bpp::PhylogeneticsApplicationTools Class Reference

This class provides some common tools for applications. More...

#include <Bpp/Phyl/App/PhylogeneticsApplicationTools.h>

Public Member Functions
	PhylogeneticsApplicationTools ()
virtual	~PhylogeneticsApplicationTools ()

Static Public Member Functions
static std::unique_ptr< Tree >	getTree (const std::map< std::string, std::string > &params, const std::string &prefix="input.", const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)
	Build a Tree object according to options. More...
static std::vector< std::unique_ptr< Tree > >	getTrees (const std::map< std::string, std::string > &params, const std::string &prefix="input.", const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)
	Build a list of Tree objects according to options. More...
static std::map< size_t, std::shared_ptr< PhyloTree > >	getPhyloTrees (const std::map< std::string, std::string > &params, const std::map< size_t, std::shared_ptr< const AlignmentDataInterface >> &mSeq, std::map< std::string, std::string > &unparsedParams, const std::string &prefix="input.", const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)
	Build a map of <number,PhyloTree> according to options. More...
static std::unique_ptr< BranchModelInterface >	getBranchModel (std::shared_ptr< const Alphabet > alphabet, std::shared_ptr< const GeneticCode > gCode, std::shared_ptr< const AlignmentDataInterface > data, const std::map< std::string, std::string > &params, std::map< std::string, std::string > &unparsedparams, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)
	Build a BranchModel (most general class of branch models) object according to options. More...
static std::unique_ptr< SubstitutionModelInterface >	getSubstitutionModel (std::shared_ptr< const Alphabet > alphabet, std::shared_ptr< const GeneticCode > gCode, std::shared_ptr< const AlignmentDataInterface > data, const std::map< std::string, std::string > &params, std::map< std::string, std::string > &unparsedparams, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)
	Build a SubstitutionModel object according to options (ie a BranchModel with a generator). More...
static std::map< size_t, std::unique_ptr< BranchModelInterface > >	getBranchModels (std::shared_ptr< const Alphabet > alphabet, std::shared_ptr< const GeneticCode > gCode, const std::map< size_t, std::shared_ptr< const AlignmentDataInterface >> &mData, const std::map< std::string, std::string > &params, std::map< std::string, std::string > &unparsedparams, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)
	The same as before, but returns a map <number, branch model>. More...
static std::unique_ptr< FrequencySetInterface >	getRootFrequencySet (std::shared_ptr< const Alphabet > alphabet, std::shared_ptr< const GeneticCode > gCode, const std::map< size_t, std::shared_ptr< const AlignmentDataInterface >> &mData, size_t nData, const std::map< std::string, std::string > &params, std::map< std::string, std::string > &sharedparams, const std::vector< double > &rateFreqs, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)
	Get A FrequencySet object for root frequencies (NH models) according to options. More...
static std::unique_ptr< FrequencySetInterface >	getRootFrequencySet (std::shared_ptr< const Alphabet > alphabet, std::shared_ptr< const GeneticCode > gCode, std::shared_ptr< const AlignmentDataInterface > data, const std::map< std::string, std::string > &params, std::map< std::string, std::string > &sharedparams, const std::vector< double > &rateFreqs, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)
static std::map< size_t, std::unique_ptr< FrequencySetInterface > >	getRootFrequencySets (std::shared_ptr< const Alphabet > alphabet, std::shared_ptr< const GeneticCode > gCode, const std::map< size_t, std::shared_ptr< const AlignmentDataInterface >> &mData, const std::map< std::string, std::string > &params, std::map< std::string, std::string > &sharedparams, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)
	The same, but returns a map <number, shared_ptr<FrequencySetInterface>>. More...
static std::unique_ptr< FrequencySetInterface >	getFrequencySet (std::shared_ptr< const Alphabet > alphabet, std::shared_ptr< const GeneticCode > gCode, const std::string &freqDescription, std::shared_ptr< const AlignmentDataInterface > data, std::map< std::string, std::string > &sharedParams, const std::vector< double > &rateFreqs, bool verbose=true, int warn=1)
	Get A FrequencySet object according to options. More...
static std::unique_ptr< FrequencySetInterface >	getFrequencySet (std::shared_ptr< const Alphabet > alphabet, std::shared_ptr< const GeneticCode > gCode, const std::string &freqDescription, const std::map< size_t, std::shared_ptr< const AlignmentDataInterface >> &mData, size_t nData, std::map< std::string, std::string > &sharedParams, const std::vector< double > &rateFreqs, bool verbose=true, int warn=1)
	Get A FrequencySet object according to options. More...
static map< size_t, std::unique_ptr< ModelPath > >	getModelPaths (const std::map< std::string, std::string > &params, const map< size_t, std::shared_ptr< BranchModelInterface >> &mModel, const string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)
	Build map of ModelPaths from a map of BranchModel. More...
static map< size_t, std::unique_ptr< ModelScenario > >	getModelScenarios (const std::map< std::string, std::string > &params, const map< size_t, std::shared_ptr< ModelPath >> &mModelPath, const map< size_t, std::shared_ptr< BranchModelInterface >> &mModel, const string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)
	Build map of ModelScenarios from a map of ModelPaths. More...
static std::unique_ptr< SubstitutionRegisterInterface >	getSubstitutionRegister (const std::string &regTypeDesc, std::shared_ptr< const StateMapInterface > stateMap, std::shared_ptr< const GeneticCode > genCode, std::shared_ptr< AlphabetIndex2 > &weights, std::shared_ptr< AlphabetIndex2 > &distances, bool verbose=true)
	Get a Register instance. More...
static std::unique_ptr< AutonomousSubstitutionProcessInterface >	getSubstitutionProcess (std::shared_ptr< const Alphabet > alphabet, std::shared_ptr< const GeneticCode > gCode, std::shared_ptr< const AlignmentDataInterface > data, const vector< std::shared_ptr< PhyloTree >> &vTree, const std::map< std::string, std::string > &params, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)
	Sets a SubstitutionProcess object according to options. More...
static std::unique_ptr< SubstitutionProcessCollection >	getSubstitutionProcessCollection (std::shared_ptr< const Alphabet > alphabet, std::shared_ptr< const GeneticCode > gCode, const map< size_t, std::shared_ptr< PhyloTree >> &mTree, const map< size_t, std::shared_ptr< BranchModelInterface >> &mMod, const map< size_t, std::shared_ptr< FrequencySetInterface >> &mRootFreq, const map< size_t, std::shared_ptr< DiscreteDistributionInterface >> &mDist, const map< size_t, std::shared_ptr< ModelScenario >> &mScen, const std::map< std::string, std::string > &params, map< string, string > &unparsedparams, const string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)
	Builds a SubstitutionProcessCollection from many maps of relevant objects. More...
static bool	addSubstitutionProcessCollectionMember (SubstitutionProcessCollection &SubProColl, size_t procNum, const std::map< std::string, std::string > &params, bool verbose=true, int warn=1)
	Adds a SubstitutionProcessCollectionMember to a Collection, under a given number. More...
static std::map< size_t, std::unique_ptr< SequenceEvolution > >	getSequenceEvolutions (std::shared_ptr< SubstitutionProcessCollection > SPC, const std::map< std::string, std::string > &params, map< string, string > &unparsedParams, const string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)
	Build a map of Sequence Evolution, ie ways how sequence evolve, which may use several processes. More...
static std::shared_ptr< PhyloLikelihoodContainer >	getPhyloLikelihoodContainer (Context &context, std::shared_ptr< SubstitutionProcessCollection > SPC, std::map< size_t, std::shared_ptr< SequenceEvolution >> &mSeqEvol, const std::map< size_t, std::shared_ptr< const AlignmentDataInterface >> &mData, const std::map< std::string, std::string > &params, const string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)
	Build a Phylogeny container from parameters map. More...
static MultipleDiscreteDistribution *	getMultipleDistributionDefaultInstance (const std::string &distDescription, std::map< std::string, std::string > &unparsedParameterValues, bool verbose=true)
	Build a multi-dimension distribution as a MultipleDiscreteDistribution object with default parameter values according to a keyval description. More...
static std::unique_ptr< DiscreteDistributionInterface >	getRateDistribution (const std::map< std::string, std::string > &params, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true)
	Build a DiscreteDistribution object according to options. More...
static std::map< size_t, std::shared_ptr< DiscreteDistributionInterface > >	getRateDistributions (const std::map< std::string, std::string > &params, const string &suffix="", bool suffixIsOptional=true, bool verbose=true)
static std::shared_ptr< PhyloLikelihoodInterface >	optimizeParameters (std::shared_ptr< PhyloLikelihoodInterface > lik, const std::map< std::string, std::string > &params, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)
	Optimize parameters according to options. More...
static void	checkEstimatedParameters (const ParameterList &pl)
	Check if parameter values are close to their definition boundary. More...
static std::unique_ptr< SubstitutionCountInterface >	getSubstitutionCount (std::shared_ptr< const Alphabet > alphabet, std::shared_ptr< const SubstitutionModelInterface > model, const std::map< std::string, std::string > &params, string suffix="", bool verbose=true, int warn=1)
	Get a SubstitutionCount instance. More...
template<class T >
static std::map< size_t, std::shared_ptr< T > >	uniqueToSharedMap (std::map< size_t, std::unique_ptr< T >> &mu)
static void	writeTree (const TreeTemplate< Node > &tree, const std::map< std::string, std::string > &params, const std::string &prefix="output.", const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, bool checkOnly=false, int warn=1)
	Output methods: More...
static void	writePhyloTrees (const std::vector< const PhyloTree * > &trees, const std::map< std::string, std::string > &params, const std::string &prefix="output.", const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, bool checkOnly=false, int warn=1)
	Write a tree according to options. More...
static void	writePhyloTrees (const SubstitutionProcessCollection &spc, const std::map< std::string, std::string > &params, const std::string &prefix="output.", const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, bool checkOnly=false, bool withIds=false, int warn=1)
	Write a tree according to options. More...
static void	printParameters (const BranchModelInterface &model, OutputStream &out, int warn=1)
	Output a SubstitutionModel description to a file. More...
static void	printParameters (const SubstitutionProcessInterface &process, OutputStream &out, int warn=1)
	Output a SubstitutionProcess description to a file. More...
static void	printParameters (const SubstitutionProcessCollection &collection, OutputStream &out, int warn=1, bool withAlias=true)
	Output a SubstitutionProcessCollection description to a file. More...
static void	printParameters (const PhyloLikelihoodContainer &phylocont, OutputStream &out, int warn=1)
	Output the description of the PhyloLikelihoods IN USE a a PhyloLikelihoodContainer to a file. More...
static void	printParameters (const SingleDataPhyloLikelihoodInterface &phylolike, OutputStream &out, size_t nPhylo=1, int warn=1)
static void	printParameters (const SequenceEvolution &evol, OutputStream &out, size_t nEvol=1, int warn=1)
	Output a Sequence Evolution description to a file. More...
static void	printParameters (const DiscreteDistributionInterface &rDist, OutputStream &out, bool withAlias=true)
	Output a DiscreteDistribution description to a file. More...
static void	printAnalysisInformation (const PhyloLikelihoodContainer &phylocont, const std::string &infosFile, int warn=1)
	Output information on the computation to a file. More...
static void	printAnalysisInformation (const SingleDataPhyloLikelihoodInterface &phylolike, const std::string &infosFile, int warn=1)
static void	printAnalysisInformation (const AlignedPhyloLikelihoodSetInterface &sOAP, const std::string &infosFile, int warn=1)

Detailed Description

This class provides some common tools for applications.

The functions parse some option file, create corresponding objects and send a pointer toward it.

The option files are supposed to follow this simple format:

parameterName = parameterContent

with one parameter per line.

See also

ApplicationTools

Definition at line 57 of file PhylogeneticsApplicationTools.h.

Constructor & Destructor Documentation

PhylogeneticsApplicationTools()

bpp::PhylogeneticsApplicationTools::PhylogeneticsApplicationTools

(

)

~PhylogeneticsApplicationTools()

virtual bpp::PhylogeneticsApplicationTools::~PhylogeneticsApplicationTools ( )

virtual

Member Function Documentation

addSubstitutionProcessCollectionMember()

bool PhylogeneticsApplicationTools::addSubstitutionProcessCollectionMember ( SubstitutionProcessCollection &  SubProColl, size_t  procNum, const std::map< std::string, std::string > &  params, bool  verbose = true, int  warn = 1  )

static

Adds a SubstitutionProcessCollectionMember to a Collection, under a given number.

Parameters

SubProColl	SubstitutionProcessCollection where the SubstitutionProcessCollectionMember will be added.
procNum	the number of the process
params	The attribute map where options may be found.
verbose	Print some info to the 'message' output stream.
warn	Set the warning level (0: always display warnings, >0 display warnings on demand).

Returns

if the addition has been successful.

Definition at line 1190 of file PhylogeneticsApplicationTools.cpp.

References bpp::SubstitutionProcessCollection::addDistribution(), bpp::SubstitutionProcessCollection::addOnePerBranchSubstitutionProcess(), bpp::SubstitutionProcessCollection::addSubstitutionProcess(), bpp::VectorTools::diff(), bpp::ApplicationTools::displayMessage(), bpp::ApplicationTools::displayResult(), bpp::ApplicationTools::displayWarning(), bpp::AssociationTreeGraphImplObserver< class, class, class >::getAllEdgesIndexes(), bpp::DiscreteDistributionInterface::getCategory(), bpp::ApplicationTools::getIntParameter(), bpp::DiscreteDistributionInterface::getName(), bpp::SubstitutionProcessCollection::getRateDistributionNumbers(), bpp::ApplicationTools::getStringParameter(), bpp::SubstitutionProcessCollection::getTree(), bpp::SubstitutionProcessCollection::hasDistributionNumber(), bpp::SubstitutionProcessCollection::hasFrequenciesNumber(), bpp::SubstitutionProcessCollection::hasModelNumber(), bpp::SubstitutionProcessCollection::hasModelScenario(), bpp::SubstitutionProcessCollection::hasTreeNumber(), bpp::KeyvalTools::parseProcedure(), bpp::SubstitutionProcessCollection::rateDistribution(), bpp::SubstitutionProcessCollectionMember::setModelScenario(), bpp::SubstitutionProcessCollection::substitutionProcess(), bpp::TextTools::toString(), and bpp::SubstitutionProcessCollection::tree().

checkEstimatedParameters()

void PhylogeneticsApplicationTools::checkEstimatedParameters ( const ParameterList &  pl )

static

Check if parameter values are close to their definition boundary.

This allows the detection of potential optimization issues. A warning message will be output for each problematic parameter.

Parameters

pl	A list of parameters. Parameters without constraint will be ignored.

Definition at line 2408 of file PhylogeneticsApplicationTools.cpp.

References bpp::ApplicationTools::displayWarning(), bpp::ParameterList::size(), and bpp::TextTools::toString().

getBranchModel()

std::unique_ptr< BranchModelInterface > PhylogeneticsApplicationTools::getBranchModel ( std::shared_ptr< const Alphabet >  alphabet, std::shared_ptr< const GeneticCode >  gCode, std::shared_ptr< const AlignmentDataInterface >  data, const std::map< std::string, std::string > &  params, std::map< std::string, std::string > &  unparsedparams, const std::string &  suffix = "", bool  suffixIsOptional = true, bool  verbose = true, int  warn = 1  )

static

Build a BranchModel (most general class of branch models) object according to options.

Creates a new branch model object according to model description syntax (see the Bio++ Program Suite manual for a detailed description of this syntax). The function also parses the parameter values and set them accordingly.

Parameters

alphabet	The alphabet to use in the model.
gCode	The genetic code to use (only for codon models, otherwise can be set to 0). If set to NULL and a codon model is requested, an Exception will be thrown.
data	A pointer toward an AlignmentDataInterface<std::string> used for the initialization of substitution model when this data is needed (typically use_observed_freq option). The alphabet associated to the data must be of the same type as the one specified for the model. May be equal to NULL, but in this case will be unavailable.
params	The attribute map where options may be found.
unparsedparams	the map of the aliases between parameters names.
suffix	A suffix to be applied to each attribute name.
suffixIsOptional	Tell if the suffix is absolutely required.
verbose	Print some info to the 'message' output stream.
warn	Set the warning level (0: always display warnings, >0 display warnings on demand).

Returns

A new BranchModel object.

Definition at line 502 of file PhylogeneticsApplicationTools.cpp.

References bpp::BppOSubstitutionModelFormat::ALL, bpp::ApplicationTools::getStringParameter(), bpp::BppOSubstitutionModelFormat::getUnparsedArguments(), bpp::AlphabetTools::isWordAlphabet(), bpp::BppOBranchModelFormat::readBranchModel(), and bpp::BppOSubstitutionModelFormat::setGeneticCode().

getBranchModels()

map< size_t, std::unique_ptr< BranchModelInterface > > PhylogeneticsApplicationTools::getBranchModels ( std::shared_ptr< const Alphabet >  alphabet, std::shared_ptr< const GeneticCode >  gCode, const std::map< size_t, std::shared_ptr< const AlignmentDataInterface >> &  mData, const std::map< std::string, std::string > &  params, std::map< std::string, std::string > &  unparsedparams, const std::string &  suffix = "", bool  suffixIsOptional = true, bool  verbose = true, int  warn = 1  )

static

The same as before, but returns a map <number, branch model>.

Definition at line 607 of file PhylogeneticsApplicationTools.cpp.

References bpp::BppOSubstitutionModelFormat::ALL, bpp::ApplicationTools::displayMessage(), bpp::ApplicationTools::displayResult(), bpp::ApplicationTools::getAFilePath(), bpp::AttributesTools::getAttributesMapFromFile(), bpp::ApplicationTools::getStringParameter(), bpp::BppOSubstitutionModelFormat::getUnparsedArguments(), bpp::ApplicationTools::matchingParameters(), bpp::BppOBranchModelFormat::readBranchModel(), bpp::BppOSubstitutionModelFormat::setGeneticCode(), bpp::BppOSubstitutionModelFormat::setVerbose(), and bpp::TextTools::toString().

getFrequencySet() [1/2]

std::unique_ptr< FrequencySetInterface > PhylogeneticsApplicationTools::getFrequencySet ( std::shared_ptr< const Alphabet >  alphabet, std::shared_ptr< const GeneticCode >  gCode, const std::string &  freqDescription, const std::map< size_t, std::shared_ptr< const AlignmentDataInterface >> &  mData, size_t  nData, std::map< std::string, std::string > &  sharedParams, const std::vector< double > &  rateFreqs, bool  verbose = true, int  warn = 1  )

static

Get A FrequencySet object according to options.

Parameters

alphabet	The alphabet to use.
gCode	The genetic code to use (only for codon alphabets, otherwise can be set to 0). If set to NULL and a codon frequencies set is requested, an Exception will be thrown.
freqDescription	A string in the keyval syntax describing the frequency set to use.
mData	A map <size_t, AlignmentDataInterface> used for the initialization of the frequency set when this data is needed (typically use_observed_freq option). The alphabet associated to the data must be of the same type as the one specified for the frequency set. May be equal to NULL, but in this case will be unavailable.
nData	the number of the AlignmentDataInterface used in the mData map. 0 if this number has not been defined.
sharedParams	(out) remote parameters will be recorded here.
rateFreqs	A vector of rate categories frequencies in case of a Markov Modulated Markov Model. Ignored if a vector with size 0 is passed.
verbose	Print some info to the 'message' output stream.
warn	Set the warning level (0: always display warnings, >0 display warnings on demand).

Returns

A new FrequencySet object according to options specified.

Definition at line 686 of file PhylogeneticsApplicationTools.cpp.

References bpp::BppOFrequencySetFormat::ALL, bpp::BppOFrequencySetFormat::getUnparsedArguments(), bpp::AlphabetTools::isCodonAlphabet(), bpp::BppOFrequencySetFormat::readFrequencySet(), and bpp::BppOFrequencySetFormat::setGeneticCode().

getFrequencySet() [2/2]

static std::unique_ptr<FrequencySetInterface> bpp::PhylogeneticsApplicationTools::getFrequencySet ( std::shared_ptr< const Alphabet >  alphabet, std::shared_ptr< const GeneticCode >  gCode, const std::string &  freqDescription, std::shared_ptr< const AlignmentDataInterface >  data, std::map< std::string, std::string > &  sharedParams, const std::vector< double > &  rateFreqs, bool  verbose = true, int  warn = 1  )

inlinestatic

Get A FrequencySet object according to options.

Parameters

alphabet	The alphabet to use.
gCode	The genetic code to use (only for codon alphabets, otherwise can be set to 0). If set to NULL and a codon frequencies set is requested, an Exception will be thrown.
freqDescription	A string in the keyval syntax describing the frequency set to use.
data	A pointer toward an AlignmentDataInterface used for the initialization of the frequency set when this data is needed (typically use_observed_freq option). The alphabet associated to the data must be of the same type as the one specified for the frequency set. May be equal to NULL, but in this case will be unavailable.
sharedParams	(out) remote parameters will be recorded here.
rateFreqs	A vector of rate categories frequencies in case of a Markov Modulated Markov Model. Ignored if a vector with size 0 is passed.
verbose	Print some info to the 'message' output stream.
warn	Set the warning level (0: always display warnings, >0 display warnings on demand).

Returns

A new FrequencySet object according to options specified.

Definition at line 325 of file PhylogeneticsApplicationTools.h.

getModelPaths()

map< size_t, std::unique_ptr< ModelPath > > PhylogeneticsApplicationTools::getModelPaths ( const std::map< std::string, std::string > &  params, const map< size_t, std::shared_ptr< BranchModelInterface >> &  mModel, const string &  suffix = "", bool  suffixIsOptional = true, bool  verbose = true, int  warn = 1  )

static

Build map of ModelPaths from a map of BranchModel.

See the Bio++ Program Suite manual for a description of available options.

Parameters

params	The attribute map where options may be found.
mModel	A map of shared pointers of BranchModels.
suffix	A suffix to be applied to each attribute name.
suffixIsOptional	Tell if the suffix is absolutely required.
verbose	Print some info to the 'message' output stream.
warn	Set the warning level (0: always display warnings, >0 display warnings on demand).

Warning: the model FIRST described in a ModelPath will be the leading model (ie on which the submodel probabilities are chosen).

Returns

A map of ModelPath shared_pointers objects according to the specified options.

Definition at line 847 of file PhylogeneticsApplicationTools.cpp.

References bpp::ApplicationTools::displayMessage(), bpp::ApplicationTools::displayResult(), bpp::ApplicationTools::getAFilePath(), bpp::AttributesTools::getAttributesMapFromFile(), bpp::ApplicationTools::getStringParameter(), bpp::StringTokenizer::hasMoreToken(), bpp::ApplicationTools::matchingParameters(), bpp::StringTokenizer::nextToken(), bpp::TextTools::toString(), and bpp::VectorTools::vectorIntersection().

getModelScenarios()

map< size_t, std::unique_ptr< ModelScenario > > PhylogeneticsApplicationTools::getModelScenarios ( const std::map< std::string, std::string > &  params, const map< size_t, std::shared_ptr< ModelPath >> &  mModelPath, const map< size_t, std::shared_ptr< BranchModelInterface >> &  mModel, const string &  suffix = "", bool  suffixIsOptional = true, bool  verbose = true, int  warn = 1  )

static

Build map of ModelScenarios from a map of ModelPaths.

See the Bio++ Program Suite manual for a description of available options.

Parameters

params	The attribute map where options may be found.
mModelPath	A map of shared pointers of ModelPaths.
mModel	A map of shared pointers of BranchModels.
suffix	A suffix to be applied to each attribute name.
suffixIsOptional	Tell if the suffix is absolutely required.
verbose	Print some info to the 'message' output stream.
warn	Set the warning level (0: always display warnings, >0 display warnings on demand).

Returns

A map of ModelScenarios shared_pointers objects according to the specified options.

Definition at line 964 of file PhylogeneticsApplicationTools.cpp.

References bpp::ApplicationTools::displayMessage(), bpp::ApplicationTools::displayResult(), bpp::ApplicationTools::getAFilePath(), bpp::AttributesTools::getAttributesMapFromFile(), bpp::ApplicationTools::getStringParameter(), bpp::StringTokenizer::hasMoreToken(), bpp::ApplicationTools::matchingParameters(), bpp::StringTokenizer::nextToken(), and bpp::TextTools::toString().

getMultipleDistributionDefaultInstance()

MultipleDiscreteDistribution * PhylogeneticsApplicationTools::getMultipleDistributionDefaultInstance ( const std::string &  distDescription, std::map< std::string, std::string > &  unparsedParameterValues, bool  verbose = true  )

static

Build a multi-dimension distribution as a MultipleDiscreteDistribution object with default parameter values according to a keyval description.

Check the Bio++ Program Suite documentation for a description of the syntax. It is mainly for internal usage, you're probably looking for the getRateDistribution function.

Parameters

distDescription	A string describing the model in the keyval syntax.
unparsedParameterValues	[out] a map that will contain all the distribution parameters names and their corresponding unparsed value, if they were found.
verbose	Print some info to the 'message' output stream.

Returns

A new MultipleDiscreteDistribution object according to options specified.

Definition at line 2252 of file PhylogeneticsApplicationTools.cpp.

References bpp::ParameterList::getParameterNames(), bpp::MultipleDiscreteDistribution::getParameterNameWithoutNamespace(), bpp::MultipleDiscreteDistribution::getParameters(), bpp::MultipleDiscreteDistribution::getParameterValue(), bpp::StringTokenizer::hasMoreToken(), bpp::StringTokenizer::nextToken(), bpp::KeyvalTools::parseProcedure(), bpp::TextTools::toDouble(), and bpp::TextTools::toString().

getPhyloLikelihoodContainer()

std::shared_ptr< PhyloLikelihoodContainer > PhylogeneticsApplicationTools::getPhyloLikelihoodContainer ( Context &  context, std::shared_ptr< SubstitutionProcessCollection >  SPC, std::map< size_t, std::shared_ptr< SequenceEvolution >> &  mSeqEvol, const std::map< size_t, std::shared_ptr< const AlignmentDataInterface >> &  mData, const std::map< std::string, std::string > &  params, const string &  suffix = "", bool  suffixIsOptional = true, bool  verbose = true, int  warn = 1  )

static

Build a Phylogeny container from parameters map.

Default data compression is simple.

The PhyloLikelihood with number 0 is a specific PhyloLikelihood, with name "result" in the BppO file.

Definition at line 1837 of file PhylogeneticsApplicationTools.cpp.

References bpp::ParameterList::addParameter(), bpp::ApplicationTools::displayMessage(), bpp::ApplicationTools::displayResult(), bpp::ApplicationTools::displayWarning(), bpp::ApplicationTools::getIntParameter(), bpp::FullHmmTransitionMatrix::getParameters(), bpp::ApplicationTools::getStringParameter(), bpp::ApplicationTools::matchingParameters(), bpp::PhyloLikelihoodFormula::output(), bpp::KeyvalTools::parseProcedure(), bpp::VectorTools::paste(), bpp::FullHmmTransitionMatrix::setTransitionProbabilities(), and bpp::TextTools::toString().

getPhyloTrees()

map< size_t, std::shared_ptr< PhyloTree > > PhylogeneticsApplicationTools::getPhyloTrees ( const std::map< std::string, std::string > &  params, const std::map< size_t, std::shared_ptr< const AlignmentDataInterface >> &  mSeq, std::map< std::string, std::string > &  unparsedParams, const std::string &  prefix = "input.", const std::string &  suffix = "", bool  suffixIsOptional = true, bool  verbose = true, int  warn = 1  )

static

Build a map of <number,PhyloTree> according to options.

See the Bio++ Program Suite manual for a description of available options.

Parameters

params	The attribute map where options may be found.
mSeq	A map of pointers of AlignmentDataInterface<std::string>s, necessary in case of random trees.
unparsedParams	A map of parameters (BrLen) that will be aliased after.
prefix	A prefix to be applied to each attribute name.
suffix	A suffix to be applied to each attribute name.
suffixIsOptional	Tell if the suffix is absolutely required.
verbose	Print some info to the 'message' output stream.
warn	Set the warning level (0: always display warnings, >0 display warnings on demand).

Returns

A new vector of Tree objects according to the specified options.

Definition at line 150 of file PhylogeneticsApplicationTools.cpp.

References bpp::PhyloTreeTools::buildFromTreeTemplate(), bpp::PhyloTreeTools::computeBranchLengthsGrafen(), bpp::PhyloTreeTools::constrainedMidPointRooting(), bpp::PhyloTreeTools::convertToClockTree(), bpp::ApplicationTools::displayMessage(), bpp::ApplicationTools::displayResult(), bpp::ApplicationTools::displayWarning(), bpp::ApplicationTools::getAFilePath(), bpp::ApplicationTools::getDoubleParameter(), bpp::PhyloTreeTools::getHeight(), bpp::TreeTemplateTools::getRandomTree(), bpp::ApplicationTools::getStringParameter(), bpp::TextTools::isDecimalInteger(), bpp::ApplicationTools::matchingParameters(), bpp::KeyvalTools::parseProcedure(), bpp::IMultiPhyloTree::readPhyloTrees(), bpp::TextTools::toDouble(), bpp::TextTools::toInt(), and bpp::TextTools::toString().

getRateDistribution()

unique_ptr< DiscreteDistributionInterface > PhylogeneticsApplicationTools::getRateDistribution ( const std::map< std::string, std::string > &  params, const std::string &  suffix = "", bool  suffixIsOptional = true, bool  verbose = true  )

static

Build a DiscreteDistribution object according to options.

Creates a new rate distribution object according to distribution description syntax (see the Bio++ Program Suite manual for a detailed description of this syntax). The function also parses the parameter values and set them accordingly.

Parameters

params	The attribute map where options may be found.
suffix	A suffix to be applied to each attribute name.
suffixIsOptional	Tell if the suffix is absolutely required.
verbose	Print some info to the 'message' output stream.

Returns

A new DiscreteDistribution object according to options specified.

Definition at line 2298 of file PhylogeneticsApplicationTools.cpp.

References bpp::ApplicationTools::displayResult(), bpp::ApplicationTools::getStringParameter(), bpp::KeyvalTools::parseProcedure(), bpp::BppORateDistributionFormat::readDiscreteDistribution(), and bpp::TextTools::toString().

getRateDistributions()

map< size_t, std::shared_ptr< DiscreteDistributionInterface > > PhylogeneticsApplicationTools::getRateDistributions ( const std::map< std::string, std::string > &  params, const string &  suffix = "", bool  suffixIsOptional = true, bool  verbose = true  )

static

brief Same as before, but using several distributions.

Definition at line 541 of file PhylogeneticsApplicationTools.cpp.

References bpp::ApplicationTools::displayMessage(), bpp::ApplicationTools::getAFilePath(), bpp::AttributesTools::getAttributesMapFromFile(), bpp::ApplicationTools::getStringParameter(), bpp::TextTools::isDecimalInteger(), bpp::ApplicationTools::matchingParameters(), bpp::BppORateDistributionFormat::readDiscreteDistribution(), bpp::TextTools::toInt(), and bpp::TextTools::toString().

getRootFrequencySet() [1/2]

std::unique_ptr< FrequencySetInterface > PhylogeneticsApplicationTools::getRootFrequencySet ( std::shared_ptr< const Alphabet >  alphabet, std::shared_ptr< const GeneticCode >  gCode, const std::map< size_t, std::shared_ptr< const AlignmentDataInterface >> &  mData, size_t  nData, const std::map< std::string, std::string > &  params, std::map< std::string, std::string > &  sharedparams, const std::vector< double > &  rateFreqs, const std::string &  suffix = "", bool  suffixIsOptional = true, bool  verbose = true, int  warn = 1  )

static

Get A FrequencySet object for root frequencies (NH models) according to options.

Parameters

alphabet	The alphabet to use.
gCode	The genetic code to use (only for codon alphabets, otherwise can be set to 0). If set to NULL and a codon frequencies set is requested, an Exception will be thrown.
mData	A map <size_t, AlignmentDataInterface> used for the initialization of the frequency set when this data is needed (typically use_observed_freq option). The alphabet associated to the data must be of the same type as the one specified for the frequency set. May be equal to NULL, but in this case will be unavailable.
nData	the number of the AlignmentDataInterface used in the mData map. 0 if this number has not been defined.
params	The attribute map where options may be found.
sharedparams	The attribute map of aliases (out).
rateFreqs	A vector of rate categories frequencies in case of a Markov Modulated Markov Model. Ignored if a vector with size 0 is passed.
suffix	A suffix to be applied to each attribute name.
suffixIsOptional	Tell if the suffix is absolutely required.
verbose	Print some info to the 'message' output stream.
warn	Set the warning level (0: always display warnings, >0 display warnings on demand).

Returns

A new FrequencySet object according to options specified.

Definition at line 722 of file PhylogeneticsApplicationTools.cpp.

References bpp::ApplicationTools::displayResult(), and bpp::ApplicationTools::getStringParameter().

Referenced by getRootFrequencySet(), and bpp::LegacyPhylogeneticsApplicationTools::setSubstitutionModelSet().

getRootFrequencySet() [2/2]

static std::unique_ptr<FrequencySetInterface> bpp::PhylogeneticsApplicationTools::getRootFrequencySet ( std::shared_ptr< const Alphabet >  alphabet, std::shared_ptr< const GeneticCode >  gCode, std::shared_ptr< const AlignmentDataInterface >  data, const std::map< std::string, std::string > &  params, std::map< std::string, std::string > &  sharedparams, const std::vector< double > &  rateFreqs, const std::string &  suffix = "", bool  suffixIsOptional = true, bool  verbose = true, int  warn = 1  )

inlinestatic

Definition at line 271 of file PhylogeneticsApplicationTools.h.

References getRootFrequencySet().

getRootFrequencySets()

map< size_t, std::unique_ptr< FrequencySetInterface > > PhylogeneticsApplicationTools::getRootFrequencySets ( std::shared_ptr< const Alphabet >  alphabet, std::shared_ptr< const GeneticCode >  gCode, const std::map< size_t, std::shared_ptr< const AlignmentDataInterface >> &  mData, const std::map< std::string, std::string > &  params, std::map< std::string, std::string > &  sharedparams, const std::string &  suffix = "", bool  suffixIsOptional = true, bool  verbose = true, int  warn = 1  )

static

The same, but returns a map <number, shared_ptr<FrequencySetInterface>>.

Definition at line 759 of file PhylogeneticsApplicationTools.cpp.

References bpp::BppOFrequencySetFormat::ALL, bpp::ApplicationTools::displayMessage(), bpp::ApplicationTools::displayResult(), bpp::ApplicationTools::getAFilePath(), bpp::AttributesTools::getAttributesMapFromFile(), bpp::ApplicationTools::getStringParameter(), bpp::BppOFrequencySetFormat::getUnparsedArguments(), bpp::ApplicationTools::matchingParameters(), bpp::KeyvalTools::parseProcedure(), bpp::BppOFrequencySetFormat::readFrequencySet(), bpp::BppOFrequencySetFormat::setGeneticCode(), and bpp::TextTools::toString().

getSequenceEvolutions()

map< size_t, unique_ptr< SequenceEvolution > > PhylogeneticsApplicationTools::getSequenceEvolutions ( std::shared_ptr< SubstitutionProcessCollection >  SPC, const std::map< std::string, std::string > &  params, map< string, string > &  unparsedParams, const string &  suffix = "", bool  suffixIsOptional = true, bool  verbose = true, int  warn = 1  )

static

Build a map of Sequence Evolution, ie ways how sequence evolve, which may use several processes.

Definition at line 1625 of file PhylogeneticsApplicationTools.cpp.

References bpp::ParameterList::addParameter(), bpp::ApplicationTools::displayMessage(), bpp::ApplicationTools::displayResult(), bpp::ApplicationTools::getIntParameter(), bpp::FullHmmTransitionMatrix::getParameters(), bpp::ApplicationTools::getStringParameter(), bpp::ApplicationTools::matchingParameters(), bpp::KeyvalTools::parseProcedure(), bpp::VectorTools::paste(), bpp::FullHmmTransitionMatrix::setTransitionProbabilities(), and bpp::TextTools::toString().

getSubstitutionCount()

unique_ptr< SubstitutionCountInterface > PhylogeneticsApplicationTools::getSubstitutionCount ( std::shared_ptr< const Alphabet >  alphabet, std::shared_ptr< const SubstitutionModelInterface >  model, const std::map< std::string, std::string > &  params, string  suffix = "", bool  verbose = true, int  warn = 1  )

static

Get a SubstitutionCount instance.

Parameters

alphabet	The alphabet to use.
model	The model to use.
params	The attribute map where options may be found.
suffix	Optional suffix for command name.
verbose	Print some info to the 'message' output stream.
warn	Set the warning level (0: always display warnings, >0 display warnings on demand).

Returns

A SubstitutionCount object.

Definition at line 3631 of file PhylogeneticsApplicationTools.cpp.

References bpp::ApplicationTools::displayError(), bpp::ApplicationTools::displayMessage(), bpp::ApplicationTools::displayResult(), bpp::SequenceApplicationTools::getAlphabetIndex2(), bpp::ApplicationTools::getStringParameter(), and bpp::KeyvalTools::parseProcedure().

getSubstitutionModel()

std::unique_ptr< SubstitutionModelInterface > PhylogeneticsApplicationTools::getSubstitutionModel ( std::shared_ptr< const Alphabet >  alphabet, std::shared_ptr< const GeneticCode >  gCode, std::shared_ptr< const AlignmentDataInterface >  data, const std::map< std::string, std::string > &  params, std::map< std::string, std::string > &  unparsedparams, const std::string &  suffix = "", bool  suffixIsOptional = true, bool  verbose = true, int  warn = 1  )

static

Build a SubstitutionModel object according to options (ie a BranchModel with a generator).

Creates a new substitution model object according to model description syntax (see the Bio++ Program Suite manual for a detailed description of this syntax). The function also parses the parameter values and set them accordingly.

Parameters

alphabet	The alphabet to use in the model.
gCode	The genetic code to use (only for codon models, otherwise can be set to 0). If set to NULL and a codon model is requested, an Exception will be thrown.
data	A pointer toward an AlignmentDataInterface<std::string> used for the initialization of substitution model when this data is needed (typically use_observed_freq option). The alphabet associated to the data must be of the same type as the one specified for the model. May be equal to NULL, but in this case will be unavailable.
params	The attribute map where options may be found.
unparsedparams	the map of the aliases between parameters names.
suffix	A suffix to be applied to each attribute name.
suffixIsOptional	Tell if the suffix is absolutely required.
verbose	Print some info to the 'message' output stream.
warn	Set the warning level (0: always display warnings, >0 display warnings on demand).

Returns

A new SubstitutionModel object.

Definition at line 466 of file PhylogeneticsApplicationTools.cpp.

References bpp::BppOSubstitutionModelFormat::ALL, bpp::ApplicationTools::getStringParameter(), bpp::BppOSubstitutionModelFormat::getUnparsedArguments(), bpp::AlphabetTools::isWordAlphabet(), bpp::BppOSubstitutionModelFormat::readSubstitutionModel(), and bpp::BppOSubstitutionModelFormat::setGeneticCode().

getSubstitutionProcess()

unique_ptr< AutonomousSubstitutionProcessInterface > PhylogeneticsApplicationTools::getSubstitutionProcess ( std::shared_ptr< const Alphabet >  alphabet, std::shared_ptr< const GeneticCode >  gCode, std::shared_ptr< const AlignmentDataInterface >  data, const vector< std::shared_ptr< PhyloTree >> &  vTree, const std::map< std::string, std::string > &  params, const std::string &  suffix = "", bool  suffixIsOptional = true, bool  verbose = true, int  warn = 1  )

static

Sets a SubstitutionProcess object according to options.

See the Bio++ Program Suite manual for a description of available options.

Parameters

alphabet	The alphabet to use in all models.
gCode	The genetic code to use (only for codon alphabets, otherwise can be set to 0). If set to NULL and a codon frequencies set is requested, an Exception will be thrown.
data	an AlignmentDataInterface<std::string> used for the initialization of process set when this data is needed (typically use_observed_freq option). The alphabet associated to the data must be of the same type as the one specified for the process set. May be equal to NULL, but in this case will be unavailable.
vTree	A vector of pointers of Trees, used to set processes.
params	The attribute map where options may be found.
suffix	A suffix to be applied to each attribute name.
suffixIsOptional	Tell if the suffix is absolutely required.
verbose	Print some info to the 'message' output stream.
warn	Set the warning level (0: always display warnings, >0 display warnings on demand).

Returns

A pointer to a AutonomousSubstitutionProcess.

Definition at line 1097 of file PhylogeneticsApplicationTools.cpp.

References bpp::SubstitutionProcessCollectionMember::getModel(), bpp::SubstitutionProcessCollectionMember::getModelNumbers(), bpp::SubstitutionProcessCollectionMember::getModelScenario(), bpp::SubstitutionProcessCollectionMember::getNodesWithModel(), bpp::SubstitutionProcessCollectionMember::getParametrizablePhyloTree(), bpp::SubstitutionProcessCollectionMember::getRateDistribution(), and bpp::SubstitutionProcessCollectionMember::getRootFrequencySet().

getSubstitutionProcessCollection()

unique_ptr< SubstitutionProcessCollection > PhylogeneticsApplicationTools::getSubstitutionProcessCollection ( std::shared_ptr< const Alphabet >  alphabet, std::shared_ptr< const GeneticCode >  gCode, const map< size_t, std::shared_ptr< PhyloTree >> &  mTree, const map< size_t, std::shared_ptr< BranchModelInterface >> &  mMod, const map< size_t, std::shared_ptr< FrequencySetInterface >> &  mRootFreq, const map< size_t, std::shared_ptr< DiscreteDistributionInterface >> &  mDist, const map< size_t, std::shared_ptr< ModelScenario >> &  mScen, const std::map< std::string, std::string > &  params, map< string, string > &  unparsedparams, const string &  suffix = "", bool  suffixIsOptional = true, bool  verbose = true, int  warn = 1  )

static

Builds a SubstitutionProcessCollection from many maps of relevant objects.

Parameters

alphabet	The alphabet to use in all models.
gCode	The genetic code to use (only for codon alphabets, otherwise can be set to 0). If set to NULL and a codon frequencies set is requested, an Exception will be thrown.
mTree	Map of the PhyloTrees
mMod	Map of Branch Models
mRootFreq	Map of FrequencySet
mDist	Map of Rate Distributions
mScen	Map of Scenarios
params	The attribute map where options may be found.
unparsedparams	map of the attributes that will not be parsed there
suffix	A suffix to be applied to each attribute name.
suffixIsOptional	Tell if the suffix is absolutely required.
verbose	Print some info to the 'message' output stream.
warn	Set the warning level (0: always display warnings, >0 display warnings on demand).

Returns

A shared pointer to a SubstitutionProcessCollection.

Definition at line 1475 of file PhylogeneticsApplicationTools.cpp.

References bpp::ApplicationTools::displayMessage(), bpp::ApplicationTools::displayResult(), bpp::TextTools::isDecimalInteger(), bpp::ApplicationTools::matchingParameters(), bpp::TextTools::toDouble(), and bpp::TextTools::toString().

getSubstitutionRegister()

unique_ptr< SubstitutionRegisterInterface > PhylogeneticsApplicationTools::getSubstitutionRegister ( const std::string &  regTypeDesc, std::shared_ptr< const StateMapInterface >  stateMap, std::shared_ptr< const GeneticCode >  genCode, std::shared_ptr< AlphabetIndex2 > &  weights, std::shared_ptr< AlphabetIndex2 > &  distances, bool  verbose = true  )

static

Get a Register instance.

Parameters

regTypeDesc	The description of the register.
stateMap	The stateMap to use.
genCode	when codon Alphabet, the genetic Code (otherwise, default : 0)
weights	[out] AlphabetIndex2 pointer if "weights" argument is provided, null otherwise
distances	[out] AlphabetIndex2 pointer if "distances" argument is provided, null otherwise
verbose	if outputs reading

Returns

A SubstitutionRegister object.

Definition at line 3704 of file PhylogeneticsApplicationTools.cpp.

References bpp::ApplicationTools::displayResult(), bpp::SequenceApplicationTools::getAlphabetIndex2(), bpp::ApplicationTools::getBooleanParameter(), bpp::ApplicationTools::getStringParameter(), bpp::AlphabetTools::isCodonAlphabet(), bpp::AlphabetTools::isNucleicAlphabet(), bpp::AlphabetTools::isProteicAlphabet(), bpp::KeyvalTools::parseProcedure(), bpp::CategorySubstitutionRegister::setStationarity(), and bpp::TextTools::toString().

Referenced by bpp::BppOSubstitutionModelFormat::readSubstitutionModel(), and bpp::BppOTransitionModelFormat::readTransitionModel().

getTree()

unique_ptr< Tree > PhylogeneticsApplicationTools::getTree ( const std::map< std::string, std::string > &  params, const std::string &  prefix = "input.", const std::string &  suffix = "", bool  suffixIsOptional = true, bool  verbose = true, int  warn = 1  )

static

Build a Tree object according to options.

See the Bio++ Program Suite manual for a description of available options.

Parameters

params	The attribute map where options may be found.
prefix	A prefix to be applied to each attribute name.
suffix	A suffix to be applied to each attribute name.
suffixIsOptional	Tell if the suffix is absolutely required.
verbose	Print some info to the 'message' output stream.
warn	Set the warning level (0: always display warnings, >0 display warnings on demand).

Returns

A new Tree object according to the specified options.

Definition at line 97 of file PhylogeneticsApplicationTools.cpp.

References bpp::ApplicationTools::displayResult(), bpp::ApplicationTools::getAFilePath(), bpp::ApplicationTools::getStringParameter(), and bpp::BppOTreeReaderFormat::readITree().

getTrees()

vector< unique_ptr< Tree > > PhylogeneticsApplicationTools::getTrees ( const std::map< std::string, std::string > &  params, const std::string &  prefix = "input.", const std::string &  suffix = "", bool  suffixIsOptional = true, bool  verbose = true, int  warn = 1  )

static

Build a list of Tree objects according to options.

See the Bio++ Program Suite manual for a description of available options.

Parameters

params	The attribute map where options may be found.
prefix	A prefix to be applied to each attribute name.
suffix	A suffix to be applied to each attribute name.
suffixIsOptional	Tell if the suffix is absolutely required.
verbose	Print some info to the 'message' output stream.
warn	Set the warning level (0: always display warnings, >0 display warnings on demand).

Returns

A new vector of Tree objects according to the specified options.

Definition at line 120 of file PhylogeneticsApplicationTools.cpp.

References bpp::ApplicationTools::displayResult(), bpp::ApplicationTools::getAFilePath(), bpp::ApplicationTools::getStringParameter(), and bpp::BppOMultiTreeReaderFormat::readIMultiTree().

optimizeParameters()

std::shared_ptr< PhyloLikelihoodInterface > PhylogeneticsApplicationTools::optimizeParameters ( std::shared_ptr< PhyloLikelihoodInterface >  lik, const std::map< std::string, std::string > &  params, const std::string &  suffix = "", bool  suffixIsOptional = true, bool  verbose = true, int  warn = 1  )

static

Optimize parameters according to options.

Parameters

lik	The PhyloLikelihood function to optimize.
params	The attribute map where options may be found.
suffix	A suffix to be applied to each attribute name.
suffixIsOptional	Tell if the suffix is absolutely required.
verbose	Print some info to the 'message' output stream.
warn	Set the warning level (0: always display warnings, >0 display warnings on demand).

Returns

A pointer toward the final likelihood object.

This pointer may be the same as passed in argument (tl), but in some cases the algorithm clone this object. We may change this behavior in the future... You hence should write something like

tl = PhylogeneticsApplicationTools::optimizeParameters(tl, ...);

Definition at line 2327 of file PhylogeneticsApplicationTools.cpp.

References bpp::OptimizationTools::OptimizationOptions::backupFile, bpp::AutoParameter::CONSTRAINTS_AUTO, bpp::ApplicationTools::displayResult(), bpp::ApplicationTools::getStringParameter(), bpp::ParameterList::matchParametersValues(), bpp::OptimizationTools::OptimizationOptions::messenger, bpp::OptimizationTools::OptimizationOptions::nbEvalMax, bpp::OptimizationTools::OptimizationOptions::nstep, bpp::OptimizationTools::OPTIMIZATION_BFGS, bpp::OptimizationTools::OPTIMIZATION_BRENT, bpp::OptimizationTools::OPTIMIZATION_NEWTON, bpp::OptimizationTools::optimizeNumericalParameters(), bpp::OptimizationTools::optimizeNumericalParameters2(), bpp::OptimizationTools::OptimizationOptions::optMethodModel, bpp::OptimizationTools::OptimizationOptions::parameters, bpp::OptimizationTools::OptimizationOptions::profiler, bpp::OptimizationTools::OptimizationOptions::tolerance, and bpp::TextTools::toString().

printAnalysisInformation() [1/3]

void PhylogeneticsApplicationTools::printAnalysisInformation ( const AlignedPhyloLikelihoodSetInterface &  sOAP, const std::string &  infosFile, int  warn = 1  )

static

Definition at line 3240 of file PhylogeneticsApplicationTools.cpp.

References bpp::DataTable::addRow(), bpp::exp(), bpp::AlignedPhyloLikelihoodInterface::getLogLikelihoodForASite(), bpp::AlignedPhyloLikelihoodSetInterface::getLogLikelihoodForASiteForAPhyloLikelihood(), bpp::AlignedPhyloLikelihoodInterface::getNumberOfSites(), bpp::PhyloLikelihoodSetInterface::getNumbersOfPhyloLikelihoods(), bpp::AlignedPhyloLikelihoodMixture::getPhyloProbabilities(), bpp::AlignedPhyloLikelihoodAutoCorrelation::getPosteriorProbabilitiesForASitePerAligned(), bpp::AlignedPhyloLikelihoodHmm::getPosteriorProbabilitiesForASitePerAligned(), bpp::VectorTools::sumExp(), bpp::TextTools::toString(), and bpp::DataTable::write().

printAnalysisInformation() [2/3]

void PhylogeneticsApplicationTools::printAnalysisInformation ( const PhyloLikelihoodContainer &  phylocont, const std::string &  infosFile, int  warn = 1  )

static

Output information on the computation to a file.

Parameters

phylocont	The phylolikelihood to serialize.
infosFile	The name of the file where to print.
warn	Set the warning level (0: always display warnings, >0 display warnings on demand).

Definition at line 3187 of file PhylogeneticsApplicationTools.cpp.

References bpp::PhyloLikelihoodContainer::getNumbersOfPhyloLikelihoods(), bpp::TextTools::toString(), and bpp::VectorTools::unique().

printAnalysisInformation() [3/3]

void PhylogeneticsApplicationTools::printAnalysisInformation ( const SingleDataPhyloLikelihoodInterface &  phylolike, const std::string &  infosFile, int  warn = 1  )

static

Definition at line 3334 of file PhylogeneticsApplicationTools.cpp.

References bpp::DataTable::addRow(), bpp::CoreSiteInterface::getCoordinate(), bpp::SingleDataPhyloLikelihoodInterface::getData(), bpp::AlignedPhyloLikelihoodInterface::getLogLikelihoodForASite(), bpp::SymbolListTools::isComplete(), bpp::SymbolListTools::isConstant(), bpp::numeric::log(), bpp::PartitionSequenceEvolution::mapOfProcessSites(), bpp::TextTools::toString(), bpp::VectorTools::whichMax(), and bpp::DataTable::write().

printParameters() [1/7]

void PhylogeneticsApplicationTools::printParameters ( const BranchModelInterface &  model, OutputStream &  out, int  warn = 1  )

static

Output a SubstitutionModel description to a file.

Parameters

model	The model to serialize.
out	The stream where to print.
warn	Set the warning level (0: always display warnings, >0 display warnings on demand).

Definition at line 2549 of file PhylogeneticsApplicationTools.cpp.

References bpp::BppOSubstitutionModelFormat::ALL, bpp::OutputStream::endLine(), and bpp::BppOSubstitutionModelFormat::write().

printParameters() [2/7]

void PhylogeneticsApplicationTools::printParameters ( const DiscreteDistributionInterface &  rDist, OutputStream &  out, bool  withAlias = true  )

static

Output a DiscreteDistribution description to a file.

Parameters

rDist	The rate distribution to serialize.
out	The stream where to print.
withAlias	outputs the alias names of the aliased Parameters instead of the values (default : true).

Definition at line 3617 of file PhylogeneticsApplicationTools.cpp.

References bpp::OutputStream::endLine(), and bpp::BppORateDistributionFormat::writeDiscreteDistribution().

printParameters() [3/7]

void PhylogeneticsApplicationTools::printParameters ( const PhyloLikelihoodContainer &  phylocont, OutputStream &  out, int  warn = 1  )

static

Output the description of the PhyloLikelihoods IN USE a a PhyloLikelihoodContainer to a file.

Starting from PhyloLikelihood with number 0 (with name "result"), PhyloLikelihoods involved in the computation are successively serialized.

Parameters

phylocont	The PhyloLikelihoodContainer to serialize.
out	The stream where to print.
warn	Set the warning level (0: always display warnings, >0 display warnings on demand).

Definition at line 2914 of file PhylogeneticsApplicationTools.cpp.

References bpp::copyEigenToBpp(), bpp::OutputStream::endLine(), bpp::StringTokenizer::hasMoreToken(), bpp::StringTokenizer::nextToken(), bpp::VectorTools::paste(), bpp::MatrixTools::print(), bpp::OutputStream::setPrecision(), and bpp::TextTools::toString().

printParameters() [4/7]

void PhylogeneticsApplicationTools::printParameters ( const SequenceEvolution &  evol, OutputStream &  out, size_t  nEvol = 1, int  warn = 1  )

static

Output a Sequence Evolution description to a file.

Parameters

evol	The Sequence Evolution to serialize.
out	The stream where to print.
nEvol	The number of the evolution
warn	Set the warning level (0: always display warnings, >0 display warnings on demand).

Definition at line 3090 of file PhylogeneticsApplicationTools.cpp.

References bpp::OutputStream::endLine(), bpp::MultiProcessSequenceEvolution::getNumberOfSubstitutionProcess(), bpp::FullHmmTransitionMatrix::getPij(), bpp::MixtureSequenceEvolution::getSubProcessProbabilities(), bpp::OneProcessSequenceEvolution::getSubstitutionProcessNumber(), bpp::MultiProcessSequenceEvolution::getSubstitutionProcessNumbers(), bpp::AutoCorrelationSequenceEvolution::hmmTransitionMatrix(), bpp::HmmSequenceEvolution::hmmTransitionMatrix(), bpp::PartitionSequenceEvolution::mapOfProcessSites(), bpp::VectorTools::paste(), bpp::AutoCorrelationTransitionMatrix::Pij(), bpp::MatrixTools::print(), bpp::VectorTools::printRange(), and bpp::TextTools::toString().

printParameters() [5/7]

void PhylogeneticsApplicationTools::printParameters ( const SingleDataPhyloLikelihoodInterface &  phylolike, OutputStream &  out, size_t  nPhylo = 1, int  warn = 1  )

static

Definition at line 3062 of file PhylogeneticsApplicationTools.cpp.

References bpp::OutputStream::endLine(), bpp::SingleDataPhyloLikelihoodInterface::getNData(), and bpp::TextTools::toString().

printParameters() [6/7]

void PhylogeneticsApplicationTools::printParameters ( const SubstitutionProcessCollection &  collection, OutputStream &  out, int  warn = 1, bool  withAlias = true  )

static

Output a SubstitutionProcessCollection description to a file.

Parameters

collection	The process collection to serialize.
out	The stream where to print.
warn	Set the warning level (0: always display warnings, >0 display warnings on demand).
withAlias	outputs the alias names of the aliased Parameters instead of the values (default : true).

Definition at line 2695 of file PhylogeneticsApplicationTools.cpp.

References bpp::BppOFrequencySetFormat::ALL, bpp::BppOSubstitutionModelFormat::ALL, bpp::OutputStream::endLine(), bpp::SubstitutionProcessCollection::getFrequenciesNumbers(), bpp::SubstitutionProcessCollection::getFrequencySet(), bpp::AbstractParameterAliasable::getFrom(), bpp::SubstitutionProcessCollection::getModel(), bpp::SubstitutionProcessCollection::getModelIndex(), bpp::SubstitutionProcessCollection::getModelNumbers(), bpp::ModelPath::getModels(), bpp::SubstitutionProcessCollection::getModelScenario(), bpp::ModelPath::getPathNode(), bpp::SubstitutionProcessCollection::getRateDistribution(), bpp::SubstitutionProcessCollection::getRateDistributionNumbers(), bpp::SubstitutionProcessCollection::getScenarioNumbers(), bpp::SubstitutionProcessCollection::getSubstitutionProcessNumbers(), bpp::ParameterList::size(), bpp::SubstitutionProcessCollection::substitutionProcess(), bpp::ModelPath::PathNode::to_string(), bpp::TextTools::toString(), bpp::BppOSubstitutionModelFormat::write(), bpp::BppORateDistributionFormat::writeDiscreteDistribution(), and bpp::BppOFrequencySetFormat::writeFrequencySet().

printParameters() [7/7]

void PhylogeneticsApplicationTools::printParameters ( const SubstitutionProcessInterface &  process, OutputStream &  out, int  warn = 1  )

static

Output a SubstitutionProcess description to a file.

Parameters

process	The process to serialize.
out	The stream where to print.
warn	Set the warning level (0: always display warnings, >0 display warnings on demand).

Definition at line 2559 of file PhylogeneticsApplicationTools.cpp.

References bpp::BppOFrequencySetFormat::ALL, bpp::BppOSubstitutionModelFormat::ALL, bpp::OutputStream::endLine(), bpp::AbstractParameterAliasable::getFrom(), bpp::NonHomogeneousSubstitutionProcess::getModel(), bpp::NonHomogeneousSubstitutionProcess::getNodesWithModel(), bpp::NonHomogeneousSubstitutionProcess::getNumberOfModels(), bpp::ParameterAliasable::getParameters(), bpp::RateAcrossSitesSubstitutionProcess::getRateDistribution(), bpp::AbstractAutonomousSubstitutionProcess::getRootFrequencySet(), bpp::SubstitutionProcessInterface::model(), bpp::NonHomogeneousSubstitutionProcess::rateDistribution(), bpp::AbstractAutonomousSubstitutionProcess::rootFrequencySet(), bpp::ParameterList::size(), bpp::TextTools::toString(), bpp::BppOSubstitutionModelFormat::write(), bpp::BppORateDistributionFormat::writeDiscreteDistribution(), and bpp::BppOFrequencySetFormat::writeFrequencySet().

uniqueToSharedMap()

template<class T >

static std::map<size_t, std::shared_ptr<T> > bpp::PhylogeneticsApplicationTools::uniqueToSharedMap ( std::map< size_t, std::unique_ptr< T >> &  mu )

inlinestatic

Definition at line 862 of file PhylogeneticsApplicationTools.h.

writePhyloTrees() [1/2]

void PhylogeneticsApplicationTools::writePhyloTrees ( const std::vector< const PhyloTree * > &  trees, const std::map< std::string, std::string > &  params, const std::string &  prefix = "output.", const std::string &  suffix = "", bool  suffixIsOptional = true, bool  verbose = true, bool  checkOnly = false, int  warn = 1  )

static

Write a tree according to options.

See the Bio++ Program Suite manual for a description of all available options.

Parameters

trees	The trees to write.
params	The attribute map where options may be found.
prefix	A prefix to be applied to each attribute name.
suffix	A suffix to be applied to each attribute name.
suffixIsOptional	Tell if the suffix is absolutely required.
verbose	Print some info to the 'message' output stream.
checkOnly	If this parameter is set to true, then all options are checked and error messages sent, but no file is written.
warn	Set the warning level (0: always display warnings, >0 display warnings on demand).

Definition at line 2459 of file PhylogeneticsApplicationTools.cpp.

References bpp::ApplicationTools::displayResult(), bpp::ApplicationTools::getAFilePath(), bpp::ApplicationTools::getStringParameter(), and bpp::OMultiPhyloTree::writePhyloTrees().

writePhyloTrees() [2/2]

void PhylogeneticsApplicationTools::writePhyloTrees ( const SubstitutionProcessCollection &  spc, const std::map< std::string, std::string > &  params, const std::string &  prefix = "output.", const std::string &  suffix = "", bool  suffixIsOptional = true, bool  verbose = true, bool  checkOnly = false, bool  withIds = false, int  warn = 1  )

static

Write a tree according to options.

See the Bio++ Program Suite manual for a description of all available options.

Parameters

spc	The SubstitutionProcessCollection of all objects
params	The attribute map where options may be found.
prefix	A prefix to be applied to each attribute name.
suffix	A suffix to be applied to each attribute name.
suffixIsOptional	Tell if the suffix is absolutely required.
verbose	Print some info to the 'message' output stream.
checkOnly	If this parameter is set to true, then all options are checked and error messages sent, but no file is written.
withIds	If this parameter is set to true, ids are added to the names of the nodes in output.
warn	Set the warning level (0: always display warnings, >0 display warnings on demand).

Definition at line 2494 of file PhylogeneticsApplicationTools.cpp.

References bpp::ApplicationTools::displayResult(), bpp::Newick::enableExtendedBootstrapProperty(), bpp::ApplicationTools::getAFilePath(), bpp::ApplicationTools::getStringParameter(), bpp::SubstitutionProcessCollection::getTree(), bpp::SubstitutionProcessCollection::getTreeNumbers(), bpp::TextTools::toString(), and bpp::OPhyloTree::writePhyloTree().

writeTree()

void PhylogeneticsApplicationTools::writeTree ( const TreeTemplate< Node > &  tree, const std::map< std::string, std::string > &  params, const std::string &  prefix = "output.", const std::string &  suffix = "", bool  suffixIsOptional = true, bool  verbose = true, bool  checkOnly = false, int  warn = 1  )

static

Output methods:

Write a tree according to options.

See the Bio++ Program Suite manual for a description of all available options.

Parameters

tree	The tree to write.
params	The attribute map where options may be found.
prefix	A prefix to be applied to each attribute name.
suffix	A suffix to be applied to each attribute name.
suffixIsOptional	Tell if the suffix is absolutely required.
verbose	Print some info to the 'message' output stream.
checkOnly	If this parameter is set to true, then all options are checked and error messages sent, but no file is written.
warn	Set the warning level (0: always display warnings, >0 display warnings on demand).

Definition at line 2429 of file PhylogeneticsApplicationTools.cpp.

References bpp::ApplicationTools::displayResult(), bpp::ApplicationTools::getAFilePath(), bpp::ApplicationTools::getStringParameter(), and bpp::OTree::writeTree().

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The documentation for this class was generated from the following files:

• Bpp/Phyl/App/PhylogeneticsApplicationTools.h
• Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp