Parameters container, implemented in each SimComponent. More...

#include <param.h>

Collaboration diagram for ParamSet:

Public Member Functions
	ParamSet ()

	ParamSet (const ParamSet &PS)

	~ParamSet ()

void	reset ()
	Put the container in the unset state, reset each Param it contains. More...

void	clear ()
	Empties the parameter containers (no delete). More...

bool	check_consistency ()
	Checks for the status of the required parameters. More...

void	show_up ()
	print info to stdout. More...

void	print (ofstream &FILE, bool commentOut=false)
	print all set parameters to the outpout file stream More...

int	size ()
	Returns the number of parameters contained. More...

map< string, Param * > &	getAllParams ()
	Returns the complete list of parameters. More...

ParamSet &	operator= (const ParamSet &PS)

Accessors to Param members.
void	add_param (Param *param)
	Adds the param argument to the list. More...

void	add_param (string Name, param_t Type, bool mandatory, bool isBounded, double low_bnd, double up_bnd)
	Adds a new param specified by arguments to the list. More...

void	add_param (string Name, param_t Type, bool mandatory, bool isBounded, double low_bnd, double up_bnd, ParamUpdaterBase *updater)

bool	set_param (string Name, string Arg)
	Look for a param named "Name" and try to set it with the "Arg" argument string. More...

Param *	find_param (string name)
	Look for a param "name" in its parameters list. More...

Param *	get_param (string name)
	Look for a param "name" in its parameters list. More...

bool	has_param (string name)
	Look for a param "name" in its parameters list. More...

bool	update_param (string Name, unsigned int generation)
	Calls the updating procedure of each of its Param. More...

void	setName (string value)
	Sets the container's name. More...

void	setIsRequired (bool value)
	Sets the _isRequired flag meaning this container is mandatory and must be set in order to run a simulation. More...

void	setOwner (SimComponent *owner)
	Sets the pointer to the SimComponents that owns this set. More...

bool	isSet ()
	Accessor to the status flag. More...

string	getName ()
	Name accessor. More...

bool	isRequired ()
	Accessor to the mandatory flag. More...

bool	isSet (string name)
	Accessor to the parameters status flag. More...

bool	isMatrix (string name)
	Check if the parameter "name" is of matrix type. More...

bool	isTemporal (string name)
	Check if the parameter "name" has temporal arguments. More...

string	getArg (string name)
	Accessor to the parameters argument string. More...

double	getValue (string name)
	Accessor the parameters value. More...

void	getMatrix (string name, TMatrix *mat)
	Accessor to the parameters matrix. More...

list< ParamUpdaterBase * >	getUpdaters ()
	Collects the parameter updaters from the set of parameters. More...

Private Attributes
string	_name
	The name of the component. More...

bool	_isSet
	Flag is true if all mandatory parameters are correctly set from user's input file. More...

bool	_isRequired
	Flaf is true if component is required (mandatory) to run a simulation (e.g. More...

map< string, Param * >	_params
	List of parameters indexed by name. More...

SimComponent *	_myOwner
	Pointer to the component that declared this parameter. More...

Detailed Description

Parameters container, implemented in each SimComponent.

A SimComponent is added to the set of active components of a simulation only if all its required parameters are set (isSet = true).

Constructor & Destructor Documentation

◆ ParamSet() [1/2]

ParamSet::ParamSet ( )

inline

229 : _isSet(0), _isRequired(0), _myOwner(0) { }

ParamSet::_myOwner

SimComponent * _myOwner

Pointer to the component that declared this parameter.

Definition: param.h:225

ParamSet::_isRequired

bool _isRequired

Flaf is true if component is required (mandatory) to run a simulation (e.g.

Definition: param.h:221

ParamSet::_isSet

bool _isSet

Flag is true if all mandatory parameters are correctly set from user's input file.

Definition: param.h:219

◆ ParamSet() [2/2]

ParamSet::ParamSet ( const ParamSet & PS )

 : _name(PS._name), _isSet(PS._isSet), _isRequired(PS._isRequired)
 {
   map<string, Param*>::iterator param;
   
   if( _params.size() ) {
     param =  _params.begin();
     while(param != _params.end()) {
       delete param->second;
       param++;
     }
     _params.clear();
   }
   map<string, Param*> PS_params = PS._params;
   param =  PS_params.begin();
   while(param != PS_params.end()) {
     _params[param->first] = new Param( *param->second );
     param++;
   }
   
 }

References _params.

◆ ~ParamSet()

ParamSet::~ParamSet ( )

 {
   map<string, Param*>::iterator param =  _params.begin();
   while(param != _params.end()) {
     delete param->second;
     param++;
   }
 }

References _params.

Member Function Documentation

◆ add_param() [1/3]

void ParamSet::add_param ( Param * param )

inline

Adds the param argument to the list.

252 {_params[param->getName()] = param;}

Param::getName

string getName()

Definition: param.h:142

References Param::getName().

Referenced by SimComponent::add_parameter(), and ParamManager::ParamManager().

Here is the caller graph for this function:

◆ add_param() [2/3]

void ParamSet::add_param	(	string	Name,
		param_t	Type,
		bool	mandatory,
		bool	isBounded,
		double	low_bnd,
		double	up_bnd
	)

inline

Adds a new param specified by arguments to the list.

Parameters

Name	the name of the parameter
Type	the type of the parameter
mandatory	specifies if this parameter is required and must be set for the container to gain the "set" status
isBounded	specified whether this parameter is bounded
low_bnd	the lower value the parameter can take, used if isBounded is true
up_bnd	the upper value the parameter can take, used if isBounded is true

263 {add_param(Name, Type, mandatory, isBounded, low_bnd, up_bnd, 0);}

ParamSet::add_param

void add_param(Param *param)

Adds the param argument to the list.

Definition: param.h:252

◆ add_param() [3/3]

void ParamSet::add_param	(	string	Name,
		param_t	Type,
		bool	mandatory,
		bool	isBounded,
		double	low_bnd,
		double	up_bnd,
		ParamUpdaterBase *	updater
	)

 {
   //  if(!_name.empty()) Name = _name + "_" + Name; //not yet...
   Param* param = new Param(Name, Type, mandatory, isBounded, low_bnd, up_bnd, _myOwner, updater);
   if(updater) updater->addParam(param);
   _params[Name] = param;
 }

References _myOwner, _params, and ParamUpdaterBase::addParam().

◆ check_consistency()

bool ParamSet::check_consistency ( )

Checks for the status of the required parameters.

Returns: TRUE if all required parameters are or if nothing is set and the container is not required

 {
   map<string, Param*>::iterator param = _params.begin();
   bool isOK = true;
   bool touched = false;
   bool ignore = false;
   
   vector<string> mandatory;
  
   while(param != _params.end()) {
  
     //check if all mandatory parameters have been set properly
     if(param->second->isRequired()) {
  
       isOK &= param->second->isSet();
  
       if( !param->second->isSet() ) {
         //ignore LCE name when not added in life cycle (not wanted) to avoid error messages from inherited classes (composite LCE)
         //e.g. if breed_disperse is set, all LCE derived from breed_base will be touched but not set and will complain
         if (_name == param->second->getName()) {
  
           ignore = true;
  
         } else
           mandatory.push_back(param->second->getName());
       }
     }
  
     //check if at least one param has been set
     touched |= param->second->isSet();
     param++;
   }
   _isSet = isOK;
  
   // issue warning in case of partial OK, or partial set
   if( touched && !isOK && !ignore) {
     warning("Mandatory parameters of component \"%s\" were not properly set.", _name.c_str());
     warning("This component will not be added to the simulation!");
     warning("The missing parameters are:\n");
  
     for(unsigned int i = 0; i < mandatory.size(); ++i)
       message(">>>> \"%s\"\n", mandatory[i].c_str());
  
     message("\n");
  
     for(unsigned int i = 10; i > 0; i--) {
       message("\rIf you want to abort now, press Ctrl-C, or wait for %is  ", i);
       fflush(stdout);
       sleep(1);
     }
  
     message("\n\n");
   }
   //return isOk or check if _isRequired in case no params are set (untouched params)
   return ( isOK | (!_isRequired));
 }

References _isRequired, _isSet, _name, _params, message(), and warning().

◆ clear()

void ParamSet::clear ( )

inline

Empties the parameter containers (no delete).

236 {_params.clear();}

◆ find_param()

Param * ParamSet::find_param ( string name )

Look for a param "name" in its parameters list.

Returns: NULL if no Param with _name = name exists

 {
   map<string, Param*>::iterator param = _params.find(Name);
  
   if(param != _params.end())
     return param->second;
   else
     return NULL;
 }

References _params.

◆ get_param()

Param * ParamSet::get_param ( string name )

Look for a param "name" in its parameters list.

Returns: NULL if no Param with _name = name exists

 {
   map<string, Param*>::iterator param = _params.find(Name);
   
   if(param != _params.end())
     return param->second;
   else
     fatal("parameter \"%s\" is not a member of \"%s\".\n", Name.c_str(), _name.c_str());
   //return NULL;
   return NULL;
 }

References _name, _params, and fatal().

Referenced by SimComponent::get_parameter(), LCE_StatServiceNotifier::setOccurence(), LCE_PhenotypeExpression::setParameters(), and update_param().

Here is the caller graph for this function:

◆ getAllParams()

map<string, Param*>& ParamSet::getAllParams ( )

inline

Returns the complete list of parameters.

248 {return _params;}

◆ getArg()

string ParamSet::getArg ( string name )

inline

Accessor to the parameters argument string.

309 {return (get_param(name))->getArg();}

ParamSet::get_param

Param * get_param(string name)

Look for a param "name" in its parameters list.

Definition: param.cc:692

Referenced by LCE_Resize::execute(), SimRunner::init(), LCE_Selection_base::set_fit_model(), LCE_Disperse_EvolDisp::setParameters(), LCE_Patch_Extinction::setParameters(), LCE_StatServiceNotifier::setParameters(), TProtoDeletMutations_bitstring::setSelectionParameters(), Metapop::setSourceParameters(), and LCE_Resize::updateParameters().

Here is the caller graph for this function:

◆ getMatrix()

void ParamSet::getMatrix	(	string	name,
		TMatrix *	mat
	)

inline

Accessor to the parameters matrix.

313 {return (get_param(name))->getMatrix(mat);}

Referenced by LCE_PhenotypeExpression::set_env_cue(), LCE_Selection_base::set_local_optima(), LCE_Disperse_base::setBaseParameters(), LCE_Breed_Disperse::setParameters(), LCE_Resize::setParameters(), LCE_PhenotypeExpression::setParameters(), LCE_QuantiInit::setParameters(), LCE_Init_BDMI::setParameters(), LCE_NtrlInit::setParameters(), Metapop::setPatchCapacities(), LCE_Selection_base::setSelectionMatrix(), and LCE_Resize::updateParameters().

Here is the caller graph for this function:

◆ getName()

string ParamSet::getName ( )

inline

Name accessor.

299 {return _name;}

Referenced by SimComponent::get_name().

Here is the caller graph for this function:

◆ getUpdaters()

list< ParamUpdaterBase * > ParamSet::getUpdaters ( )

Collects the parameter updaters from the set of parameters.

 {
   list<ParamUpdaterBase*> updaters;
   map<string, Param*>::iterator param = _params.begin();
   for(;param != _params.end(); param++) {
     if(param->second->getUpdater() != 0)
       updaters.push_back(param->second->getUpdater());
   }
   return updaters;
 }

References _params.

Referenced by SimComponent::loadUpdaters().

Here is the caller graph for this function:

◆ getValue()

double ParamSet::getValue ( string name )

inline

Accessor the parameters value.

311 {return (get_param(name))->getValue();}

Referenced by SimComponent::get_parameter_value(), SimRunner::init(), SimRunner::init_random_seed(), LCE_Disperse_base::setBaseParameters(), LCE_Disperse_base::setLatticeMatrix(), LCE_Breed_base::setMatingSystem(), LCE_Disperse_EvolDisp::setParameters(), LCE_PhenotypeExpression::setParameters(), LCE_StatServiceNotifier::setParameters(), Metapop::setPopulationParameters(), and Metapop::setSourceParameters().

Here is the caller graph for this function:

◆ has_param()

bool ParamSet::has_param ( string name )

Look for a param "name" in its parameters list.

Returns: false if no Param with _name = name exists, true otherwise

 {
   map<string, Param*>::iterator param = _params.find(Name);
  
   return (param != _params.end());
 }

References _params.

Referenced by SimComponent::has_parameter().

Here is the caller graph for this function:

◆ isMatrix()

bool ParamSet::isMatrix ( string name )

inline

Check if the parameter "name" is of matrix type.

305 {return (get_param(name))->isMatrix();}

Referenced by LCE_Breed_Disperse::setParameters(), LCE_Resize::setParameters(), Metapop::setPopulationParameters(), and LCE_FileServicesNotifier::setSamplingParameters().

Here is the caller graph for this function:

◆ isRequired()

bool ParamSet::isRequired ( )

inline

Accessor to the mandatory flag.

301 {return _isRequired;}

◆ isSet() [1/2]

bool ParamSet::isSet ( )

inline

Accessor to the status flag.

297 {return _isSet;}

Referenced by Metapop::init(), SimRunner::init(), SimRunner::init_random_seed(), LCE_Selection_base::loadFileServices(), LCE_StatServiceNotifier::loadStatServices(), LCE_Selection_base::set_fit_model(), LCE_Selection_base::set_local_optima(), LCE_Selection_base::set_sel_model(), LCE_Disperse_base::setBaseParameters(), LCE_Disperse_base::setIsland_PropagulePool_Matrix(), LCE_Disperse_base::setLatticeMatrix(), LCE_Breed_base::setMatingSystem(), TProtoQuanti::setMutationModel_no_pleio(), LCE_Breed_Disperse::setParameters(), LCE_Disperse_EvolDisp::setParameters(), LCE_PhenotypeExpression::setParameters(), LCE_QuantiInit::setParameters(), LCE_StatServiceNotifier::setParameters(), Metapop::setPopulationParameters(), LCE_FileServicesNotifier::setSamplingParameters(), LCE_Selection_base::setSelectionMatrix(), and Metapop::setSourceParameters().

◆ isSet() [2/2]

bool ParamSet::isSet ( string name )

inline

Accessor to the parameters status flag.

303 {return (get_param(name))->isSet();}

◆ isTemporal()

bool ParamSet::isTemporal ( string name )

inline

Check if the parameter "name" has temporal arguments.

307 {return (get_param(name))->isTemporal();}

◆ operator=()

ParamSet & ParamSet::operator= ( const ParamSet & PS )

 {
   if(this != &PS) {
     _name = PS._name;
     _isSet = PS._isSet;
     _isRequired = PS._isRequired;
     
     map<string, Param*>::iterator param;
     
     if( _params.size() ) {
       param =  _params.begin();
       while(param != _params.end()) {
         delete param->second;
         param++;
       }
       _params.clear();
     }
     map<string, Param*> PS_params = PS._params;
     param =  PS_params.begin();
     while(param != PS_params.end()) {
       _params[param->first] = new Param( *param->second );
       param++;
     }
   }
   return *this;
 }

References _isRequired, _isSet, _name, and _params.

◆ print()

void ParamSet::print	(	ofstream &	FILE,
		bool	commentOut = `false`
	)

print all set parameters to the outpout file stream

 {
   map<string, Param*>::iterator paramRec = _params.begin();
   Param* param;
   
   while(paramRec != _params.end()) {
     
     param = paramRec->second;
     
     if(param->isSet())
     {
       if(commentOut)
         FILE<<"#";
       
       FILE<<param->getName()<<" "<<param->getInputArg()<<endl;
     }
     
     paramRec++;
   }
 }

References _params, Param::getInputArg(), Param::getName(), and Param::isSet().

◆ reset()

void ParamSet::reset ( )

Put the container in the unset state, reset each Param it contains.

 {
   _isSet = 0;
   map<string, Param*>::iterator param =  _params.begin();
   while(param != _params.end()) {
     param->second->reset();
     param++;
   }
 }

References _isSet, and _params.

◆ set_param()

bool ParamSet::set_param	(	string	Name,
		string	Arg
	)

Look for a param named "Name" and try to set it with the "Arg" argument string.

Returns: TRUE if param Name has been found and set with Arg; FALSE otherwise

Parameters

Name	the name of the parameter to find in the list
Arg	the argument string as found in the init params

 {
   map<string, Param*>::iterator param = _params.find(Name);
   string error_msg;
   
   if(param == _params.end()) {
     //    error("could not set \"%s\": parameter not found.\n",Name.c_str());
     //exist silently
     return false;
   }
   
   if( !param->second->set(Arg, error_msg) ) {
     error("could not set \"%s\": %s.\n", Name.c_str(), error_msg.c_str());
     return false;
   } else
     return true;
 }

References _params, and error().

Referenced by LCE_Resize::execute().

Here is the caller graph for this function:

◆ setIsRequired()

void ParamSet::setIsRequired ( bool value )

inline

Sets the _isRequired flag meaning this container is mandatory and must be set in order to run a simulation.

293 {_isRequired = value;}

Referenced by ParamManager::ParamManager(), and SimComponent::set_paramset().

Here is the caller graph for this function:

◆ setName()

void ParamSet::setName ( string value )

inline

Sets the container's name.

291 {_name = value;}

Referenced by ParamManager::ParamManager(), and SimComponent::set_paramset().

Here is the caller graph for this function:

◆ setOwner()

void ParamSet::setOwner ( SimComponent * owner )

inline

Sets the pointer to the SimComponents that owns this set.

295 {_myOwner = owner;}

Referenced by ParamManager::ParamManager(), and SimComponent::set_paramset().

Here is the caller graph for this function:

◆ show_up()

void ParamSet::show_up ( )

print info to stdout.

 {
   message("%s\n",_name.c_str());
   map<string, Param*>::iterator param = _params.begin();
   while(param != _params.end()) {
     param->second->show_up();
     param++;
   }
 }

References _name, _params, and message().

◆ size()

int ParamSet::size ( )

inline

Returns the number of parameters contained.

246 {return _params.size();}

◆ update_param()

bool ParamSet::update_param	(	string	Name,
		unsigned int	generation
	)

Calls the updating procedure of each of its Param.

 {
   Param* param = get_param(Name);
   if(param) return param->update( generation );
   return false;
 }

References get_param(), and Param::update().

Member Data Documentation

◆ _isRequired

bool ParamSet::_isRequired

private

Flaf is true if component is required (mandatory) to run a simulation (e.g.

SimRunner, Metapop).

Referenced by check_consistency(), and operator=().

◆ _isSet

bool ParamSet::_isSet

private

Flag is true if all mandatory parameters are correctly set from user's input file.

Referenced by check_consistency(), operator=(), and reset().

◆ _myOwner

SimComponent* ParamSet::_myOwner

private

Pointer to the component that declared this parameter.

Referenced by add_param().

◆ _name

string ParamSet::_name

private

The name of the component.

Referenced by check_consistency(), get_param(), operator=(), and show_up().

◆ _params

map<string, Param*> ParamSet::_params

private

List of parameters indexed by name.

Referenced by add_param(), check_consistency(), find_param(), get_param(), getUpdaters(), has_param(), operator=(), ParamSet(), print(), reset(), set_param(), show_up(), and ~ParamSet().

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

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ ParamSet() [1/2]

◆ ParamSet() [2/2]

◆ ~ParamSet()

Member Function Documentation

◆ add_param() [1/3]

◆ add_param() [2/3]

◆ add_param() [3/3]

◆ check_consistency()

◆ clear()

◆ find_param()

◆ get_param()

◆ getAllParams()

◆ getArg()

◆ getMatrix()

◆ getName()

◆ getUpdaters()

◆ getValue()

◆ has_param()

◆ isMatrix()

◆ isRequired()

◆ isSet() [1/2]

◆ isSet() [2/2]

◆ isTemporal()

◆ operator=()

◆ print()

◆ reset()

◆ set_param()

◆ setIsRequired()

◆ setName()

◆ setOwner()

◆ show_up()

◆ size()

◆ update_param()

Member Data Documentation

◆ _isRequired

◆ _isSet

◆ _myOwner

◆ _name

◆ _params