sets, rate distributions and trees.
This class contains a set of substitution models sets, linking models, rates and trees.
This object has the same parameters names as the owned objects. The updating of the parameters is done through the ParametrizableCollection objects.
This class also deals with the parameters associated to the models, distribution, frequencies.
It will deal with the parameters associated to the trees when they are parametrized.
Definition at line 47 of file SubstitutionProcessCollection.h.
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Create empty collections.
Definition at line 119 of file SubstitutionProcessCollection.h.
Referenced by clone().
SubstitutionProcessCollection::SubstitutionProcessCollection | ( | const SubstitutionProcessCollection & | set | ) |
Definition at line 15 of file SubstitutionProcessCollection.cpp.
References bpp::SubstitutionProcessCollectionMember::clone(), and mSubProcess_.
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Definition at line 138 of file SubstitutionProcessCollection.h.
References clear().
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Definition at line 201 of file SubstitutionProcessCollection.h.
References addParametrizable(), and mVConstDist_.
Referenced by bpp::PhylogeneticsApplicationTools::addSubstitutionProcessCollectionMember().
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Definition at line 191 of file SubstitutionProcessCollection.h.
References addParametrizable().
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specific methods to add specific objects.
? operator[] ?
Definition at line 181 of file SubstitutionProcessCollection.h.
References addParametrizable(), and model().
Referenced by addOnePerBranchSubstitutionProcess().
void SubstitutionProcessCollection::addOnePerBranchSubstitutionProcess | ( | size_t | nProc, |
size_t | nMod, | ||
size_t | nTree, | ||
size_t | nRate, | ||
const std::vector< std::string > & | sharedParameterNames | ||
) |
Definition at line 370 of file SubstitutionProcessCollection.cpp.
References addModel(), addSubstitutionProcess(), aliasParameters(), bpp::BranchModelInterface::clone(), distColl_, bpp::AssociationTreeGraphImplObserver< class, class, class >::getAllEdgesIndexes(), bpp::ParameterAliasable::getIndependentParameters(), getModel(), getModelNumbers(), getTree(), bpp::StringTokenizer::hasMoreToken(), bpp::ParameterList::hasParameter(), model(), mSubProcess_, bpp::StringTokenizer::nextToken(), bpp::ParameterList::size(), bpp::TextTools::toString(), tree(), and treeColl_.
void SubstitutionProcessCollection::addOnePerBranchSubstitutionProcess | ( | size_t | nProc, |
size_t | nMod, | ||
size_t | nTree, | ||
size_t | nRate, | ||
size_t | nFreq, | ||
const std::vector< std::string > & | sharedParameterNames | ||
) |
Definition at line 356 of file SubstitutionProcessCollection.cpp.
References freqColl_, mFreqToSubPro_, bpp::SubstitutionProcessCollectionMember::setRootFrequencies(), and substitutionProcess().
Referenced by bpp::PhylogeneticsApplicationTools::addSubstitutionProcessCollectionMember().
void SubstitutionProcessCollection::addParametrizable | ( | std::shared_ptr< Parametrizable > | parametrizable, |
size_t | parametrizableIndex, | ||
bool | withParameters = true |
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Add a new parametrizable to the matching collection with a given number.
Exception | if the number is already used. See replace function instead. |
parametrizable | A shared pointer toward a parametrizable, that will added to the collection. |
parametrizableIndex | The number of the parametrizable in the Collection. Must be >= 1. |
withParameters | boolean if the parameters of the object should be added (default: true) |
Definition at line 75 of file SubstitutionProcessCollection.cpp.
References bpp::AbstractParameterAliasable::addParameters_(), distColl_, freqColl_, modelColl_, and treeColl_.
Referenced by addDistribution(), addFrequencies(), addModel(), addTree(), replaceFrequencies(), and replaceParametrizable().
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Definition at line 220 of file SubstitutionProcessCollection.h.
References mModelScenario_.
void SubstitutionProcessCollection::addSubstitutionProcess | ( | size_t | nProc, |
std::map< size_t, std::vector< unsigned int >> | mModBr, | ||
size_t | nTree, | ||
size_t | nRate | ||
) |
Definition at line 314 of file SubstitutionProcessCollection.cpp.
References distColl_, mDistToSubPro_, mModelToSubPro_, mSubProcess_, mTreeToSubPro_, and treeColl_.
void SubstitutionProcessCollection::addSubstitutionProcess | ( | size_t | nProc, |
std::map< size_t, std::vector< unsigned int >> | mModBr, | ||
size_t | nTree, | ||
size_t | nRate, | ||
size_t | nFreq | ||
) |
Definition at line 301 of file SubstitutionProcessCollection.cpp.
References freqColl_, mFreqToSubPro_, bpp::SubstitutionProcessCollectionMember::setRootFrequencies(), and substitutionProcess().
Referenced by addOnePerBranchSubstitutionProcess(), and bpp::PhylogeneticsApplicationTools::addSubstitutionProcessCollectionMember().
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Definition at line 210 of file SubstitutionProcessCollection.h.
References addParametrizable(), and tree().
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Reimplemented from bpp::AbstractParameterAliasable.
Definition at line 263 of file SubstitutionProcessCollection.cpp.
References bpp::AbstractParameterAliasable::aliasParameters(), and mSubProcess_.
Referenced by addOnePerBranchSubstitutionProcess().
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Reimplemented from bpp::AbstractParameterAliasable.
Definition at line 285 of file SubstitutionProcessCollection.cpp.
References bpp::AbstractParameterAliasable::aliasParameters(), and mSubProcess_.
void SubstitutionProcessCollection::clear | ( | ) |
Resets all the information contained in this object.
Definition at line 58 of file SubstitutionProcessCollection.cpp.
References distColl_, freqColl_, mDistToSubPro_, mFreqToSubPro_, mModelToSubPro_, modelColl_, mSubProcess_, mTreeToSubPro_, mVConstDist_, bpp::AbstractParameterAliasable::resetParameters_(), and treeColl_.
Referenced by operator=(), and ~SubstitutionProcessCollection().
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Implements bpp::AbstractParameterAliasable.
Definition at line 143 of file SubstitutionProcessCollection.h.
References SubstitutionProcessCollection().
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AbstractParameterAliasable functions, redirected towards the process members.
To be called when a parameter has changed. This will call fireParameterChanged on the collections and the process members.
parameters | The modified parameters. |
Reimplemented from bpp::AbstractParameterAliasable.
Definition at line 181 of file SubstitutionProcessCollection.cpp.
References bpp::ParameterList::addParameter(), bpp::ParameterList::addParameters(), distColl_, freqColl_, bpp::AbstractParameterAliasable::getAliasedParameters(), getRateDistribution(), mDistToSubPro_, modelColl_, mSubProcess_, mTreeToSubPro_, mVConstDist_, bpp::TextTools::toString(), and treeColl_.
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Get a FrequencySet from the collection.
frequenciesIndex | The index of the frequencies set in the collection. |
Definition at line 281 of file SubstitutionProcessCollection.h.
References freqColl_.
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Definition at line 286 of file SubstitutionProcessCollection.h.
References freqColl_.
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Methods to retrieve parameters.
Definition at line 588 of file SubstitutionProcessCollection.h.
References bpp::ParameterList::getCommonParametersWith(), bpp::AbstractParameterAliasable::getIndependentParameters(), and treeColl_.
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Definition at line 598 of file SubstitutionProcessCollection.h.
References bpp::ParameterList::getCommonParametersWith(), bpp::AbstractParameterAliasable::getIndependentParameters(), and treeColl_.
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Definition at line 407 of file SubstitutionProcessCollection.h.
References freqColl_.
Referenced by bpp::PhylogeneticsApplicationTools::printParameters().
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Definition at line 291 of file SubstitutionProcessCollection.h.
References freqColl_.
Referenced by bpp::PhylogeneticsApplicationTools::printParameters().
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Definition at line 296 of file SubstitutionProcessCollection.h.
References freqColl_.
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Definition at line 241 of file SubstitutionProcessCollection.h.
References modelColl_.
Referenced by addOnePerBranchSubstitutionProcess(), and bpp::PhylogeneticsApplicationTools::printParameters().
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Definition at line 246 of file SubstitutionProcessCollection.h.
References modelColl_.
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Return the number of a BranchModel in the collection.
model | The model looked for in the collection. |
Definition at line 257 of file SubstitutionProcessCollection.h.
References model(), and modelColl_.
Referenced by bpp::PhylogeneticsApplicationTools::printParameters().
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Get the numbers of the specified objects from the collections.
Definition at line 402 of file SubstitutionProcessCollection.h.
References modelColl_.
Referenced by addOnePerBranchSubstitutionProcess(), and bpp::PhylogeneticsApplicationTools::printParameters().
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Definition at line 377 of file SubstitutionProcessCollection.h.
References hasModelScenario(), and mModelScenario_.
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Get a ModelScenario from the set.
numPath | The number of the model path in the set. |
Definition at line 369 of file SubstitutionProcessCollection.h.
References hasModelScenario(), and mModelScenario_.
Referenced by bpp::PhylogeneticsApplicationTools::printParameters().
ParameterList SubstitutionProcessCollection::getNonDerivableParameters | ( | ) | const |
Get the Non-derivable parameters.
Definition at line 169 of file SubstitutionProcessCollection.cpp.
References bpp::ParameterList::addParameters(), distColl_, freqColl_, bpp::AbstractParameterAliasable::getAliasedParameters(), bpp::AbstractParameterAliasable::getFromParameters(), bpp::ParameterList::includeParameters(), and modelColl_.
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Methods to retrieve Substitution Process.
Definition at line 553 of file SubstitutionProcessCollection.h.
References mSubProcess_.
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Get a DiscreteDistribution from the collection.
distributionIndex | The index of the distribution in the collection. |
Definition at line 307 of file SubstitutionProcessCollection.h.
References distColl_.
Referenced by fireParameterChanged(), and bpp::PhylogeneticsApplicationTools::printParameters().
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Definition at line 312 of file SubstitutionProcessCollection.h.
References distColl_.
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Definition at line 412 of file SubstitutionProcessCollection.h.
References distColl_.
Referenced by bpp::PhylogeneticsApplicationTools::addSubstitutionProcessCollectionMember(), and bpp::PhylogeneticsApplicationTools::printParameters().
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Definition at line 679 of file SubstitutionProcessCollection.h.
References distColl_, bpp::ParameterList::getCommonParametersWith(), and bpp::AbstractParameterAliasable::getIndependentParameters().
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Get the parameters associated to the rate distribution(s).
Definition at line 669 of file SubstitutionProcessCollection.h.
References distColl_, bpp::ParameterList::getCommonParametersWith(), and bpp::AbstractParameterAliasable::getIndependentParameters().
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Definition at line 704 of file SubstitutionProcessCollection.h.
References freqColl_, bpp::ParameterList::getCommonParametersWith(), and bpp::AbstractParameterAliasable::getIndependentParameters().
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Get the parameters associated to the root frequencies(s).
Definition at line 694 of file SubstitutionProcessCollection.h.
References freqColl_, bpp::ParameterList::getCommonParametersWith(), and bpp::AbstractParameterAliasable::getIndependentParameters().
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Definition at line 385 of file SubstitutionProcessCollection.h.
References mModelScenario_.
Referenced by bpp::PhylogeneticsApplicationTools::printParameters().
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Definition at line 645 of file SubstitutionProcessCollection.h.
References bpp::ParameterList::getCommonParametersWith(), bpp::AbstractParameterAliasable::getIndependentParameters(), and modelColl_.
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Get the parameters associated to substitution model(s).
Definition at line 635 of file SubstitutionProcessCollection.h.
References bpp::ParameterList::getCommonParametersWith(), bpp::AbstractParameterAliasable::getIndependentParameters(), and modelColl_.
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Definition at line 567 of file SubstitutionProcessCollection.h.
References mSubProcess_.
Referenced by bpp::ProcessTree::makeProcessTree().
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Definition at line 572 of file SubstitutionProcessCollection.h.
References mSubProcess_.
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Definition at line 422 of file SubstitutionProcessCollection.h.
References mSubProcess_.
Referenced by bpp::PhylogeneticsApplicationTools::printParameters().
ParameterList SubstitutionProcessCollection::getSubstitutionProcessParameters | ( | ) | const |
Definition at line 345 of file SubstitutionProcessCollection.cpp.
References bpp::ParameterList::addParameters(), distColl_, freqColl_, modelColl_, and treeColl_.
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Get the parameters associated to substitution process(es).
Definition at line 613 of file SubstitutionProcessCollection.h.
References bpp::ParameterList::getCommonParametersWith(), bpp::AbstractParameterAliasable::getIndependentParameters(), and mSubProcess_.
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Definition at line 343 of file SubstitutionProcessCollection.h.
References treeColl_.
Referenced by addOnePerBranchSubstitutionProcess(), bpp::PhylogeneticsApplicationTools::addSubstitutionProcessCollectionMember(), and bpp::PhylogeneticsApplicationTools::writePhyloTrees().
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Definition at line 348 of file SubstitutionProcessCollection.h.
References treeColl_.
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Definition at line 417 of file SubstitutionProcessCollection.h.
References treeColl_.
Referenced by bpp::PhylogeneticsApplicationTools::writePhyloTrees().
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Definition at line 444 of file SubstitutionProcessCollection.h.
References distColl_.
Referenced by bpp::PhylogeneticsApplicationTools::addSubstitutionProcessCollectionMember(), and replaceParametrizable().
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Definition at line 439 of file SubstitutionProcessCollection.h.
References freqColl_.
Referenced by bpp::PhylogeneticsApplicationTools::addSubstitutionProcessCollectionMember(), and replaceParametrizable().
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Return if a BranchModel is in the collection.
model | The model looked for in the collection. |
Definition at line 270 of file SubstitutionProcessCollection.h.
References model(), and modelColl_.
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Definition at line 434 of file SubstitutionProcessCollection.h.
References modelColl_.
Referenced by bpp::PhylogeneticsApplicationTools::addSubstitutionProcessCollectionMember(), and replaceParametrizable().
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checks if the set has a ModelScenario
numPath | The number of the model path in the set. |
Definition at line 358 of file SubstitutionProcessCollection.h.
References mModelScenario_.
Referenced by bpp::PhylogeneticsApplicationTools::addSubstitutionProcessCollectionMember(), and getModelScenario().
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Definition at line 454 of file SubstitutionProcessCollection.h.
References mSubProcess_.
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Definition at line 449 of file SubstitutionProcessCollection.h.
References treeColl_.
Referenced by bpp::PhylogeneticsApplicationTools::addSubstitutionProcessCollectionMember(), and replaceParametrizable().
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Get a BranchModel from the collection.
modelIndex | The index of the model in the collection. |
Definition at line 231 of file SubstitutionProcessCollection.h.
References modelColl_.
Referenced by addModel(), addOnePerBranchSubstitutionProcess(), getModelIndex(), hasModel(), and replaceModel().
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Definition at line 236 of file SubstitutionProcessCollection.h.
References modelColl_.
SubstitutionProcessCollection & SubstitutionProcessCollection::operator= | ( | const SubstitutionProcessCollection & | set | ) |
Definition at line 35 of file SubstitutionProcessCollection.cpp.
References clear(), distColl_, freqColl_, mDistToSubPro_, mFreqToSubPro_, mModelToSubPro_, modelColl_, mSubProcess_, mTreeToSubPro_, mVConstDist_, bpp::AbstractParameterAliasable::operator=(), and treeColl_.
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Definition at line 317 of file SubstitutionProcessCollection.h.
References distColl_.
Referenced by bpp::PhylogeneticsApplicationTools::addSubstitutionProcessCollectionMember().
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Definition at line 322 of file SubstitutionProcessCollection.h.
References distColl_.
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Definition at line 196 of file SubstitutionProcessCollection.h.
References addParametrizable().
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Definition at line 186 of file SubstitutionProcessCollection.h.
References model(), and replaceParametrizable().
void SubstitutionProcessCollection::replaceParametrizable | ( | std::shared_ptr< Parametrizable > | parametrizable, |
size_t | parametrizableIndex, | ||
bool | withParameters = true |
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Definition at line 109 of file SubstitutionProcessCollection.cpp.
References bpp::AbstractParameterAliasable::addParameters_(), addParametrizable(), bpp::ParameterList::deleteParameters(), distColl_, freqColl_, bpp::AbstractParameterAliasable::getParameters_(), hasDistributionNumber(), hasFrequenciesNumber(), hasModelNumber(), hasTreeNumber(), modelColl_, and treeColl_.
Referenced by replaceModel(), and replaceTree().
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Definition at line 215 of file SubstitutionProcessCollection.h.
References replaceParametrizable(), and tree().
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Reimplemented from bpp::AbstractParameterAliasable.
Definition at line 254 of file SubstitutionProcessCollection.cpp.
References mSubProcess_, and bpp::AbstractParameterAliasable::setNamespace().
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Definition at line 555 of file SubstitutionProcessCollection.h.
References mSubProcess_.
Referenced by addOnePerBranchSubstitutionProcess(), addSubstitutionProcess(), bpp::PhylogeneticsApplicationTools::addSubstitutionProcessCollectionMember(), bpp::LikelihoodCalculationSingleProcess::makeProcessNodes_(), and bpp::PhylogeneticsApplicationTools::printParameters().
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Definition at line 560 of file SubstitutionProcessCollection.h.
References mSubProcess_.
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Get a tree from the set.
treeIndex | The index of the model in the set. |
Definition at line 333 of file SubstitutionProcessCollection.h.
References treeColl_.
Referenced by addOnePerBranchSubstitutionProcess(), bpp::PhylogeneticsApplicationTools::addSubstitutionProcessCollectionMember(), addTree(), and replaceTree().
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Definition at line 338 of file SubstitutionProcessCollection.h.
References treeColl_.
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Reimplemented from bpp::AbstractParameterAliasable.
Definition at line 276 of file SubstitutionProcessCollection.cpp.
References mSubProcess_, and bpp::AbstractParameterAliasable::unaliasParameters().
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A collection of DiscreteDistributions
Definition at line 77 of file SubstitutionProcessCollection.h.
Referenced by addOnePerBranchSubstitutionProcess(), addParametrizable(), addSubstitutionProcess(), clear(), fireParameterChanged(), getNonDerivableParameters(), getRateDistribution(), getRateDistributionNumbers(), getRateDistributionParameters(), getSubstitutionProcessParameters(), hasDistributionNumber(), operator=(), rateDistribution(), and replaceParametrizable().
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A collection of Frequencies Sets
Definition at line 66 of file SubstitutionProcessCollection.h.
Referenced by addOnePerBranchSubstitutionProcess(), addParametrizable(), addSubstitutionProcess(), clear(), fireParameterChanged(), frequencySet(), getFrequenciesNumbers(), getFrequencySet(), getNonDerivableParameters(), getRootFrequenciesParameters(), getSubstitutionProcessParameters(), hasFrequenciesNumber(), operator=(), and replaceParametrizable().
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A map from each DiscreteDistribution number to the SubProcess members that are linked to it.
Definition at line 92 of file SubstitutionProcessCollection.h.
Referenced by addSubstitutionProcess(), clear(), fireParameterChanged(), and operator=().
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A map from each FrequencySet number to the SubProcess members that are linked to it.
Definition at line 72 of file SubstitutionProcessCollection.h.
Referenced by addOnePerBranchSubstitutionProcess(), addSubstitutionProcess(), clear(), and operator=().
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A map of ModelScenario
Definition at line 108 of file SubstitutionProcessCollection.h.
Referenced by addScenario(), getModelScenario(), getScenarioNumbers(), and hasModelScenario().
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A map from each BranchModel number to the SubProcess members that are linked to it.
Definition at line 61 of file SubstitutionProcessCollection.h.
Referenced by addSubstitutionProcess(), clear(), and operator=().
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A collection of Transition Models
Definition at line 55 of file SubstitutionProcessCollection.h.
Referenced by addParametrizable(), clear(), fireParameterChanged(), getModel(), getModelIndex(), getModelNumbers(), getNonDerivableParameters(), getSubstitutionModelParameters(), getSubstitutionProcessParameters(), hasModel(), hasModelNumber(), model(), operator=(), and replaceParametrizable().
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A map of SubstitutionProcessCollectionMember
Definition at line 113 of file SubstitutionProcessCollection.h.
Referenced by addOnePerBranchSubstitutionProcess(), addSubstitutionProcess(), aliasParameters(), clear(), fireParameterChanged(), getNumberOfSubstitutionProcess(), getSubstitutionProcess(), getSubstitutionProcessNumbers(), getSubstitutionProcessParameters(), hasSubstitutionProcessNumber(), operator=(), setNamespace(), substitutionProcess(), SubstitutionProcessCollection(), and unaliasParameters().
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A map from each Tree number to the SubProcess members that are linked to it.
Definition at line 103 of file SubstitutionProcessCollection.h.
Referenced by addSubstitutionProcess(), clear(), fireParameterChanged(), and operator=().
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A map from the DiscreteDistribution numbers to the numbers of categories that are used independently as ConstantDistributions.
These ConstantDistributions are stored in distColl_ with numbers 10000*(numberOfDiscreteDistribution+1) + numberOfTheCategory.
Definition at line 86 of file SubstitutionProcessCollection.h.
Referenced by addDistribution(), clear(), fireParameterChanged(), and operator=().
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A collection of trees
Definition at line 97 of file SubstitutionProcessCollection.h.
Referenced by addOnePerBranchSubstitutionProcess(), addParametrizable(), addSubstitutionProcess(), clear(), fireParameterChanged(), getBranchLengthParameters(), getSubstitutionProcessParameters(), getTree(), getTreeNumbers(), hasTreeNumber(), operator=(), replaceParametrizable(), and tree().