FileHandler Class Reference

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

#include <filehandler.h>

Inheritance diagram for FileHandler:

[legend]

Collaboration diagram for FileHandler:

[legend]

List of all members.

Public Member Functions
	FileHandler (const char *ext)
virtual	~FileHandler ()
virtual void	init ()
	Called by notifier during simulation setup, performs file checking.
virtual bool	ifExist ()
	Checks if any file associated with the current file name already exists on disk.
virtual void	set (bool rpl_per, bool gen_per, int rpl_occ, int gen_occ, int rank, string path)
	Sets the hanlder parameters.
virtual void	FHwrite ()=0
	Default behavior of the class, called by Handler::update().
virtual void	FHread (string &filename)=0
	Default input function.
virtual void	update ()
	Updates the inner replicate and generation counters and calls FHwrite if needed by the the periodicity of the file.
Accessors
Metapop *	get_pop_ptr ()
	Returns the pointer to the current metapop through the FileServices interface.
void	set_pop_ptr (Metapop *pop_ptr)
FileServices *	get_service ()
	Returns pointer to the FileServices.
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.
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.
void	set_ExecRank (int val)
bool	get_isMasterExec ()
void	set_isMasterExec (bool is)
Protected Attributes
Metapop *	_pop
	Pointer to the current metapop, set during initialization within the init function.
Private Attributes
FileServices *	_service
	Link to the files manager.
bool	_isMasterExec
	Flag telling if the file must be written by the master or the slave node.
bool	_isInputHandler
	Writing mode flag.
bool	_isReplicatePeriodic
	Flag telling if the file should be written each replicate.
bool	_isGenerationPeriodic
	Flag setting the per generation periodicity behaviour of the file.
unsigned int	_ReplicateOccurrence
	Tells every what replicate the file should be written.
unsigned int	_GenerationOccurrence
	Tells every what generation the file should be written.
unsigned int	_current_replicate
	The current replicate number of the simulation.
unsigned int	_current_generation
	The current generation number of the simulation.
unsigned int	_ExecRank
	unused.
std::string	_path
	File path as set during initialization.
std::string	_extension
	File extension, should be specific to the implementation.
std::string	_current_filename
	The current filename as set by FileHandler::get_filename().

---

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...).

Definition at line 52 of file filehandler.h.

---

Constructor & Destructor Documentation

FileHandler::FileHandler

(

const char *

ext

)

[inline]

Definition at line 99 of file filehandler.h.

    : _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)
    {}

virtual FileHandler::~FileHandler

(

)

[inline, virtual]

Definition at line 113 of file filehandler.h.

{ }

---

Member Function Documentation

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, TraitFileHandler< TP >, EventFileHandler< LCE >, FHLogWriter, LCE_StatFH, TTDeletMutBitstrFH, TTNeutralGenesFH, TraitFileHandler< TProtoNeutralGenes >, and TraitFileHandler< TProtoDeletMutations_bitstring >.

Referenced by Metapop::loadPopFromTraitFile().

virtual void FileHandler::FHwrite

(

)

[pure virtual]

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

Implemented in BinaryDataSaver, TraitFileHandler< TP >, EventFileHandler< LCE >, FHLogWriter, LCE_StatFH, TTDeletMutBitstrFH, TTNeutralGenesFH, TraitFileHandler< TProtoNeutralGenes >, and TraitFileHandler< TProtoDeletMutations_bitstring >.

Referenced by update().

unsigned int FileHandler::get_ExecRank

(

)

[inline]

unused yet.

..

Definition at line 157 of file filehandler.h.

{return _ExecRank;}

std::string& FileHandler::get_extension

(

)

[inline]

Definition at line 135 of file filehandler.h.

Referenced by TTDeletMutBitstrFH::FHwrite(), LCE_StatFH::FHwrite(), TTNeutralGenesFH::write_freq(), TTNeutralGenesFH::write_Fst_i(), TTNeutralGenesFH::write_FSTAT(), and TTNeutralGenesFH::write_varcompWC().

{return _extension;}

string & FileHandler::get_filename

(

)

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

Definition at line 138 of file filehandler.cc.

Referenced by BinaryDataSaver::finish(), BinaryDataSaver::printData(), BinaryDataSaver::printHeader(), and FHLogWriter::save_simparams().

{
  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;
}

unsigned int FileHandler::get_GenerationOccurrence

(

)

[inline]

Definition at line 154 of file filehandler.h.

{return _GenerationOccurrence;}

bool FileHandler::get_isGenerationPeriodic

(

)

[inline]

Definition at line 151 of file filehandler.h.

{return _isGenerationPeriodic;}

bool FileHandler::get_isInputHandler

(

)

[inline]

Definition at line 142 of file filehandler.h.

Referenced by FileServices::attach().

{return _isInputHandler;}

bool FileHandler::get_isMasterExec

(

)

[inline]

Definition at line 160 of file filehandler.h.

{return _isMasterExec;}

bool FileHandler::get_isReplicatePeriodic

(

)

[inline]

Definition at line 145 of file filehandler.h.

{return _isReplicatePeriodic;}

std::string& FileHandler::get_path

(

)

[inline]

Definition at line 131 of file filehandler.h.

Referenced by TTDeletMutBitstrFH::FHwrite(), LCE_StatFH::FHwrite(), BinaryDataSaver::finish(), LCE_StatFH::ifExist(), LCE_StatFH::PrintStat_byGen(), TTNeutralGenesFH::write_freq(), TTNeutralGenesFH::write_Fst_i(), TTNeutralGenesFH::write_FSTAT(), and TTNeutralGenesFH::write_varcompWC().

{return _path;}

Metapop* FileHandler::get_pop_ptr

(

)

[inline]

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

Definition at line 123 of file filehandler.h.

Referenced by TTDeletMutBitstrFH::FHwrite().

{return _pop;}

unsigned int FileHandler::get_ReplicateOccurrence

(

)

[inline]

Definition at line 148 of file filehandler.h.

{return _ReplicateOccurrence;}

FileServices* FileHandler::get_service

(

)

[inline]

Returns pointer to the FileServices.

Definition at line 127 of file filehandler.h.

Referenced by TTDeletMutBitstrFH::FHwrite(), LCE_StatFH::FHwrite(), BinaryDataSaver::finish(), LCE_StatFH::ifExist(), BinaryDataSaver::printHeader(), LCE_StatFH::PrintStat_byGen(), TTNeutralGenesFH::write_freq(), TTNeutralGenesFH::write_Fst_i(), TTNeutralGenesFH::write_FSTAT(), and TTNeutralGenesFH::write_varcompWC().

{return _service;}

bool 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.

Definition at line 69 of file filehandler.cc.

{
  //check if the basefilename is already used on disk:
  string filename = _path + _service->getBaseFileName();

  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();
    return false;
  }
  ifXist.close();

  return true;
}

void FileHandler::init

(

)

[virtual]

Called by notifier during simulation setup, performs file checking.

Implements Handler.

Definition at line 51 of file filehandler.cc.

{
  _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();

  if ( _myenv->isMaster() != _isMasterExec ) return;
  //@todo check FileHandler::init with MPI, set_path() has moved from set() to init()!
  set_path();
//  message("     %s*%s\n",get_path().c_str(),get_extension().c_str());
}

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

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

Definition at line 175 of file filehandler.h.

Referenced by FileServices::init(), LCE_StatFH::LCE_StatFH(), LCE_StatServiceNotifier::setParameters(), and BinaryDataSaver::setParameters().

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

void FileHandler::set_ExecRank

(

int

val

)

[inline]

Definition at line 158 of file filehandler.h.

{_ExecRank = val;}

void FileHandler::set_extension

(

const char *

ext

)

[inline]

Definition at line 137 of file filehandler.h.

Referenced by TProtoNeutralGenes::loadFileServices().

{_extension = ext;}

void FileHandler::set_GenerationOccurrence

(

unsigned int

val

)

[inline]

Definition at line 155 of file filehandler.h.

{_GenerationOccurrence = val;}

void FileHandler::set_isGenerationPeriodic

(

bool

val

)

[inline]

Definition at line 152 of file filehandler.h.

{_isGenerationPeriodic = val;}

void FileHandler::set_isInputHandler

(

bool

val

)

[inline]

Definition at line 143 of file filehandler.h.

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

{_isInputHandler = val;}

void FileHandler::set_isMasterExec

(

bool

is

)

[inline]

Definition at line 164 of file filehandler.h.

Referenced by LCE_StatFH::LCE_StatFH().

{_isMasterExec = true;}

void FileHandler::set_isReplicatePeriodic

(

bool

val

)

[inline]

Definition at line 146 of file filehandler.h.

{_isReplicatePeriodic = val;}

void FileHandler::set_path

(

)

Definition at line 108 of file filehandler.cc.

Referenced by init().

{
  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;
  
  //check if we have to create the directory:
  if(_path.size() != 0 && opendir(_path.c_str()) == 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 wd.\n",_path.c_str());
      _path = "";
    }
  }
}

void FileHandler::set_pop_ptr

(

Metapop *

pop_ptr

)

[inline]

Definition at line 125 of file filehandler.h.

Referenced by Metapop::loadPopFromTraitFile().

{ _pop = pop_ptr;}

void FileHandler::set_ReplicateOccurrence

(

unsigned int

val

)

[inline]

Definition at line 149 of file filehandler.h.

{_ReplicateOccurrence = val;}

void FileHandler::set_service

(

FileServices *

srv

)

[inline]

Definition at line 129 of file filehandler.h.

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

{_service = srv;}

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.

Definition at line 153 of file filehandler.cc.

{
    _current_replicate = _pop->getCurrentReplicate();

    _current_generation = _pop->getCurrentGeneration();

    if ( ( (_isReplicatePeriodic && !(_current_replicate % _ReplicateOccurrence))
           || (_current_replicate == _ReplicateOccurrence) ) 
         && 
         ( (_isGenerationPeriodic && !(_current_generation % _GenerationOccurrence)) 
           || (_current_generation == _GenerationOccurrence) ) )
      if( _myenv->isMaster() == _isMasterExec)
        FHwrite();
}

---

Member Data Documentation

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.

Definition at line 91 of file filehandler.h.

Referenced by get_filename().

unsigned int FileHandler::_current_generation [private]

The current generation number of the simulation.

Set by FileHandler::update().

Definition at line 78 of file filehandler.h.

Referenced by update().

unsigned int FileHandler::_current_replicate [private]

The current replicate number of the simulation.

Set by FileHandler::update().

Definition at line 76 of file filehandler.h.

Referenced by update().

unsigned int FileHandler::_ExecRank [private]

unused.

.. yet

Definition at line 80 of file filehandler.h.

Referenced by get_ExecRank(), and set_ExecRank().

std::string FileHandler::_extension [private]

File extension, should be specific to the implementation.

Is set during construction.

Definition at line 85 of file filehandler.h.

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

unsigned int FileHandler::_GenerationOccurrence [private]

Tells every what generation the file should be written.

Set by the set() method below.

Definition at line 74 of file filehandler.h.

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

bool FileHandler::_isGenerationPeriodic [private]

Flag setting the per generation periodicity behaviour of the file.

Definition at line 70 of file filehandler.h.

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

bool FileHandler::_isInputHandler [private]

Writing mode flag.

Must be true

Definition at line 66 of file filehandler.h.

Referenced by get_isInputHandler(), and set_isInputHandler().

bool FileHandler::_isMasterExec [private]

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

Definition at line 64 of file filehandler.h.

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

bool FileHandler::_isReplicatePeriodic [private]

Flag telling if the file should be written each replicate.

Definition at line 68 of file filehandler.h.

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

std::string FileHandler::_path [private]

File path as set during initialization.

Usually user-defined.

Definition at line 82 of file filehandler.h.

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

Metapop* FileHandler::_pop [protected]

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

Definition at line 95 of file filehandler.h.

Referenced by TTNeutralGenesFH::FHread(), TTDeletMutBitstrFH::FHread(), get_pop_ptr(), ifExist(), init(), set_pop_ptr(), update(), TTNeutralGenesFH::write_freq(), TTNeutralGenesFH::write_Fst_i(), TTNeutralGenesFH::write_FSTAT(), and TTNeutralGenesFH::write_varcompWC().

unsigned int FileHandler::_ReplicateOccurrence [private]

Tells every what replicate the file should be written.

Set by the set() method below.

Definition at line 72 of file filehandler.h.

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

FileServices* FileHandler::_service [private]

Link to the files manager.

Definition at line 56 of file filehandler.h.

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