FileServices Class Reference

A class to manage the files associated with each components of the simulation. More...

#include <fileservices.h>

Inheritance diagram for FileServices:

Collaboration diagram for FileServices:

Public Types
typedef std::list< FileHandler * >::const_iterator	file_it

Public Member Functions
	FileServices ()
virtual	~FileServices ()
virtual bool	init ()
virtual void	notify ()
bool	init (list< ParamSet * > &params)
	Checks if files with _basename already exist and save the simulation parameters in log files. More...
virtual Metapop *	get_pop_ptr ()
	Accessor to the pointer to the main population. More...
virtual void	set_pop_ptr (Metapop *pop)
	Sets the Metapop reference. More...
void	setMode (unsigned int m)
	Mode setter, determines if file will get overwritten or not. More...
unsigned int	getMode ()
	Writting mode getter. More...
void	setBasename (string name)
	Sets the base file name of the simulation. More...
void	setRootDir (string name)
	Sets the root directory of the simulation. More...
void	log_simparams ()
	Saves the current simulation parameters to the default parameter logfile. More...
void	log (string message)
	Write to the parameter logfile. More...
list< ParamSet * > &	get_params ()
	Accessor to the list of the current parameters of the simulation. More...
file_it	getFirstWriter ()
	Accessor to first element of the list of output FileHandlers. More...
file_it	getLastWriter ()
	Accessor to last element of the list of output FileHandlers. More...
file_it	getFirstReader ()
	Accessor to first element of the list of input FileHandlers. More...
file_it	getLastReader ()
	Accessor to last element of the list of input FileHandlers. More...
FileHandler *	getReader (string &type)
	Accessor to a specific file handler specified by its extension string. More...
string &	getBaseFileName ()
	Accessor to the base file name of the simulation. More...
string &	getRootDir ()
	Accessor to the name of the simulation's root output directory. More...
string	getReplicateCounter ()
	Accessor to the current replicate counter string. More...
string &	getFirstReplicateFileName ()
	Accessor to the first replicate file name. More...
string &	getReplicateFileName ()
	Accessor to the current replicate file name. More...
string	getGenerationCounter ()
	Accessor to the current generation counter string. More...
string	getGenerationReplicateFileName ()
	Accessor to the current file name with generation and replicate counters added. More...
virtual void	load (SimComponent *sc)
	Tells the SimComponent to load its file handlers. More...
virtual void	attach (Handler *FH)
	Attaches the FileHandler to the current list (_writers) of the FileServices. More...
virtual void	attach_reader (FileHandler *FH)
	Attaches the FileHandler to the current list (_readers) of the FileServices. More...
virtual void	reset ()
	Clears the list of FileHandlers. More...
population sampling for output files
void	set_sampling_params (TMatrix *size, TMatrix *age, TMatrix *patches)
	Set the population sampling params. More...
void	empty_sampled_pop ()
	Empty the sampled pop without deleting the individuals since they are also in the main population. More...
void	reset_sampled_pop ()
	Remove the existing sampled metapop, if it has been allocated previously. More...
Metapop *	getSampledPop ()
	Sets the down-sampled population and provides accessor to file handlers. More...
void	subSamplePatch (sex_t SEX, age_idx AGE, unsigned int num, Patch *source_patch, Patch *patch)
	Create a patch from a sample of the corresponding patch in the main metapopulation. More...
Public Member Functions inherited from Service
	Service ()
virtual	~Service ()

Private Attributes
Metapop *	_popPtr
	a pointer to the current Metapop More...
FHLogWriter *	_logWriter
	a FileHandler used to save the simulation parameters on disk. More...
list< FileHandler * >	_writers
	the list of the FileHandler's registered by the SimComponent in output mode More...
list< FileHandler * >	_readers
	the list of the FileHandler's registered by the SimComponent in input mode More...
string	_rep_filename
	the file name associated with the current simulation replicate More...
string	_basename
	the base file name of the simulation, read from the init file (param "filename") More...
string	_root_dir
	the root directory for the simulation's results, read from the init file (param "root_dir") More...
list< ParamSet * >	_params
	the list of the parameters of the current simulation. More...
unsigned int	_mode
	File mode, sets behavior when file must be overwritten or not. More...
TMatrix *	_patch_sample_size
	Number of individuals to sample from each patch for the file handlers. More...
TMatrix *	_patch_sample_age
TMatrix *	_patch_sampled
int	_sampled_at_replicate
int	_sampled_at_generation
Metapop *	_sample_pop

Detailed Description

A class to manage the files associated with each components of the simulation.

Implements the Observer design pattern (is the concrete subject), stores the base filename of the simulation and updates the replicate filenames. It also performs files checking and saves the simulation parameters on init.

Member Typedef Documentation

file_it

typedef std::list< FileHandler* >::const_iterator FileServices::file_it

Constructor & Destructor Documentation

FileServices()

FileServices::FileServices

(

)

                            : _popPtr(0), _rep_filename(""), _basename(""), _root_dir(""),
    _patch_sample_size(0), _patch_sample_age(0), _patch_sampled(0), _sample_pop(0), _sampled_at_replicate(-1),
    _sampled_at_generation(-1)
{
  _logWriter = new FHLogWriter();
  attach(_logWriter);
}

References _logWriter, and attach().

~FileServices()

FileServices::~FileServices ( )

virtual

                            {
  if(_logWriter) delete _logWriter;
  if(_sample_pop) delete _sample_pop;
}

References _logWriter, and _sample_pop.

Member Function Documentation

attach()

void FileServices::attach ( Handler *  FH )

virtual

Attaches the FileHandler to the current list (_writers) of the FileServices.

Parameters

FH	the FileHandler

Implements Service.

{
//  Service::attach(FH);
  FileHandler* FH = dynamic_cast<FileHandler*> (H);
  _writers.push_back(FH);
  
  if(FH->get_isInputHandler()) attach_reader(FH);
  
  FH->set_service(this);
}

References _writers, attach_reader(), FileHandler::get_isInputHandler(), and FileHandler::set_service().

Referenced by FileServices(), BinaryDataSaver::loadFileServices(), LCE_Selection_base::loadFileServices(), Metapop::loadFileServices(), LCE_FileServicesNotifier::loadFileServices(), LCE_StatServiceNotifier::loadFileServices(), TProtoBDMI::loadFileServices(), TProtoDeletMutations_bitstring::loadFileServices(), TProtoNeutralGenes::loadFileServices(), TProtoQuanti::loadFileServices(), and LCE_Breed_Wolbachia::loadFileServices().

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attach_reader()

void FileServices::attach_reader ( FileHandler *  FH )

virtual

Attaches the FileHandler to the current list (_readers) of the FileServices.

Parameters

FH	the FileHandler

{
  _readers.push_back(FH);
  FH->set_service(this);
}

References _readers, and FileHandler::set_service().

Referenced by attach(), LCE_Cross::loadFileServices(), TProtoDeletMutations_bitstring::loadFileServices(), TProtoNeutralGenes::loadFileServices(), and TProtoQuanti::loadFileServices().

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empty_sampled_pop()

void FileServices::empty_sampled_pop

(

)

Empty the sampled pop without deleting the individuals since they are also in the main population.

                                      {
 
  if(_sample_pop) {
 
    // the sample pop need to be emptied without destroying the individuals because they
    // are also in the patch containers in the main pop.
    Patch* patch;
    // remove the patches :
    for(unsigned int i = 0; i < _sample_pop->getPatchArraySize(); ) {
      // removePatch() resizes the array, i must stay = 0 to mimic pop_front() until array is empty
      patch = _sample_pop->removePatch(i);
      patch->clear(); // this resets all container's size to 0 without deleting content
      delete patch;   // delete the patch, without deleting individuals
    }
 
  }
 
}

References _sample_pop, Patch::clear(), Metapop::getPatchArraySize(), and Metapop::removePatch().

Referenced by getSampledPop(), reset(), and reset_sampled_pop().

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get_params()

list< ParamSet* >& FileServices::get_params ( )

inline

Accessor to the list of the current parameters of the simulation.

{return _params;};

References _params.

Referenced by BinaryDataSaver::printHeader().

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get_pop_ptr()

virtual Metapop* FileServices::get_pop_ptr ( )

inlinevirtual

Accessor to the pointer to the main population.

Returns

the pointer to the current Metapop as set during simulation setup.

{return _popPtr;}

References _popPtr.

Referenced by GenotyperFH::FHwrite(), TTBDMI_FH::FHwrite(), TTDeletMutBitstrFH::FHwrite(), TTNeutralGenesFH::FHwrite(), TTQuantiFH::FHwrite(), TTQFreqExtractor::FHwrite(), TTNeutralGenesFH::write_Fst_i(), and TTNeutralGenesFH::write_varcompWC().

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getBaseFileName()

string & FileServices::getBaseFileName

(

)

Accessor to the base file name of the simulation.

{
  return _basename;
}

References _basename.

Referenced by LCE_StatFH::FHwrite(), BinaryDataSaver::finish(), BinaryDataSaver::ifExist(), LCE_StatFH::ifExist(), SimRunner::printLog(), LCE_StatFH::PrintStat_byGen(), SimRunner::run(), and SimRunner::runPostExecReplicateWise().

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getFirstReader()

file_it FileServices::getFirstReader ( )

inline

Accessor to first element of the list of input FileHandlers.

{return _readers.begin();}

References _readers.

Referenced by getReader().

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getFirstReplicateFileName()

string & FileServices::getFirstReplicateFileName

(

)

Accessor to the first replicate file name.

{
  ostringstream rpl;
 
  rpl.fill('0');
  rpl.width( (int)log10((double)_popPtr->getReplicates()) + 1);
  rpl<< max( 1, _myenv->workerRank() );
 
  _rep_filename = _basename + "_" + rpl.str();
 
  return _rep_filename;
}

References _basename, _myenv, _popPtr, _rep_filename, Metapop::getReplicates(), and MPIenv::workerRank().

getFirstWriter()

file_it FileServices::getFirstWriter ( )

inline

Accessor to first element of the list of output FileHandlers.

{return _writers.begin();}

References _writers.

Referenced by SimRunner::printLog().

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getGenerationCounter()

string FileServices::getGenerationCounter

(

)

Accessor to the current generation counter string.

{
  ostringstream gen;
  
  gen.fill('0');
  gen.width( (int)log10((double)_popPtr->getGenerations()) + 1);
  gen<<_popPtr->getCurrentGeneration();
  
  return gen.str();
}

References _popPtr, Metapop::getCurrentGeneration(), and Metapop::getGenerations().

Referenced by getGenerationReplicateFileName().

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getGenerationReplicateFileName()

string FileServices::getGenerationReplicateFileName

(

)

Accessor to the current file name with generation and replicate counters added.

{
  string name = _basename + "_" + getGenerationCounter() + "_" + getReplicateCounter();
  return name;
}

References _basename, getGenerationCounter(), and getReplicateCounter().

Referenced by GenotyperFH::FHwrite(), TTDeletMutBitstrFH::FHwrite(), GenotyperFH::print_PLINK(), TTNeutralGenesFH::write_Fst_i(), TTNeutralGenesFH::write_FSTAT(), TTNeutralGenesFH::write_GENEPOP(), TTNeutralGenesFH::write_PLINK(), TTQuantiFH::write_PLINK(), TTNeutralGenesFH::write_TAB(), and TTNeutralGenesFH::write_varcompWC().

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getLastReader()

file_it FileServices::getLastReader ( )

inline

Accessor to last element of the list of input FileHandlers.

{return _readers.end();}

References _readers.

Referenced by getReader().

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getLastWriter()

file_it FileServices::getLastWriter ( )

inline

Accessor to last element of the list of output FileHandlers.

{return _writers.end();}  

References _writers.

Referenced by SimRunner::printLog().

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getMode()

unsigned int FileServices::getMode ( )

inline

Writting mode getter.

{return _mode;}

References _mode.

Referenced by BinaryDataSaver::finish().

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getReader()

FileHandler * FileServices::getReader

(

string &

type

)

Accessor to a specific file handler specified by its extension string.

{
  file_it file = getFirstReader(), last = getLastReader() ;
    
  for(;file != last; file++) {
    if( (*file)->get_extension().compare( type ) == 0) {
      return (*file);
    }
  }
  return 0;
}

References getFirstReader(), and getLastReader().

Referenced by Metapop::loadPopFromTraitFile().

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getReplicateCounter()

string FileServices::getReplicateCounter

(

)

Accessor to the current replicate counter string.

{
  ostringstream rpl;
  
  rpl.fill('0');
  rpl.width( (int)log10((double)_popPtr->getReplicates()) + 1);
  rpl<<_popPtr->getCurrentReplicate();
  
  return rpl.str();
}

References _popPtr, Metapop::getCurrentReplicate(), and Metapop::getReplicates().

Referenced by getGenerationReplicateFileName(), and getReplicateFileName().

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getReplicateFileName()

string & FileServices::getReplicateFileName

(

)

Accessor to the current replicate file name.

{
  _rep_filename = _basename + "_" + getReplicateCounter();
 
  return _rep_filename;
}

References _basename, _rep_filename, and getReplicateCounter().

Referenced by TTQFreqExtractor::FHwrite().

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getRootDir()

std::string & FileServices::getRootDir

(

)

Accessor to the name of the simulation's root output directory.

{
  return _root_dir;
}

References _root_dir.

getSampledPop()

Metapop * FileServices::getSampledPop

(

)

Sets the down-sampled population and provides accessor to file handlers.

{
  // if the sampling parameters haven't been set, we return the main pop ptr
  if(_patch_sample_size->length() == 0 )
    return _popPtr;
 
  // if we already created a population sample, we return it:
  if( _popPtr->getCurrentReplicate() == _sampled_at_replicate &&
      _popPtr->getCurrentGeneration() == _sampled_at_generation )
  {
    return _sample_pop;
  }
 
#ifdef _DEBUG_
  message("FileServices::setting sub-sampled pop in %i patches and %i age classes: ", _patch_sample_size->nrows(), _patch_sample_size->ncols());
#endif
 
  // else, population hasn't been sampled yet, create sample:
 
  Patch *sample_patch, *src_patch;
 
  //first time it is called, the pointer should be NULL upon instantiation of FileServices
  if(!_sample_pop) {
 
    _sample_pop = new Metapop();
 
  } else {
 
    empty_sampled_pop();
 
    _sample_pop->setCurrentAge( age_t(NONE) );
 
  }
 
  // set the age flag as the union of all age classes selected
  unsigned int length = _patch_sample_age->length();
  const double* age_selected = _patch_sample_age->get();
 
  age_t age_flag = 0;
 
  if(length > 0){
    int mask = 1;
    for(unsigned int i = 0; i < length; ++i) {
      mask <<= int(age_selected[i]);
      age_flag |= mask;
      mask = 1;
    }
  }
  // check the age flag:
  if( age_flag != 0) {
 
    // check if current pop age flag is compatible with user's choice:
 
    if(!(age_flag &  _popPtr->getCurrentAge())) {
      warning("Cannot sub-sample the population for output file writers: no individual present within age class(es) selected at time of sampling.\n");
    }
 
  } else { // the age flag wasn't set by the user
 
    age_flag = _popPtr->getCurrentAge();
 
  }
 
  //need to set the age flag of the population
  _sample_pop->setCurrentAge( age_flag );
 
  // stop here if age flag is null after checking:
  if( age_flag == 0 )
    fatal("The population cannot be sub-sampled for the age-class chosen (parameter \"files_sample_age\")\n             Check your parameter file or contact the developers\n");
 
#ifdef _DEBUG_
  message("after check, sampling age is %i; ", age_flag);
#endif
 
  // add some double checking on matrix sizes:
  if(_patch_sample_size->nrows() != _patch_sampled->ncols())
    fatal("The patch sampling parameters are mis-specified: number of patches don't match between size and patch-id input parameters\n.");
 
  if(_patch_sample_size->ncols() != _patch_sample_age->ncols())
    fatal("The patch sampling parameters are mis-specified: number of stages don't match between size and age-class input parameters\n.");
 
  if(_patch_sample_size->nrows() != _patch_sample_age->nrows())
    fatal("The patch sampling parameters are mis-specified: number of patches don't match between size and age-class input parameters\n.");
 
  // add patches to match current parameters and patch sizes (discard empty patches)
  age_idx age;
  unsigned int patchID;
  for(unsigned int i = 0; i < _patch_sampled->ncols(); ++i) {
 
    patchID = _patch_sampled->get(0, i);
 
//    cout << " --- sampling patch "<< patchID << endl;
 
    if( _popPtr->size(age_flag, patchID) == 0 ) continue; //skip empty patches
 
    src_patch = _popPtr->getPatch(patchID);
    // allocate new patches
    sample_patch = new Patch();
    sample_patch->setID(patchID);
    sample_patch->set_K(src_patch->get_K());
    sample_patch->set_KFem(src_patch->get_KFem());
    sample_patch->set_KMal(src_patch->get_KMal());
 
    // sample in each age class selected (has been expanded at set up to hold the necessary number of values)
    for(unsigned int j = 0; j < _patch_sample_size->ncols(); ++j) {
 
      age = age_idx(_patch_sample_age->get(i, j));
 
//      cout << "   ... in age container "<<age<<" (age flag "<<age_flag<<")\n";
 
      if(age_flag & age_t(pow(2,_patch_sample_age->get(i, j)))) {
        subSamplePatch(FEM, age, _patch_sample_size->get(i,j), src_patch, sample_patch);
        subSamplePatch(MAL, age, _patch_sample_size->get(i,j), src_patch, sample_patch);
      }
 
    }
 
    _sample_pop->addPatch( sample_patch );
 
  }
 
  _sample_pop->setPatchNbr(_sample_pop->getPatchArraySize());
  _sample_pop->setPatchSizes(*_popPtr->getPatchCapacities());
 
#ifdef _DEBUG_
  message("sampled pop is: \n");
  _sample_pop->show_up();
#endif
 
 
  _sampled_at_replicate = _popPtr->getCurrentReplicate();
  _sampled_at_generation = _popPtr->getCurrentGeneration();
 
  return _sample_pop;
}

References _patch_sample_age, _patch_sample_size, _patch_sampled, _popPtr, _sample_pop, _sampled_at_generation, _sampled_at_replicate, Metapop::addPatch(), empty_sampled_pop(), fatal(), FEM, TMatrix::get(), Patch::get_K(), Patch::get_KFem(), Patch::get_KMal(), Metapop::getCurrentAge(), Metapop::getCurrentGeneration(), Metapop::getCurrentReplicate(), Metapop::getPatch(), Metapop::getPatchArraySize(), Metapop::getPatchCapacities(), TMatrix::length(), MAL, message(), TMatrix::ncols(), NONE, TMatrix::nrows(), Patch::set_K(), Patch::set_KFem(), Patch::set_KMal(), Metapop::setCurrentAge(), Patch::setID(), Metapop::setPatchNbr(), Metapop::setPatchSizes(), Metapop::show_up(), Metapop::size(), subSamplePatch(), and warning().

Referenced by GenotyperFH::FHwrite(), TTBDMI_FH::FHwrite(), TTDeletMutBitstrFH::FHwrite(), TTNeutralGenesFH::FHwrite(), TTQuantiFH::FHwrite(), and TTQOhtaStats::FHwrite().

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init() [1/2]

virtual bool FileServices::init ( )

inlinevirtual

Implements Service.

{return false;}

Referenced by SimRunner::run().

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init() [2/2]

bool FileServices::init

(

list< ParamSet * > &

params

)

Checks if files with _basename already exist and save the simulation parameters in log files.

Parameters

params

a ref to the list of the current parameters of the simulation

Returns

true if the files check is ok

false if the user wants to skip this simulation

{
  char yn;
  bool ok;
  file_it HIT;
 
  _params = params;
  
  _logWriter->set(0, 0, 0, 0, 0, "");
 
  //first, build path and filename for each file handler
  HIT = _writers.begin();
 
  if(_myenv->isMaster()) message("    outputs: %s{",_root_dir.c_str());
 
  while(HIT != _writers.end()) {
    if(_myenv->isMaster())  message("%s%s*%s",
                                    (*HIT)->get_path().c_str(),
                                    ((*HIT)->get_path().size() !=0? "/":""),
                                    (*HIT)->get_extension().c_str());
    (*HIT)->init();
    HIT++;
 
    if(HIT != _writers.end() && _myenv->isMaster()) message(", ");
  }
  if(_myenv->isMaster()) message("}\n");
 
  //then check if any file already exists
check:
 
  ok = true;
  HIT = _writers.begin();
  vector<string> local_files, Xing_files;
 
  //we have to skip the first writer, it is the log-writer (always overwritten)
  while(++HIT != _writers.end()) {
 
    Xing_files = (*HIT)->ifExist();
 
    if( Xing_files.size() != 0 ) {
      local_files.insert(local_files.end(), Xing_files.begin(), Xing_files.end() );
      ok = false;
    } else
      ok &= true;
  }
 
  if(!ok) {
 
//    warning("simulation filename \"%s\" already used on disc!", getBaseFileName().c_str());
 
    for(unsigned int i=0; i < local_files.size(); ++i)
      warning("\"%s\" exists", local_files[i].c_str());
 
    //file mode is set during simulation setup, in SimRunner::init()
    if(_mode == 0) { //"run"
 
#if defined(_R_OUTPUT_) || defined(LOW_VERBOSE) || defined(USE_MPI)
      yn = 's';
      message("\nPlease choose an other base filename or move the existing file(s)\n");
#else
 
      message("\nDo you want to overwrite all the files that use it ? (y/n/s(kip)): ");
      cin>>yn;
#endif
 
    } else if( _mode == 1 ) { //"overwrite"
 
      warning("Overwriting existing files.\n\n");
      yn = 'y';
 
    } else if( _mode == 2 ) { //"skip" & "silent_run"
 
      error("Files with the same simulation name already exist on disk!\n");
      error("Choose another base filename or move the existing file(s)\n");
      yn = 's';
 
    } else if( _mode == 3 || _mode == 4) { // "dryrun" & "create_init"
      //dryrun, pretend overwriting, silently
      yn = 'y';      
    } else {
      fatal("Run mode not properly set, check simulation parameter \"run_mode\".\n");
    }
 
 
    switch(yn) {
      case 'y':
        break;
      case 's':
        error("Skipping this simulation\n");
        return false;
      default: {
        message("Please give a new output filename : ");
        cin>>_basename;
        goto check;
      }
    }
  }
  
  return true;
}

References _basename, _logWriter, _mode, _myenv, _params, _root_dir, _writers, error(), fatal(), MPIenv::isMaster(), message(), FileHandler::set(), and warning().

load()

void FileServices::load ( SimComponent *  sc )

virtual

Tells the SimComponent to load its file handlers.

Parameters

sc	the SimComponent

Implements Service.

{sc->loadFileServices(this);}

References SimComponent::loadFileServices().

Referenced by SimRunner::register_component().

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log()

void FileServices::log

(

string

message

)

Write to the parameter logfile.

{
  _logWriter->log_message(message);
}

References _logWriter, FHLogWriter::log_message(), and message().

Referenced by Metapop::loadPopFromBinarySource(), SimRunner::run(), and LCE_Selection_base::set_std_rate_of_change().

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log_simparams()

void FileServices::log_simparams

(

)

Saves the current simulation parameters to the default parameter logfile.

{
  if(_mode == 4)
    _logWriter->createInitFile(_params);
  else
    _logWriter->save_simparams(_params);
}

References _logWriter, _mode, _params, FHLogWriter::createInitFile(), and FHLogWriter::save_simparams().

Referenced by SimRunner::run().

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notify()

void FileServices::notify ( )

virtual

Implements Service.

{
  for (file_it file = _writers.begin(); file != _writers.end(); ++file) {
    (*file)->update();
  }
}

References _writers.

Referenced by LCE_FileServicesNotifier::execute(), and SimRunner::Replicate_LOOP().

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reset()

void FileServices::reset ( )

virtual

Clears the list of FileHandlers.

Implements Service.

{
#ifdef _DEBUG_
  message("FileServices::reset\n");
#endif
  //Service::reset(); 
  _writers.clear(); _writers.push_back(_logWriter);
  _readers.clear();
 
  if(_sample_pop != NULL) {
    empty_sampled_pop();
    delete _sample_pop;
  }
 
  _sample_pop = NULL;
 
#ifdef _DEBUG_
  message("FileServices::reset done\n");
#endif
}

References _logWriter, _readers, _sample_pop, _writers, empty_sampled_pop(), and message().

Referenced by SimRunner::reset_services().

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reset_sampled_pop()

void FileServices::reset_sampled_pop

(

)

Remove the existing sampled metapop, if it has been allocated previously.

                                      {
 
  if(_sample_pop) {
 
    empty_sampled_pop();
 
    delete _sample_pop;
  }
 
  _sample_pop = NULL;
 
  _sampled_at_generation = -1;
  _sampled_at_replicate = -1;
}

References _sample_pop, _sampled_at_generation, _sampled_at_replicate, and empty_sampled_pop().

Referenced by LCE_FileServicesNotifier::loadFileServices().

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set_pop_ptr()

virtual void FileServices::set_pop_ptr ( Metapop *  pop )

inlinevirtual

Sets the Metapop reference.

{_popPtr = pop;}

References _popPtr.

Referenced by SimRunner::init_components().

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set_sampling_params()

void FileServices::set_sampling_params ( TMatrix *  size, TMatrix *  age, TMatrix *  patches  )

inline

Set the population sampling params.

{_patch_sample_size = size; _patch_sample_age = age; _patch_sampled = patches;}

References _patch_sample_age, _patch_sample_size, and _patch_sampled.

Referenced by LCE_FileServicesNotifier::loadFileServices().

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setBasename()

void FileServices::setBasename

(

string

name

)

Sets the base file name of the simulation.

{
    _basename = name;
}

References _basename.

Referenced by SimRunner::init().

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setMode()

void FileServices::setMode ( unsigned int  m )

inline

Mode setter, determines if file will get overwritten or not.

{_mode = m;}

References _mode.

Referenced by SimRunner::init().

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setRootDir()

void FileServices::setRootDir

(

string

name

)

Sets the root directory of the simulation.

{
  _root_dir = name;
 
  if(_root_dir.size() != 0 && _root_dir[_root_dir.length()-1] != '/')
        _root_dir += "/";
  
}

References _root_dir.

Referenced by SimRunner::init().

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subSamplePatch()

void FileServices::subSamplePatch	(	sex_t	SEX,
		age_idx	AGE,
		unsigned int	num,
		Patch *	source_patch,
		Patch *	patch
	)

Create a patch from a sample of the corresponding patch in the main metapopulation.

{
 
  int* sample = NULL;
  int size = (int)source_patch->size(SEX, AGE), sample_size;
  Individual *ind = 0;
 
  sample_size = (num <  size ? num : size);
 
//  cout << "   ... SEX = "<<SEX<<"; sample size = "<<sample_size<< "; size of receiving patch container: "<< patch->size(SEX, AGE)<< endl;
  if( patch->size(SEX, AGE) != 0) fatal("FileServices::subSamplePatch::receiver patch container is not empty before sampling\n");
 
  if( sample_size != 0) {
 
    int sample[sample_size];
 
    RAND::Sample(0, size, sample_size, &sample[0], false);
 
    for(unsigned int j = 0; j < sample_size; ++j) {
 
      ind = source_patch->get(SEX, AGE, sample[j]);
 
      patch->add(SEX, AGE, ind);
    }
  }
}

References Patch::add(), fatal(), Patch::get(), RAND::Sample(), and Patch::size().

Referenced by getSampledPop().

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Member Data Documentation

_basename

string FileServices::_basename

private

the base file name of the simulation, read from the init file (param "filename")

Referenced by getBaseFileName(), getFirstReplicateFileName(), getGenerationReplicateFileName(), getReplicateFileName(), init(), and setBasename().

_logWriter

FHLogWriter* FileServices::_logWriter

private

a FileHandler used to save the simulation parameters on disk.

Referenced by FileServices(), init(), log(), log_simparams(), reset(), and ~FileServices().

_mode

unsigned int FileServices::_mode

private

File mode, sets behavior when file must be overwritten or not.

Referenced by getMode(), init(), log_simparams(), and setMode().

_params

list< ParamSet* > FileServices::_params

private

the list of the parameters of the current simulation.

The list is created when init() is called from SimRunner::run().

Referenced by get_params(), init(), and log_simparams().

_patch_sample_age

TMatrix* FileServices::_patch_sample_age

private

Referenced by getSampledPop(), and set_sampling_params().

_patch_sample_size

TMatrix* FileServices::_patch_sample_size

private

Number of individuals to sample from each patch for the file handlers.

Referenced by getSampledPop(), and set_sampling_params().

_patch_sampled

TMatrix* FileServices::_patch_sampled

private

Referenced by getSampledPop(), and set_sampling_params().

_popPtr

Metapop* FileServices::_popPtr

private

a pointer to the current Metapop

Referenced by get_pop_ptr(), getFirstReplicateFileName(), getGenerationCounter(), getReplicateCounter(), getSampledPop(), and set_pop_ptr().

_readers

list< FileHandler* > FileServices::_readers

private

the list of the FileHandler's registered by the SimComponent in input mode

Referenced by attach_reader(), getFirstReader(), getLastReader(), and reset().

_rep_filename

string FileServices::_rep_filename

private

the file name associated with the current simulation replicate

Referenced by getFirstReplicateFileName(), and getReplicateFileName().

_root_dir

string FileServices::_root_dir

private

the root directory for the simulation's results, read from the init file (param "root_dir")

Referenced by getRootDir(), init(), and setRootDir().

_sample_pop

Metapop* FileServices::_sample_pop

private

Referenced by empty_sampled_pop(), getSampledPop(), reset(), reset_sampled_pop(), and ~FileServices().

_sampled_at_generation

int FileServices::_sampled_at_generation

private

Referenced by getSampledPop(), and reset_sampled_pop().

_sampled_at_replicate

int FileServices::_sampled_at_replicate

private

Referenced by getSampledPop(), and reset_sampled_pop().

_writers

list< FileHandler* > FileServices::_writers

private

the list of the FileHandler's registered by the SimComponent in output mode

Referenced by attach(), getFirstWriter(), getLastWriter(), init(), notify(), and reset().

---

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

• fileservices.h
• fileservices.cc