FileHandler Class Reference

Interface to handle file input/output for any SimComponent. More...

#include <filehandler.h>

Inheritance diagram for FileHandler:

Collaboration diagram for FileHandler:

Public Member Functions
	FileHandler (const char *ext)
virtual	~FileHandler ()
virtual void	init ()
	Called by notifier during simulation setup, performs file checking. More...
virtual vector< string >	ifExist ()
	Checks if any file associated with the current file name already exists on disk. More...
virtual void	set (bool rpl_per, bool gen_per, int rpl_occ, int gen_occ, int rank, string path)
	Sets the hanlder parameters. More...
virtual void	set_multi (bool rpl_per, bool gen_per, int rpl_occ, TMatrix *Occ, string path)
virtual void	FHwrite ()=0
	Default behavior of the class, called by Handler::update(). More...
virtual void	FHread (string &filename)=0
	Default input function. More...
virtual void	update ()
	Updates the inner replicate and generation counters and calls FHwrite if needed by the the periodicity of the file. More...
Accessors
Metapop *	get_pop_ptr ()
	Returns the pointer to the current metapop through the FileServices interface. More...
void	set_pop_ptr (Metapop *pop_ptr)
FileServices *	get_service ()
	Returns pointer to the FileServices. More...
void	set_service (FileServices *srv)
std::string &	get_path ()
void	set_path ()
std::string &	get_extension ()
void	set_extension (const char *ext)
std::string &	get_filename ()
	Builds and returns the current file name depending on the periodicity of the file. More...
bool	get_isInputHandler ()
void	set_isInputHandler (bool val)
bool	get_isReplicatePeriodic ()
void	set_isReplicatePeriodic (bool val)
unsigned int	get_ReplicateOccurrence ()
void	set_ReplicateOccurrence (unsigned int val)
bool	get_isGenerationPeriodic ()
void	set_isGenerationPeriodic (bool val)
unsigned int	get_GenerationOccurrence ()
void	set_GenerationOccurrence (unsigned int val)
unsigned int	get_ExecRank ()
	unused yet... More...
void	set_ExecRank (int val)
TMatrix *	get_OccMatrix ()
void	set_OccMatrix (TMatrix *occ)
bool	get_isMasterExec ()
void	set_isMasterExec (bool is)
Public Member Functions inherited from Handler
virtual void	init ()=0
	Inits state. More...
virtual void	update ()=0
	Updates the handler state. More...
virtual	~Handler ()

Protected Attributes
Metapop *	_pop
	Pointer to the current metapop, set during initialization within the init function. More...

Private Attributes
FileServices *	_service
	Link to the files manager. More...
bool	_isMasterExec
	Flag telling if the file must be written by the master or the worker node. More...
bool	_isInputHandler
	Writing mode flag. More...
bool	_isReplicatePeriodic
	Flag telling if the file should be written each replicate. More...
bool	_isGenerationPeriodic
	Flag setting the per generation periodicity behaviour of the file. More...
unsigned int	_ReplicateOccurrence
	Tells every what replicate the file should be written. More...
unsigned int	_GenerationOccurrence
	Tells every what generation the file should be written. More...
unsigned int	_current_replicate
	The current replicate number of the simulation. More...
unsigned int	_current_generation
	The current generation number of the simulation. More...
TMatrix	_multipleOccurences
	Multiple occurences. More...
list< int >::const_iterator	_genITER
list< int >	_generations
unsigned int	_ExecRank
	unused... yet More...
std::string	_path
	File path as set during initialization. More...
std::string	_extension
	File extension, should be specific to the implementation. More...
std::string	_current_filename
	The current filename as set by FileHandler::get_filename(). More...

Detailed Description

Interface to handle file input/output for any SimComponent.

Stores the periodicity parameters and the file path and extension. The replicate file name is given by the FileServices. A file handler might be set to write output at a specific generation of a specific replicate or at some periodic time during the simulation. The default writing mode of a FileHandler is in output and is added as a 'writer' to the File Services as such using the FileServices::attach mode. The _isInputHandler flag is thus set to FALSE by default. To set a FileHandler as a reader instead of a writer, the method FileHandler::set_isInputHandler(TRUE) must be called prior to attaching it to the FileServices using the FileServices::attach_reader method. Furthermore, a single instance of a FileHandler can be attached as both a writer and a reader by setting the _isInputHandler flag to TRUE and then using the FileServices::attach method to add it to the list of both the reader and writers. Note on memory management: the FileServices class only deals with its lists of FileHandlers pointers and will never try to delete any one of those. All memory management must thus be taken care of by the user class (typically the TraitPrototype...).

Constructor & Destructor Documentation

FileHandler()

FileHandler::FileHandler ( const char *  ext )

inline

    : _service(0), 
#ifdef USE_MPI
    _isMasterExec(false), 
#else
    _isMasterExec(true), 
#endif
    _isInputHandler(0),
    _isReplicatePeriodic(0), _isGenerationPeriodic(0),
    _ReplicateOccurrence(0), _GenerationOccurrence(0),
    _current_replicate(0), _current_generation(0), _ExecRank(0),
    _path(), _extension(ext), _current_filename(), _pop(0)
    {}

~FileHandler()

virtual FileHandler::~FileHandler ( )

inlinevirtual

{ }

Member Function Documentation

FHread()

virtual void FileHandler::FHread ( string &  filename )

pure virtual

Default input function.

Loads a pop from the genotypes read from the input file.

Implemented in BinaryDataSaver, FHLogWriter, FHPedigreeReader, LCE_SelectionFH, MPFileHandler, FileMergerFH, LCE_StatFH, TTBDMI_FH, TTDeletMutBitstrFH, TTNeutralGenesFH, TTQuantiFH, TTQFreqExtractor, TTWolbachiaFH, TraitFileHandler< TP >, and EventFileHandler< LCE >.

Referenced by Metapop::loadPopFromTraitFile().

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FHwrite()

virtual void FileHandler::FHwrite ( )

pure virtual

Default behavior of the class, called by Handler::update().

Implemented in BinaryDataSaver, FHLogWriter, FHPedigreeReader, LCE_SelectionFH, MPFileHandler, FileMergerFH, LCE_StatFH, TTBDMI_FH, TTDeletMutBitstrFH, TTNeutralGenesFH, TTQuantiFH, TTQFreqExtractor, TTWolbachiaFH, TraitFileHandler< TP >, TraitFileHandler< TProtoBDMI >, TraitFileHandler< TProtoDeletMutations_bitstring >, TraitFileHandler< TProtoNeutralGenes >, TraitFileHandler< TProtoQuanti >, EventFileHandler< LCE >, EventFileHandler< LCE_Cross >, EventFileHandler< LCE_FileServicesNotifier >, EventFileHandler< LCE_Selection_base >, and EventFileHandler< LCE_Breed_Wolbachia >.

Referenced by SimRunner::Replicate_LOOP(), and update().

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get_ExecRank()

unsigned int FileHandler::get_ExecRank ( )

inline

unused yet...

{return _ExecRank;}

References _ExecRank.

get_extension()

std::string & FileHandler::get_extension ( )

inline

{return _extension;}

References _extension.

Referenced by LCE_StatFH::FHwrite(), TTDeletMutBitstrFH::FHwrite(), TTQFreqExtractor::FHwrite(), BinaryDataSaver::ifExist(), TTNeutralGenesFH::write_Fst_i(), TTNeutralGenesFH::write_FSTAT(), TTNeutralGenesFH::write_GENEPOP(), TTNeutralGenesFH::write_TAB(), and TTNeutralGenesFH::write_varcompWC().

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get_filename()

string & FileHandler::get_filename

(

)

Builds and returns the current file name depending on the periodicity of the file.

{
  if(_isReplicatePeriodic)
    if(_isGenerationPeriodic)
      _current_filename = _path + _service->getGenerationReplicateFileName() + _extension;
    else
      _current_filename = _path + _service->getReplicateFileName() + _extension;
  else
    _current_filename = _path + _service->getBaseFileName() + _extension;
  
  return _current_filename;
}

References _current_filename, _extension, _isGenerationPeriodic, _isReplicatePeriodic, _path, _service, FileServices::getBaseFileName(), FileServices::getGenerationReplicateFileName(), and FileServices::getReplicateFileName().

Referenced by LCE_SelectionFH::FHwrite(), MPFileHandler::FHwrite(), TTBDMI_FH::FHwrite(), TTWolbachiaFH::FHwrite(), BinaryDataSaver::finish(), FHLogWriter::open_logfile4writing(), BinaryDataSaver::printHeader(), BinaryDataSaver::setFileDescriptor(), and TTQuantiFH::write_TABLE().

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get_GenerationOccurrence()

unsigned int FileHandler::get_GenerationOccurrence ( )

inline

{return _GenerationOccurrence;}

References _GenerationOccurrence.

Referenced by TTQFreqExtractor::FHwrite(), and BinaryDataSaver::ifExist().

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get_isGenerationPeriodic()

bool FileHandler::get_isGenerationPeriodic ( )

inline

{return _isGenerationPeriodic;}

References _isGenerationPeriodic.

get_isInputHandler()

bool FileHandler::get_isInputHandler ( )

inline

{return _isInputHandler;}

References _isInputHandler.

Referenced by FileServices::attach().

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get_isMasterExec()

bool FileHandler::get_isMasterExec ( )

inline

{return _isMasterExec;}

References _isMasterExec.

get_isReplicatePeriodic()

bool FileHandler::get_isReplicatePeriodic ( )

inline

{return _isReplicatePeriodic;}

References _isReplicatePeriodic.

get_OccMatrix()

TMatrix * FileHandler::get_OccMatrix ( )

inline

{return &_multipleOccurences;}

References _multipleOccurences.

get_path()

std::string & FileHandler::get_path ( )

inline

{return _path;}

References _path.

Referenced by LCE_StatFH::FHwrite(), TTDeletMutBitstrFH::FHwrite(), TTQFreqExtractor::FHwrite(), BinaryDataSaver::finish(), BinaryDataSaver::ifExist(), LCE_StatFH::ifExist(), LCE_StatFH::PrintStat_byGen(), 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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get_pop_ptr()

Metapop * FileHandler::get_pop_ptr ( )

inline

Returns the pointer to the current metapop through the FileServices interface.

{return _pop;}

References _pop.

Referenced by TTDeletMutBitstrFH::FHwrite().

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get_ReplicateOccurrence()

unsigned int FileHandler::get_ReplicateOccurrence ( )

inline

{return _ReplicateOccurrence;}

References _ReplicateOccurrence.

Referenced by BinaryDataSaver::ifExist().

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get_service()

FileServices * FileHandler::get_service ( )

inline

Returns pointer to the FileServices.

{return _service;}

References _service.

Referenced by FHLogWriter::createInitFile(), TTNeutralGenesFH::FHread(), LCE_StatFH::FHwrite(), TTBDMI_FH::FHwrite(), TTDeletMutBitstrFH::FHwrite(), TTNeutralGenesFH::FHwrite(), TTQuantiFH::FHwrite(), TTQFreqExtractor::FHwrite(), BinaryDataSaver::finish(), BinaryDataSaver::ifExist(), LCE_StatFH::ifExist(), BinaryDataSaver::printHeader(), LCE_StatFH::PrintStat_byGen(), TTNeutralGenesFH::write_Fst_i(), TTNeutralGenesFH::write_FSTAT(), TTNeutralGenesFH::write_GENEPOP(), TTNeutralGenesFH::write_PLINK(), TTQuantiFH::write_PLINK(), TTNeutralGenesFH::write_TAB(), TTQuantiFH::write_TABLE(), and TTNeutralGenesFH::write_varcompWC().

ifExist()

vector< string > FileHandler::ifExist ( )

virtual

Checks if any file associated with the current file name already exists on disk.

Only checks wether the first replicate file is present.

Returns

false if filename already exists on disk, true otherwise.

Reimplemented in BinaryDataSaver, and LCE_StatFH.

{
  //check if the basefilename is already used on disk:
  string filename = _path + _service->getBaseFileName();
 
  vector< string > list;
 
  ostringstream rpl, gen;
    
  gen.fill('0');
  gen.width( (int)log10((double)_pop->getGenerations()) + 1);
  gen<<_GenerationOccurrence;
  
  rpl.fill('0');
  rpl.width( (int)log10((double)_pop->getReplicates()) + 1);
  rpl<<_ReplicateOccurrence;    
  
  if(!_isReplicatePeriodic)
    filename += _extension;
  else if(!_isGenerationPeriodic)
    filename += "_" + rpl.str() + _extension;
  else
    filename += "_" + gen.str() + "_" + rpl.str() + _extension;
  
  ifstream ifXist;
  ifXist.setstate(ios::failbit);
  
  ifXist.open(filename.c_str(),ios::in);
  
  if(ifXist.is_open()) {
//    warning("filename \"%s\" used by \"%s\"\n",_service->getBaseFileName().c_str(),filename.c_str());
    ifXist.close();
    list.push_back( filename );
//    return false;
  }
  ifXist.close();
 
  return list;
}

References _extension, _GenerationOccurrence, _isGenerationPeriodic, _isReplicatePeriodic, _path, _pop, _ReplicateOccurrence, _service, FileServices::getBaseFileName(), Metapop::getGenerations(), and Metapop::getReplicates().

init()

void FileHandler::init ( )

virtual

Called by notifier during simulation setup, performs file checking.

Implements Handler.

{
  _pop = _service->get_pop_ptr();
  //check if the occurrences exceed the pop parameters:
  if(_GenerationOccurrence > _pop->getGenerations())
    _GenerationOccurrence = _pop->getGenerations();
 
  if(_ReplicateOccurrence > _pop->getReplicates())
    _ReplicateOccurrence = _pop->getReplicates();
 
  set_path();
  
//  if ( _myenv->isMaster() != _isMasterExec ) return;
 
//  message("     %s*%s\n",get_path().c_str(),get_extension().c_str());
}

References _GenerationOccurrence, _pop, _ReplicateOccurrence, _service, FileServices::get_pop_ptr(), Metapop::getGenerations(), Metapop::getReplicates(), and set_path().

set()

virtual void FileHandler::set ( bool  rpl_per, bool  gen_per, int  rpl_occ, int  gen_occ, int  rank, string  path  )

inlinevirtual

Sets the hanlder parameters.

Parameters

rpl_per	replicate periodicity
gen_per	generation periodicity
rpl_occ	replicate occurence
gen_occ	generation occurence
rank	the rank in the life cycle, actualy unused...
path	the file path

                                                                                                 {
        set_isReplicatePeriodic(rpl_per); set_isGenerationPeriodic(gen_per); set_ReplicateOccurrence(rpl_occ);
        set_GenerationOccurrence(gen_occ); set_ExecRank(rank); _path = path;}

References _path, set_ExecRank(), set_GenerationOccurrence(), set_isGenerationPeriodic(), set_isReplicatePeriodic(), and set_ReplicateOccurrence().

Referenced by FileServices::init(), LCE_StatFH::LCE_StatFH(), Metapop::loadFileServices(), EventFileHandler< LCE >::set(), TraitFileHandler< TP >::set(), BinaryDataSaver::setParameters(), and LCE_StatServiceNotifier::setParameters().

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set_ExecRank()

void FileHandler::set_ExecRank ( int  val )

inline

{_ExecRank = val;}

References _ExecRank.

Referenced by set().

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set_extension()

void FileHandler::set_extension ( const char *  ext )

inline

{_extension = ext;}

References _extension.

Referenced by TProtoNeutralGenes::loadFileServices().

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set_GenerationOccurrence()

void FileHandler::set_GenerationOccurrence ( unsigned int  val )

inline

{_GenerationOccurrence = val;}

References _GenerationOccurrence.

Referenced by set(), and set_multi().

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set_isGenerationPeriodic()

void FileHandler::set_isGenerationPeriodic ( bool  val )

inline

{_isGenerationPeriodic = val;}

References _isGenerationPeriodic.

Referenced by set(), and set_multi().

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set_isInputHandler()

void FileHandler::set_isInputHandler ( bool  val )

inline

{_isInputHandler = val;}

References _isInputHandler.

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

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set_isMasterExec()

void FileHandler::set_isMasterExec ( bool  is )

inline

{_isMasterExec = true;}

References _isMasterExec.

Referenced by LCE_StatFH::LCE_StatFH().

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set_isReplicatePeriodic()

void FileHandler::set_isReplicatePeriodic ( bool  val )

inline

{_isReplicatePeriodic = val;}

References _isReplicatePeriodic.

Referenced by set(), and set_multi().

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set_multi()

virtual void FileHandler::set_multi ( bool  rpl_per, bool  gen_per, int  rpl_occ, TMatrix *  Occ, string  path  )

inlinevirtual

                                                                                              {
    set_isReplicatePeriodic(rpl_per); set_isGenerationPeriodic(gen_per); set_ReplicateOccurrence(rpl_occ);
    set_GenerationOccurrence(0); set_OccMatrix(Occ); _path = path;}

References _path, set_GenerationOccurrence(), set_isGenerationPeriodic(), set_isReplicatePeriodic(), set_OccMatrix(), and set_ReplicateOccurrence().

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

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set_OccMatrix()

void FileHandler::set_OccMatrix ( TMatrix *  occ )

inline

                                    {
    _multipleOccurences.reset(occ->nrows(), occ->ncols(), occ->getValArray());
    _generations.clear();
    for(unsigned int i = 0; i < _multipleOccurences.ncols(); i++)
      _generations.push_back((int)_multipleOccurences.get(0, i));
    _genITER = _generations.begin();
  }

References _generations, _genITER, _multipleOccurences, TMatrix::get(), TMatrix::getValArray(), TMatrix::ncols(), TMatrix::nrows(), and TMatrix::reset().

Referenced by set_multi().

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set_path()

void FileHandler::set_path

(

)

{
  string root_dir;
  
  root_dir = _service->getRootDir();
  
  if(_path.size() != 0 && _path[_path.length()-1] != '/')
        _path += "/";
  
  if(root_dir.size() != 0)
    _path = root_dir + _path;
  
  if(_path.size() != 0) {
    
    DIR *dir = opendir(_path.c_str());
    
    //check if we have to create the directory:
    if(_path.size() != 0 && dir == 0) {
      
#ifdef _WINDOWS_
      mode_t mode = S_IRUSR | S_IWUSR | S_IRGRP | S_IROTH;
      if((mkdir(_path.c_str(), mode)) == -1)
#else
        string cmd = "mkdir -p " + _path;
      if ( system( cmd.c_str() ) < 0 )
#endif
      {
        error("could not create directory \"%s\", saving in current directory.\n",_path.c_str());
        _path = "";
      }
    } else {
      if(closedir(dir) == -1)
        warning("FileHandler::set_path::closedir: %s\n",strerror(errno));
    }
  }
}

References _path, _service, error(), FileServices::getRootDir(), and warning().

Referenced by init().

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set_pop_ptr()

void FileHandler::set_pop_ptr ( Metapop *  pop_ptr )

inline

{ _pop = pop_ptr;}

References _pop.

Referenced by Metapop::loadPopFromTraitFile().

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set_ReplicateOccurrence()

void FileHandler::set_ReplicateOccurrence ( unsigned int  val )

inline

{_ReplicateOccurrence = val;}

References _ReplicateOccurrence.

Referenced by set(), and set_multi().

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set_service()

void FileHandler::set_service ( FileServices *  srv )

inline

{_service = srv;}

References _service.

Referenced by FileServices::attach(), and FileServices::attach_reader().

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update()

void FileHandler::update ( )

virtual

Updates the inner replicate and generation counters and calls FHwrite if needed by the the periodicity of the file.

Implements Handler.

{
  _current_replicate = _pop->getCurrentReplicate();
  
  _current_generation = _pop->getCurrentGeneration();
  
  // reset the generation iterator to the first in the list for new replicates
  if(_genITER == _generations.end() && _current_generation == 1)
    _genITER = _generations.begin();
  
  if ( ( (_isReplicatePeriodic && !(_current_replicate % _ReplicateOccurrence))
        || (_current_replicate == _ReplicateOccurrence) ) ) {
    if(_isGenerationPeriodic) {
      if(_GenerationOccurrence != 0) {
        if(!(_current_generation % _GenerationOccurrence) &&  _myenv->isMaster() == _isMasterExec) 
          FHwrite();
      } else if(_current_generation == (unsigned)(*_genITER)  &&  _myenv->isMaster() == _isMasterExec) {
        FHwrite();
        _genITER++;
      }
    } else if(_current_generation == _GenerationOccurrence &&  _myenv->isMaster() == _isMasterExec)
      FHwrite();
  }
}

References _current_generation, _current_replicate, _GenerationOccurrence, _generations, _genITER, _isGenerationPeriodic, _isMasterExec, _isReplicatePeriodic, _myenv, _pop, _ReplicateOccurrence, FHwrite(), Metapop::getCurrentGeneration(), Metapop::getCurrentReplicate(), and MPIenv::isMaster().

Member Data Documentation

_current_filename

std::string FileHandler::_current_filename

private

The current filename as set by FileHandler::get_filename().

Is composed by putting together the following strings: FileHandler::_path, FileServices::_basename (+ replicate and generation counters if needed), and FileHandler::_extension.

Referenced by get_filename().

_current_generation

unsigned int FileHandler::_current_generation

private

The current generation number of the simulation.

Set by FileHandler::update().

Referenced by update().

_current_replicate

unsigned int FileHandler::_current_replicate

private

The current replicate number of the simulation.

Set by FileHandler::update().

Referenced by update().

_ExecRank

unsigned int FileHandler::_ExecRank

private

unused... yet

Referenced by get_ExecRank(), and set_ExecRank().

_extension

std::string FileHandler::_extension

private

File extension, should be specific to the implementation.

Is set during construction.

Referenced by get_extension(), get_filename(), ifExist(), and set_extension().

_GenerationOccurrence

unsigned int FileHandler::_GenerationOccurrence

private

Tells every what generation the file should be written.

Set by the set() method below.

Referenced by get_GenerationOccurrence(), ifExist(), init(), set_GenerationOccurrence(), and update().

_generations

list< int > FileHandler::_generations

private

Referenced by set_OccMatrix(), and update().

_genITER

list<int>::const_iterator FileHandler::_genITER

private

Referenced by set_OccMatrix(), and update().

_isGenerationPeriodic

bool FileHandler::_isGenerationPeriodic

private

Flag setting the per generation periodicity behaviour of the file.

Referenced by get_filename(), get_isGenerationPeriodic(), ifExist(), set_isGenerationPeriodic(), and update().

_isInputHandler

bool FileHandler::_isInputHandler

private

Writing mode flag.

Must be true

Referenced by get_isInputHandler(), and set_isInputHandler().

_isMasterExec

bool FileHandler::_isMasterExec

private

Flag telling if the file must be written by the master or the worker node.

An example of master-only file is the stats files (.txt and _bygen.txt) that aggregate the stats from each node. Binary files or FSTAT files are written by the worker nodes, each file beeing written for one replicate only. The default behaviour is to be TRUE in the non-MPI version and FALSE in the MPI version.

Referenced by get_isMasterExec(), set_isMasterExec(), and update().

_isReplicatePeriodic

bool FileHandler::_isReplicatePeriodic

private

Flag telling if the file should be written each replicate.

Referenced by get_filename(), get_isReplicatePeriodic(), ifExist(), set_isReplicatePeriodic(), and update().

_multipleOccurences

TMatrix FileHandler::_multipleOccurences

private

Multiple occurences.

Referenced by get_OccMatrix(), and set_OccMatrix().

_path

std::string FileHandler::_path

private

File path as set during initialization.

Usually user-defined.

Referenced by get_filename(), get_path(), ifExist(), set(), set_multi(), and set_path().

_pop

Metapop* FileHandler::_pop

protected

Pointer to the current metapop, set during initialization within the init function.

Referenced by TTDeletMutBitstrFH::FHread(), TTQuantiFH::FHread(), LCE_SelectionFH::FHwrite(), MPFileHandler::FHwrite(), TTBDMI_FH::FHwrite(), TTDeletMutBitstrFH::FHwrite(), TTNeutralGenesFH::FHwrite(), TTQuantiFH::FHwrite(), get_pop_ptr(), BinaryDataSaver::ifExist(), ifExist(), init(), TTQuantiFH::print(), set_pop_ptr(), update(), TTNeutralGenesFH::write_FSTAT(), TTNeutralGenesFH::write_GENEPOP(), TTNeutralGenesFH::write_PLINK(), TTQuantiFH::write_PLINK(), TTNeutralGenesFH::write_PLINK_BED(), TTNeutralGenesFH::write_TAB(), and TTQuantiFH::write_TABLE().

_ReplicateOccurrence

unsigned int FileHandler::_ReplicateOccurrence

private

Tells every what replicate the file should be written.

Set by the set() method below.

Referenced by get_ReplicateOccurrence(), ifExist(), init(), set_ReplicateOccurrence(), and update().

_service

FileServices* FileHandler::_service

private

Link to the files manager.

Referenced by get_filename(), get_service(), ifExist(), init(), set_path(), and set_service().

---

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

• filehandler.h
• filehandler.cc