MPFileHandler Class Reference

#include <metapop.h>

Inheritance diagram for MPFileHandler:

Collaboration diagram for MPFileHandler:

Public Member Functions
	MPFileHandler ()
virtual	~MPFileHandler ()
void	setOption (int size)
virtual void	FHwrite ()
virtual void	FHread (string &filename)
void	createAndPrintSample (age_idx AGE, Patch *patch, ofstream &FH)
void	printNoSample (sex_t SEX, age_idx AGE, Patch *patch, ofstream &FH)
Public Member Functions inherited from FileHandler
	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...
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 ()

Private Attributes
int	_patch_sample_size

Additional Inherited Members
Protected Attributes inherited from FileHandler
Metapop *	_pop
	Pointer to the current metapop, set during initialization within the init function. More...

Constructor & Destructor Documentation

MPFileHandler()

MPFileHandler::MPFileHandler ( )

inline

: FileHandler(".ped"), _patch_sample_size(0) {}

~MPFileHandler()

virtual MPFileHandler::~MPFileHandler ( )

inlinevirtual

{}

Member Function Documentation

createAndPrintSample()

void MPFileHandler::createAndPrintSample	(	age_idx	AGE,
		Patch *	patch,
		ofstream &	FH
	)

{
        Individual* ind;
        unsigned int size_fem = patch->size(FEM, AGE);
        unsigned int size_mal = patch->size(MAL, AGE);
        unsigned int sample_size;
 
        int* sample = NULL;
 
        //Females -----------------------------------------------------------------------------
        sample_size = (_patch_sample_size < (int)size_fem ? _patch_sample_size : size_fem);
 
        if( sample_size != 0) {
 
                sample = new int[sample_size];
 
                RAND::Sample(0, size_fem, sample_size, sample, false);
 
                for(unsigned int j = 0; j < sample_size; ++j) {
 
                        ind = patch->get(FEM, AGE, sample[j]);
 
                        FH<< ind->getID() << " " << ind->getFatherID() << " " << ind->getMotherID()
                                << " " << FEM << " " << AGE << " " << ind->getHome()+1
                                << " " << patch->getID()+1 << endl;
                }
        }
 
        //Males -------------------------------------------------------------------------------
        sample_size = (_patch_sample_size < (int)size_mal ? _patch_sample_size : size_mal);
 
        if( sample_size != 0) {
 
                if(sample) delete [] sample;
 
                sample = new int[sample_size];
 
                RAND::Sample(0, size_mal, sample_size, sample, false);
 
                for(unsigned int j = 0; j < sample_size; ++j) {
 
                        ind = patch->get(MAL, AGE, sample[j]);
 
                        FH<< ind->getID() << " " << ind->getFatherID() << " " << ind->getMotherID()
                                << " " << MAL << " " << AGE << " " << ind->getHome()+1
                                << " " << patch->getID()+1 << endl;
                }
        }
 
        if(sample) delete [] sample;
}

References _patch_sample_size, FEM, Patch::get(), Individual::getFatherID(), Individual::getHome(), Individual::getID(), Patch::getID(), Individual::getMotherID(), MAL, RAND::Sample(), and Patch::size().

Referenced by FHwrite().

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FHread()

virtual void MPFileHandler::FHread ( string &  filename )

inlinevirtual

Implements FileHandler.

{}

FHwrite()

void MPFileHandler::FHwrite ( )

virtual

Implements FileHandler.

{
        if (!_pop->isAlive()) return; //don't write anything if pop is extinct
 
 
        std::string filename = get_filename();
 
        std::ofstream FILE (filename.c_str(), ios::out);
 
        if(!FILE) fatal("could not open \"%s\" output file!!\n",filename.c_str());
 
        FILE << "ID dad mum sex age home pop\n";
 
        Patch* patch;
 
        if(_patch_sample_size == 0) {
 
                for(unsigned int i = 0; i < _pop->getPatchNbr(); ++i) {
 
                        patch = _pop->getPatch(i);
 
                        for(unsigned int S = 0; S < 2; ++S){
 
                                printNoSample((sex_t)S, OFFSx, patch, FILE);
 
                                printNoSample((sex_t)S, ADLTx, patch, FILE);
 
                        }
                }
 
        } else {
 
                for(unsigned int i = 0; i < _pop->getPatchNbr(); ++i) {
 
                        patch = _pop->getPatch(i);
 
                        createAndPrintSample(OFFSx, patch, FILE);
 
                        createAndPrintSample(ADLTx, patch, FILE);
                }
        }
 
        FILE.close();
 
}

References _patch_sample_size, FileHandler::_pop, ADLTx, createAndPrintSample(), fatal(), FileHandler::get_filename(), Metapop::getPatch(), Metapop::getPatchNbr(), Metapop::isAlive(), OFFSx, and printNoSample().

printNoSample()

void MPFileHandler::printNoSample	(	sex_t	SEX,
		age_idx	AGE,
		Patch *	patch,
		ofstream &	FH
	)

{
        Individual* ind;
        for(unsigned int j = 0; j < patch->size(SEX, AGE); ++j) {
 
                ind = patch->get(SEX, AGE, j);
 
                FH<< ind->getID() << " " << ind->getFatherID() << " " << ind->getMotherID()
                        << " " << SEX << " " << AGE << " " << ind->getHome()+1
                        << " " << patch->getID()+1 << endl;
        }
}

References Patch::get(), Individual::getFatherID(), Individual::getHome(), Individual::getID(), Patch::getID(), Individual::getMotherID(), and Patch::size().

Referenced by FHwrite().

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setOption()

void MPFileHandler::setOption ( int  size )

inline

{_patch_sample_size = size;}

References _patch_sample_size.

Referenced by Metapop::loadFileServices().

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Member Data Documentation

_patch_sample_size

int MPFileHandler::_patch_sample_size

private

Referenced by createAndPrintSample(), FHwrite(), and setOption().

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

• metapop.h
• metapop.cc