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	~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... 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

121 { }

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 EventFileHandler< LCE >, TraitFileHandler< TP >, TTWolbachiaFH, TTQOhtaStats, TTQFreqExtractor, TTQuantiFH, TTNOhtaStats, TTNeutralGenesFH, TTDeletMutBitstrFH, TTBDMI_FH, LCE_StatFH, GenotyperFH, MPFileHandler, LCE_SelectionFH, FHPedigreeReader, FHLogWriter, and BinaryDataSaver.

Referenced by Metapop::loadPopFromTraitFile().

◆ FHwrite()

virtual void FileHandler::FHwrite ( )

pure virtual

◆ get_ExecRank()

unsigned int FileHandler::get_ExecRank ( )

inline

unused yet...

165 {return _ExecRank;}

References _ExecRank.

◆ get_extension()

std::string& FileHandler::get_extension ( )

inline

143 {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().

◆ 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;
 }

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

◆ get_GenerationOccurrence()

unsigned int FileHandler::get_GenerationOccurrence ( )

inline

162 {return _GenerationOccurrence;}

References _GenerationOccurrence.

Referenced by BinaryDataSaver::ifExist().

◆ get_isGenerationPeriodic()

bool FileHandler::get_isGenerationPeriodic ( )

inline

159 {return _isGenerationPeriodic;}

References _isGenerationPeriodic.

◆ get_isInputHandler()

bool FileHandler::get_isInputHandler ( )

inline

150 {return _isInputHandler;}

References _isInputHandler.

Referenced by FileServices::attach().

◆ get_isMasterExec()

bool FileHandler::get_isMasterExec ( )

inline

178 {return _isMasterExec;}

References _isMasterExec.

◆ get_isReplicatePeriodic()

bool FileHandler::get_isReplicatePeriodic ( )

inline

153 {return _isReplicatePeriodic;}

References _isReplicatePeriodic.

◆ get_OccMatrix()

TMatrix* FileHandler::get_OccMatrix ( )

inline

168 {return &_multipleOccurences;}

FileHandler::_multipleOccurences

TMatrix _multipleOccurences

Multiple occurences.

Definition: filehandler.h:82

References _multipleOccurences.

◆ get_path()

std::string& FileHandler::get_path ( )

inline

139 {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().

◆ get_pop_ptr()

Metapop* FileHandler::get_pop_ptr ( )

inline

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

131 {return _pop;}

References _pop.

Referenced by TTDeletMutBitstrFH::FHwrite(), TTNOhtaStats::FHwrite(), and TTQOhtaStats::FHwrite().

◆ get_ReplicateOccurrence()

unsigned int FileHandler::get_ReplicateOccurrence ( )

inline

156 {return _ReplicateOccurrence;}

References _ReplicateOccurrence.

Referenced by BinaryDataSaver::ifExist().

◆ get_service()

FileServices* FileHandler::get_service ( )

inline

◆ 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 LCE_StatFH, and BinaryDataSaver.

 {
   //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;
 }

◆ 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());
 }

◆ 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().

◆ set_ExecRank()

void FileHandler::set_ExecRank ( int val )

inline

166 {_ExecRank = val;}

References _ExecRank.

Referenced by set().

◆ set_extension()

void FileHandler::set_extension ( const char * ext )

inline

145 {_extension = ext;}

References _extension.

Referenced by TProtoNeutralGenes::loadFileServices().

◆ set_GenerationOccurrence()

void FileHandler::set_GenerationOccurrence ( unsigned int val )

inline

163 {_GenerationOccurrence = val;}

References _GenerationOccurrence.

Referenced by set(), and set_multi().

◆ set_isGenerationPeriodic()

void FileHandler::set_isGenerationPeriodic ( bool val )

inline

160 {_isGenerationPeriodic = val;}

References _isGenerationPeriodic.

Referenced by set(), and set_multi().

◆ set_isInputHandler()

void FileHandler::set_isInputHandler ( bool val )

inline

151 {_isInputHandler = val;}

References _isInputHandler.

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

◆ set_isMasterExec()

void FileHandler::set_isMasterExec ( bool is )

inline

182 {_isMasterExec = true;}

References _isMasterExec.

Referenced by LCE_StatFH::LCE_StatFH().

◆ set_isReplicatePeriodic()

void FileHandler::set_isReplicatePeriodic ( bool val )

inline

154 {_isReplicatePeriodic = val;}

References _isReplicatePeriodic.

Referenced by set(), and set_multi().

◆ 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(), and TraitFileHandler< TP >::set_multi().

◆ 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().

◆ 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 error(), and warning().

◆ set_pop_ptr()

void FileHandler::set_pop_ptr ( Metapop * pop_ptr )

inline

133 { _pop = pop_ptr;}

References _pop.

Referenced by Metapop::loadPopFromTraitFile().

◆ set_ReplicateOccurrence()

void FileHandler::set_ReplicateOccurrence ( unsigned int val )

inline

157 {_ReplicateOccurrence = val;}

References _ReplicateOccurrence.

Referenced by set(), and set_multi().

◆ set_service()

void FileHandler::set_service ( FileServices * srv )

inline

137 {_service = srv;}

References _service.

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

◆ 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 _myenv, 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.

◆ _current_generation

unsigned int FileHandler::_current_generation

private

The current generation number of the simulation.

Set by FileHandler::update().

◆ _current_replicate

unsigned int FileHandler::_current_replicate

private

The current replicate number of the simulation.

Set by FileHandler::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(), 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(), and set_GenerationOccurrence().

◆ _generations

list< int > FileHandler::_generations

private

Referenced by set_OccMatrix().

◆ _genITER

list< int >::const_iterator FileHandler::_genITER

private

Referenced by set_OccMatrix().

◆ _isGenerationPeriodic

bool FileHandler::_isGenerationPeriodic

private

Flag setting the per generation periodicity behaviour of the file.

Referenced by get_isGenerationPeriodic(), and set_isGenerationPeriodic().

◆ _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(), and set_isMasterExec().

◆ _isReplicatePeriodic

bool FileHandler::_isReplicatePeriodic

private

Flag telling if the file should be written each replicate.

Referenced by get_isReplicatePeriodic(), and set_isReplicatePeriodic().

◆ _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_path(), set(), and set_multi().

◆ _pop

Metapop* FileHandler::_pop

protected

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

Referenced by TTDeletMutBitstrFH::FHread(), TTNeutralGenesFH::FHread(), TTQuantiFH::FHread(), LCE_SelectionFH::FHwrite(), MPFileHandler::FHwrite(), TTBDMI_FH::FHwrite(), TTDeletMutBitstrFH::FHwrite(), TTNeutralGenesFH::FHwrite(), TTQuantiFH::FHwrite(), get_pop_ptr(), BinaryDataSaver::ifExist(), set_pop_ptr(), TTNeutralGenesFH::write_FSTAT(), TTNeutralGenesFH::write_GENEPOP(), TTNeutralGenesFH::write_PLINK(), TTQuantiFH::write_PLINK(), 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(), and set_ReplicateOccurrence().

◆ _service

FileServices* FileHandler::_service

private

Link to the files manager.

Referenced by get_service(), and set_service().

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

Public Member Functions

Protected Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ FileHandler()

◆ ~FileHandler()

Member Function Documentation

◆ FHread()

◆ FHwrite()

◆ get_ExecRank()

◆ get_extension()

◆ get_filename()

◆ get_GenerationOccurrence()

◆ get_isGenerationPeriodic()

◆ get_isInputHandler()

◆ get_isMasterExec()

◆ get_isReplicatePeriodic()

◆ get_OccMatrix()

◆ get_path()

◆ get_pop_ptr()

◆ get_ReplicateOccurrence()

◆ get_service()

◆ ifExist()

◆ init()

◆ set()

◆ set_ExecRank()

◆ set_extension()

◆ set_GenerationOccurrence()

◆ set_isGenerationPeriodic()

◆ set_isInputHandler()

◆ set_isMasterExec()

◆ set_isReplicatePeriodic()

◆ set_multi()

◆ set_OccMatrix()

◆ set_path()

◆ set_pop_ptr()

◆ set_ReplicateOccurrence()

◆ set_service()

◆ update()

Member Data Documentation

◆ _current_filename

◆ _current_generation

◆ _current_replicate

◆ _ExecRank

◆ _extension

◆ _GenerationOccurrence

◆ _generations

◆ _genITER

◆ _isGenerationPeriodic

◆ _isInputHandler

◆ _isMasterExec

◆ _isReplicatePeriodic

◆ _multipleOccurences

◆ _path

◆ _pop

◆ _ReplicateOccurrence

◆ _service