LCE_FileServicesNotifier Class Reference

Event used to notify all file handlers to update their state through the FileServices::notify() interface. More...

#include <servicenotifiers.h>

Inheritance diagram for LCE_FileServicesNotifier:

Collaboration diagram for LCE_FileServicesNotifier:

Public Member Functions
	LCE_FileServicesNotifier ()
virtual	~LCE_FileServicesNotifier ()
virtual void	execute ()
virtual bool	setParameters ()
virtual LifeCycleEvent *	clone ()
virtual void	loadFileServices (FileServices *loader)
virtual void	loadStatServices (StatServices *loader)
virtual bool	resetParameterFromSource (std::string param, SimComponent *cmpt)
virtual age_t	removeAgeClass ()
virtual age_t	addAgeClass ()
virtual age_t	requiredAgeClass ()
Public Member Functions inherited from LifeCycleEvent
	LifeCycleEvent (const char *name, const char *trait_link)
	Cstor. More...
virtual	~LifeCycleEvent ()
virtual void	init (Metapop *popPtr)
	Sets the pointer to the current Metapop and the trait link if applicable. More...
virtual bool	attach_trait (string trait)
virtual void	set_paramset (std::string name, bool required, SimComponent *owner)
virtual void	set_event_name (std::string &name)
	Set the name of the event (name of the ParamSet) and add the corresponding parameter to the set. More...
virtual void	set_event_name (const char *name)
virtual string &	get_event_name ()
	Accessor to the LCE's name. More...
virtual int	get_rank ()
	Accessor to the LCE rank in the life cycle. More...
virtual void	set_pop_ptr (Metapop *popPtr)
	Accessors for the population pointer. More...
virtual Metapop *	get_pop_ptr ()
Public Member Functions inherited from SimComponent
	SimComponent ()
virtual	~SimComponent ()
virtual void	loadUpdaters (UpdaterServices *loader)
	Loads the parameters and component updater onto the updater manager. More...
virtual void	set_paramset (ParamSet *paramset)
	Sets the ParamSet member. More...
virtual void	set_paramsetFromCopy (const ParamSet &PSet)
	Reset the set of parameters from a another set. More...
virtual ParamSet *	get_paramset ()
	ParamSet accessor. More...
virtual void	add_parameter (Param *param)
	Interface to add a parameter to the set. More...
virtual void	add_parameter (std::string Name, param_t Type, bool isRequired, bool isBounded, double low_bnd, double up_bnd)
	Interface to add a parameter to the set. More...
virtual void	add_parameter (std::string Name, param_t Type, bool isRequired, bool isBounded, double low_bnd, double up_bnd, ParamUpdaterBase *updater)
	Interface to add a parameter and its updater to the set. More...
virtual Param *	get_parameter (std::string name)
	Param getter. More...
virtual double	get_parameter_value (std::string name)
	Param value getter. More...
virtual string	get_name ()
	Returnd the name of the ParamSet, i.e. More...
virtual bool	has_parameter (std::string name)
	Param getter. More...

Private Attributes
FileServices *	_service
unsigned int	_sample_size
age_t	_sample_age
GenotyperFH *	_genotyper

Additional Inherited Members
Protected Attributes inherited from LifeCycleEvent
std::string	_event_name
	The param name to be read in the init file. More...
Metapop *	_popPtr
	The ptr to the current Metapop. More...
std::string	_LCELinkedTraitType
	The name of the linked trait. More...
int	_LCELinkedTraitIndex
	The index in the individual's trait table of the linked trait. More...
Protected Attributes inherited from SimComponent
ParamSet *	_paramSet
	The parameters container. More...

Detailed Description

Event used to notify all file handlers to update their state through the FileServices::notify() interface.

Constructor & Destructor Documentation

LCE_FileServicesNotifier()

LCE_FileServicesNotifier::LCE_FileServicesNotifier

(

)

                                                   : LifeCycleEvent("save_files",""),
    _service(0), _sample_size(0), _sample_age(0), _genotyper(0)
{
 
  add_parameter("files_sample_size", INT, false, false, 0, 0);
  add_parameter("files_sample_age", INT, false, false, 0, 0);
  add_parameter("files_genotyper_traits", STR, false, false, 0, 0);
  add_parameter("files_genotyper_format", STR, false, false, 0, 0);
  add_parameter("files_genotyper_logtime", INT, false, false, 0, 0);
  add_parameter("files_genotyper_dir", STR, false, false, 0, 0);
  add_parameter("files_genotyper_trim_fixed", BOOL, false, false, 0, 0);
 
}

References SimComponent::add_parameter(), BOOL, INT, and STR.

Referenced by clone().

~LCE_FileServicesNotifier()

LCE_FileServicesNotifier::~LCE_FileServicesNotifier ( )

virtual

{
  if(_genotyper) delete _genotyper;
}

References _genotyper.

Member Function Documentation

addAgeClass()

virtual age_t LCE_FileServicesNotifier::addAgeClass ( )

inlinevirtual

Implements LifeCycleEvent.

{return 0;}

clone()

virtual LifeCycleEvent* LCE_FileServicesNotifier::clone ( )

inlinevirtual

Implements LifeCycleEvent.

{return new LCE_FileServicesNotifier();}

References LCE_FileServicesNotifier().

execute()

void LCE_FileServicesNotifier::execute ( )

virtual

Implements LifeCycleEvent.

{
#ifdef _DEBUG_
  message("LCE_FileServicesNotifier::execute (gen: %i rpl: %i)\n",
                  this->get_pop_ptr()->getCurrentGeneration(),
                  this->get_pop_ptr()->getCurrentReplicate());
#endif
 
  _service->notify();
}

References _service, LifeCycleEvent::get_pop_ptr(), message(), and FileServices::notify().

loadFileServices()

void LCE_FileServicesNotifier::loadFileServices ( FileServices *  loader )

virtual

Implements SimComponent.

{
  _service = loader;
 
  // tell the file services to reset the sampled metapop to avoid pbs between chained simulations
  _service->reset_sampled_pop();
 
  _service->set_sampling_params(_sample_size, _sample_age);
 
  if(get_parameter("files_genotyper_traits")->isSet()) {
 
    // create FH for merged output
    if( _genotyper) delete _genotyper;
    _genotyper = new GenotyperFH(this);
 
    vector< string >  traits = get_parameter("files_genotyper_traits")->getMultiArgs();
 
    int index;
 
    for(unsigned int i = 0; i < traits.size(); i++)  {
 
      if( _popPtr->getTraitIndex(traits[i].c_str()) < 0) {
 
        fatal("Genotyper::cannot find trait \"%s\" among successfully initialized traits.\n", traits[i].c_str());
 
      }
    }
 
    _genotyper->setTraits(traits);
 
    Param* param = get_parameter("files_genotyper_logtime");
 
    if(!param->isSet()) fatal("parameter \"files_genotyper_logtime\" is missing\n");
 
    if(param->isMatrix()) {
 
      TMatrix temp;
 
      param->getMatrix(&temp);
 
      _genotyper->set_multi(true, true, 1, &temp, get_parameter("files_genotyper_dir")->getArg());
 
      //               rpl_per, gen_per, rpl_occ, gen_occ, rank, path, self-ref
    } else
      _genotyper->set(true, param->isSet(), 1, (param->isSet() ? (int)param->getValue() : 0),
                        0, get_parameter("files_genotyper_dir")->getArg(), this);
 
    loader->attach(_genotyper);
  }
 
}

References _genotyper, LifeCycleEvent::_popPtr, _sample_age, _sample_size, _service, FileServices::attach(), fatal(), SimComponent::get_parameter(), Param::getMatrix(), Param::getMultiArgs(), IndFactory::getTraitIndex(), Param::getValue(), Param::isMatrix(), Param::isSet(), FileServices::reset_sampled_pop(), EventFileHandler< LCE >::set(), FileHandler::set_multi(), FileServices::set_sampling_params(), and GenotyperFH::setTraits().

loadStatServices()

virtual void LCE_FileServicesNotifier::loadStatServices ( StatServices *  loader )

inlinevirtual

Implements SimComponent.

{}

removeAgeClass()

virtual age_t LCE_FileServicesNotifier::removeAgeClass ( )

inlinevirtual

Implements LifeCycleEvent.

{return 0;}

requiredAgeClass()

virtual age_t LCE_FileServicesNotifier::requiredAgeClass ( )

inlinevirtual

Implements LifeCycleEvent.

{return 0;}

resetParameterFromSource()

virtual bool LCE_FileServicesNotifier::resetParameterFromSource ( std::string  param, SimComponent *  cmpt  )

inlinevirtual

Implements SimComponent.

{return false;}

setParameters()

bool LCE_FileServicesNotifier::setParameters ( )

virtual

Implements SimComponent.

{
  _sample_size = 0;
  _sample_age = 0;
 
  if( get_parameter("files_sample_size")->isSet() ) {
 
    _sample_size = get_parameter_value("files_sample_size");
 
    if(get_parameter("files_sample_age")->isSet())
      _sample_age = static_cast<age_t> (get_parameter_value("files_sample_age"));
 
  } else if(get_parameter("files_sample_age")->isSet()) {
    return error("parameter \"files_sample_age\" but parameter \"files_sample_size\" is missing\n");
  }
 
 
  if(get_parameter("files_genotyper_traits")->isSet()){
 
    //read trait types, get genetic map
  }
 
  return true;
}

References _sample_age, _sample_size, error(), SimComponent::get_parameter(), SimComponent::get_parameter_value(), and Param::isSet().

Member Data Documentation

_genotyper

GenotyperFH* LCE_FileServicesNotifier::_genotyper

private

Referenced by loadFileServices(), and ~LCE_FileServicesNotifier().

_sample_age

age_t LCE_FileServicesNotifier::_sample_age

private

Referenced by loadFileServices(), and setParameters().

_sample_size

unsigned int LCE_FileServicesNotifier::_sample_size

private

Referenced by loadFileServices(), and setParameters().

_service

FileServices* LCE_FileServicesNotifier::_service

private

Referenced by execute(), and loadFileServices().

---

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

• servicenotifiers.h
• servicenotifiers.cc