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 ()
bool	setSamplingParameters ()
bool	setGenotyperParameters ()
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
TMatrix	_sample_patch
unsigned int	_sample_patch_num
TMatrix	_sample_size
TMatrix	_sample_age
vector< GenotyperFH * >	_genotypers

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_patch_num(0)
{
 
  ParamUpdater<LCE_FileServicesNotifier>* sampler = new ParamUpdater<LCE_FileServicesNotifier>(&LCE_FileServicesNotifier::setSamplingParameters);
 
  add_parameter("files_sample_patch", MAT, false, false, 0, 0, sampler);
  add_parameter("files_sample_size", INT, false, false, 0, 0, sampler);
  add_parameter("files_sample_age", INT, false, false, 0, 0, sampler);
 
  ParamUpdater<LCE_FileServicesNotifier>* genotyper = new ParamUpdater<LCE_FileServicesNotifier>(&LCE_FileServicesNotifier::setGenotyperParameters);
 
  add_parameter("files_genotyper_traits", STR, false, false, 0, 0, genotyper);
  add_parameter("files_genotyper_format", STR, false, false, 0, 0, genotyper);
  add_parameter("files_genotyper_logtime", INT, false, false, 0, 0, genotyper);
  add_parameter("files_genotyper_dir", STR, false, false, 0, 0, genotyper);
  add_parameter("files_genotyper_trim_maf", DBL, false, false, 0, 0, genotyper);
 
}

References SimComponent::add_parameter(), DBL, INT, MAT, setGenotyperParameters(), setSamplingParameters(), and STR.

Referenced by clone().

~LCE_FileServicesNotifier()

LCE_FileServicesNotifier::~LCE_FileServicesNotifier ( )

virtual

{
  if(_genotypers.size() != 0) {
    for(auto g : _genotypers)
      delete g;
    _genotypers.clear();
  }
}

References _genotypers.

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, &_sample_patch);
 
  if( !_genotypers.empty()) {
    for(auto g : _genotypers)
      loader->attach(g);
  }
 
}

References _genotypers, _sample_age, _sample_patch, _sample_size, _service, FileServices::attach(), FileServices::reset_sampled_pop(), and FileServices::set_sampling_params().

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;}

setGenotyperParameters()

bool LCE_FileServicesNotifier::setGenotyperParameters

(

)

{
 
  if(!get_parameter("files_genotyper_format")->isSet())
    return error("parameter \"files_genotyper_format\" is missing\n");
 
  if(!get_parameter("files_genotyper_logtime")->isSet())
    return error("parameter \"files_genotyper_logtime\" is missing\n");
 
  vector< string >  traits = get_parameter("files_genotyper_traits")->getMultiArgs();
 
  vector<unsigned int> trait_index;
 
  TraitPrototype* Tproto;
 
  for(unsigned int i = 0; i < traits.size(); i++)  {
 
    Tproto = _popPtr->getTraitPrototype(traits[i]);
 
    if( !Tproto )
      return error("Genotyper::cannot find trait \"%s\" among successfully initialized traits.\n", traits[i].c_str());
 
    if( !Tproto->is_mappable() )
      return error("Genotyper::cannot add the non-mappable trait \"%s\" to the joint genotype output file\n", traits[i].c_str());
 
    trait_index.push_back(Tproto->get_index());
  }
 
  // FORMAT ---------------------------------------------------------------------------------
  string format = get_parameter("files_genotyper_format")->getArg();
 
  // trim plural form of format string, check if word ends with an "s"
  if(format.find_last_of("s") == format.size()-1)
    format = format.substr(0, format.size()-1);
 
  if( format != "genotype" && format != "snp_genotype" && format != "snp_id")
    return error("Genotyper::file format \"%s\" is not a valid option. Check the manual.\n", format.c_str());
 
  // check for di-allelic loci compatible with snp-based format:
  bool is2all = true;
 
  for(unsigned int i = 0; i < traits.size(); i++)  {
    // allele number;
    is2all &= (_popPtr->getTraitPrototype(traits[i])->get_allele_number() < 3);
 
  }
 
  if( !is2all && format.find("snp") !=  string::npos) {
    return error("Genotyper:: not all traits have di-allelic loci as requested by the output format \"%s\"\n", format.c_str());
  }
 
  // create the genotyper:
  GenotyperFH* genotyper = new GenotyperFH(this);
 
  genotyper->setTraits(traits);
  genotyper->setTraitIndex(trait_index);
  genotyper->setFormat(format);
  genotyper->set_isDiallelic(is2all);
 
  bool doTrimFixedLoci = get_parameter("files_genotyper_trim_maf")->isSet();
  double trim_maf = 0;
 
  if(doTrimFixedLoci) {
 
    if(!is2all) {
      warning("Genotyper::option \"files_genotyper_trim_maf\" is set but loci are not di-allelic. Not trimming.\n");
      doTrimFixedLoci = false;
    }
 
    if(format == "genotype") {
      warning("Genotyper::option \"files_genotyper_trim_maf\" is set but data recorded is allele values (format option \"genotype\"). Not trimming.\n");
      doTrimFixedLoci = false;
    }
 
    trim_maf = get_parameter_value("files_genotyper_trim_maf");
 
    if( trim_maf <= 0) {
      warning("Genotyper::value %f for option \"files_genotyper_trim_maf\" cannot be used for trimming di-allelic loci.\n",trim_maf);
      doTrimFixedLoci = false;
      trim_maf = 0;
    }
  }
 
  genotyper->set_trimFixedLoci(doTrimFixedLoci, trim_maf);
 
  // LOGTIME -------------------------------------------------------------------------------
  Param* param = get_parameter("files_genotyper_logtime");
 
  if(param->isMatrix()) {
 
    TMatrix log_mat;
 
    param->getMatrix(&log_mat);
 
    genotyper->set_multi(true, true, 1, &log_mat, 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);
 
  if (format== "genotype")
    genotyper->set_extension(".genotype");
  else  if (format=="snp_genotype")
    genotyper->set_extension(".snp_geno");
  else  if (format== "snp_id")
    genotyper->set_extension(".snp_id");
 
  // add it to the container:
  _genotypers.push_back(genotyper);
 
  return true;
}

References _genotypers, LifeCycleEvent::_popPtr, error(), TraitPrototype::get_allele_number(), TraitPrototype::get_index(), SimComponent::get_parameter(), SimComponent::get_parameter_value(), Param::getArg(), Param::getMatrix(), Param::getMultiArgs(), IndFactory::getTraitPrototype(), Param::getValue(), TraitPrototype::is_mappable(), Param::isMatrix(), Param::isSet(), EventFileHandler< LCE >::set(), FileHandler::set_extension(), GenotyperFH::set_isDiallelic(), FileHandler::set_multi(), GenotyperFH::set_trimFixedLoci(), GenotyperFH::setFormat(), GenotyperFH::setTraitIndex(), GenotyperFH::setTraits(), and warning().

Referenced by LCE_FileServicesNotifier(), and setParameters().

setParameters()

bool LCE_FileServicesNotifier::setParameters ( )

virtual

Implements SimComponent.

{
 
 
  // _sample_size holds the number of individuals sampled in each sampled patch and age-class
  // it is mandatory for any sampling scheme to happen
  if( get_parameter("files_sample_size")->isSet() ) {
 
    if( !setSamplingParameters() ) return false;
 
  } else if( get_parameter("files_sample_age")->isSet() || get_parameter("files_sample_patch")->isSet() ) {
 
    return error("some patch sampling parameters are set but parameter \"files_sample_size\" is missing.\n");
 
  } else { // no sampling parameter present
    _sample_age.reset();
    _sample_size.reset();
    _sample_patch.reset();
    _sample_patch_num = 0;
  }
 
  // GENOTYPER ----------------------------------------------------------------------------
 
  if(_genotypers.size() != 0) {
    for(auto g : _genotypers)
      delete g;
    _genotypers.clear();
  }
 
  if(get_parameter("files_genotyper_traits")->isSet()){
 
    if( !setGenotyperParameters() ) return false;
 
  }
 
  return true;
}

References _genotypers, _sample_age, _sample_patch, _sample_patch_num, _sample_size, error(), SimComponent::get_parameter(), TMatrix::reset(), setGenotyperParameters(), and setSamplingParameters().

setSamplingParameters()

bool LCE_FileServicesNotifier::setSamplingParameters

(

)

{
 
  TMatrix tmp_mat;
 
  // 1. check which patch needs to be sampled -------------------------------------------
 
  // _sample_patch holds the IDs of patches sampled, 1-based in input, 0-based in output
  if(_paramSet->isSet("files_sample_patch")) {
 
    get_parameter("files_sample_patch")->getMatrix(&_sample_patch);
 
    if(_sample_patch.nrows() > 1)
      return error("parameter \"files_sample_patch\" awaits a single row (array) of patch-IDs (1-based) in input.\n");
 
 
    _sample_patch_num = _sample_patch.ncols();
 
    // transform 1-based values to 0-based (we're confident that no 0 was given in input?)
    _sample_patch.matrix_increment(-1.0);
 
 
  } else {
    // generate a sequence of values 0..patch_number
    double ID[_popPtr->getPatchNbr()];
 
    for(unsigned int i = 0; i < _popPtr->getPatchNbr(); ++i) ID[i] = double(i);
 
    _sample_patch.reset(1, _popPtr->getPatchNbr(), &ID[0]);
    _sample_patch_num = _popPtr->getPatchNbr();
 
  }
 
  // 2. check which age class are sampled ----------------------------------------------
 
  // _sample_age matrix has at least one array of age-class index in which to sample
  // can have one array per patch sampled
  if(get_parameter("files_sample_age")->isSet()) {
 
    if(get_parameter("files_sample_age")->isMatrix()) {
 
      get_parameter("files_sample_age")->getMatrix(&tmp_mat);
 
      if(tmp_mat.nrows() > _sample_patch_num)
        return error("parameter \"files_sample_age\" has more rows than the number of patches sampled.\n");
 
      if(tmp_mat.ncols() > _popPtr->getNumAgeClasses())
        return error("parameter \"files_sample_age\" has more age-class values than the number of stages in the population.\n");
 
      // need to copy-expand!
      _sample_age.reset(_sample_patch_num, tmp_mat.ncols());
      _sample_age.copy_recycle(tmp_mat);
 
    } else {
      // copy a single number to all elements
      _sample_age.reset(_sample_patch_num, 1, get_parameter_value("files_sample_age"));
    }
 
  } else {
    // we set the age class flags to all age class by default
    TMatrix sizes(1,_popPtr->getNumAgeClasses());
    for(unsigned int a = 0; a < sizes.ncols(); ++a) sizes.set(0, a, double(a));
    // !!! in nemo, contrary to nemo-age, adults are at position 2, not 1 !!!
    // specifically for nemo, set adults index to 2
    sizes.set(0,1,2.0);
    _sample_age.reset(_sample_patch_num, _popPtr->getNumAgeClasses());
    _sample_age.copy_recycle(sizes); // expand, copy values to all rows
  }
 
 
  // 3. now read the sampling size provided, and copy to patch and age class if needed --
 
  if( _paramSet->isMatrix("files_sample_size")) {
 
    get_parameter("files_sample_size")->getMatrix(&tmp_mat);
 
    if(tmp_mat.nrows() > _sample_patch_num)
      return error("parameter \"files_sample_size\" has more rows than the number of sampled patches specified with \"files_sample_patch\" (if any).\n");
 
    if(tmp_mat.ncols() > _sample_age.ncols())
      return error("parameter \"files_sample_size\" has more values per row than the number of sampled stages specified with \"files_sample_age\" (if any).\n");
 
    // set the matrix dimensions according to previous parameters
    _sample_size.reset(_sample_patch_num, _sample_age.ncols());
 
    // copy input values with expansion if dimensions don't match
    _sample_size.copy_recycle(tmp_mat);
 
  } else {
    // copy the sample size to all patches and age-classes sampled
    _sample_size.reset(_sample_patch_num,  _sample_age.ncols(), get_parameter("files_sample_size")->getValue());
 
  }
 
  return true;
}

References SimComponent::_paramSet, LifeCycleEvent::_popPtr, _sample_age, _sample_patch, _sample_patch_num, _sample_size, TMatrix::copy_recycle(), error(), SimComponent::get_parameter(), SimComponent::get_parameter_value(), Param::getMatrix(), Metapop::getNumAgeClasses(), Metapop::getPatchNbr(), ParamSet::isMatrix(), ParamSet::isSet(), TMatrix::matrix_increment(), TMatrix::ncols(), TMatrix::nrows(), TMatrix::reset(), and TMatrix::set().

Referenced by LCE_FileServicesNotifier(), and setParameters().

Member Data Documentation

_genotypers

vector< GenotyperFH* > LCE_FileServicesNotifier::_genotypers

private

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

_sample_age

TMatrix LCE_FileServicesNotifier::_sample_age

private

Referenced by loadFileServices(), setParameters(), and setSamplingParameters().

_sample_patch

TMatrix LCE_FileServicesNotifier::_sample_patch

private

Referenced by loadFileServices(), setParameters(), and setSamplingParameters().

_sample_patch_num

unsigned int LCE_FileServicesNotifier::_sample_patch_num

private

Referenced by setParameters(), and setSamplingParameters().

_sample_size

TMatrix LCE_FileServicesNotifier::_sample_size

private

Referenced by loadFileServices(), setParameters(), and setSamplingParameters().

_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