TTBDMI_FH Class Reference

FileHandler for the DBMI trait. More...

#include <ttbdmi.h>

Inheritance diagram for TTBDMI_FH:

Collaboration diagram for TTBDMI_FH:

Public Member Functions
	TTBDMI_FH (TProtoBDMI *TP)
virtual	~TTBDMI_FH ()
void	write_haplo (Patch *patch, sex_t SEX, age_idx AGE, ofstream &FH)
void	write_diplo (Patch *patch, sex_t SEX, age_idx AGE, ofstream &FH)
virtual void	FHwrite ()
virtual void	FHread (string &filename)
Public Member Functions inherited from TraitFileHandler< TProtoBDMI >
	TraitFileHandler (TProtoBDMI *trait_proto, const char *ext)
virtual	~TraitFileHandler ()
virtual void	FHread (string &filename)=0
virtual void	set (bool rpl_per, bool gen_per, int rpl_occ, int gen_occ, int rank, string path, TProtoBDMI *trait_proto)
virtual void	set_multi (bool rpl_per, bool gen_per, int rpl_occ, TMatrix *Occ, string path, TProtoBDMI *trait_proto)
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	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	~Handler ()

Additional Inherited Members
Protected Attributes inherited from TraitFileHandler< TProtoBDMI >
TProtoBDMI *	_FHLinkedTrait
int	_FHLinkedTraitIndex
Protected Attributes inherited from FileHandler
Metapop *	_pop
	Pointer to the current metapop, set during initialization within the init function. More...

Detailed Description

FileHandler for the DBMI trait.

Records the complete genotype in a text file.

Constructor & Destructor Documentation

TTBDMI_FH()

TTBDMI_FH::TTBDMI_FH ( TProtoBDMI *  TP )

inline

: TraitFileHandler< TProtoBDMI > (TP,".dmi") {}

~TTBDMI_FH()

virtual TTBDMI_FH::~TTBDMI_FH ( )

inlinevirtual

{ }

Member Function Documentation

FHread()

virtual void TTBDMI_FH::FHread ( string &  filename )

inlinevirtual

Implements FileHandler.

{}

FHwrite()

void TTBDMI_FH::FHwrite ( )

virtual

Implements TraitFileHandler< TProtoBDMI >.

{
  if(!_pop->isAlive()) return;
 
  // get sub sampled pop, if pop was sub sampled, otherwise points to main pop
  _pop = get_service()->getSampledPop();
 
  string filename = get_filename();
  
  ofstream FILE (filename.c_str(), ios::out);
  
  if(!FILE) fatal("could not open DMI output file\n");
  
  
  Patch* current_patch;
  int patchNbr = _pop->getPatchNbr();
  
  FILE<<"pop ";
  
  for(int i = 0; i < _FHLinkedTrait->get_num_locus(); i++)
    FILE<<"loc"<<i+1<<" ";
  
  FILE<<"W age sex home ped isMigrant father mother ID\n";
 
  for (int i = 0; i < patchNbr; ++i) {
    
    current_patch = _pop->getPatch(i);
 
    if(_FHLinkedTrait->isHaploid()) {
      write_haplo(current_patch, FEM, OFFSx, FILE);
      write_haplo(current_patch, MAL, OFFSx, FILE);
      write_haplo(current_patch, FEM, ADLTx, FILE);
      write_haplo(current_patch, MAL, ADLTx, FILE);
    } else {
      write_diplo(current_patch, FEM, OFFSx, FILE);
      write_diplo(current_patch, MAL, OFFSx, FILE);
      write_diplo(current_patch, FEM, ADLTx, FILE);
      write_diplo(current_patch, MAL, ADLTx, FILE);
    }
  }    
 
  // reset main ptr to main pop
  _pop = get_service()->get_pop_ptr();
}

References TraitFileHandler< TProtoBDMI >::_FHLinkedTrait, FileHandler::_pop, ADLTx, fatal(), FEM, FileHandler::get_filename(), TProtoBDMI::get_num_locus(), FileServices::get_pop_ptr(), FileHandler::get_service(), Metapop::getPatch(), Metapop::getPatchNbr(), FileServices::getSampledPop(), Metapop::isAlive(), TProtoBDMI::isHaploid(), MAL, OFFSx, write_diplo(), and write_haplo().

write_diplo()

void TTBDMI_FH::write_diplo	(	Patch *	patch,
		sex_t	SEX,
		age_idx	AGE,
		ofstream &	FH
	)

{
  const bitstring* seq;
  Individual *ind;
  TT_BDMI* trait;
  for (unsigned int j = 0, size = patch->size(SEX, AGE); j < size; ++j) {
    
    FH<<patch->getID()+1<<" ";
    ind = patch->get(SEX, AGE, j);
    trait = dynamic_cast<TT_BDMI*>(ind->getTrait(_FHLinkedTraitIndex));
    seq = trait->get_genome_sequence();
    
    for(int k = 0; k < _FHLinkedTrait->get_num_locus(); ++k)
      FH<<seq[0][k]<<seq[1][k]<<" ";
    
    FH <<*(double*)trait->getValue()<<" "<<AGE<<" "<<ind->getSex()<<" "<<ind->getHome()+1<<" "<<ind->getPedigreeClass()<<" "
        << (ind->getFather() && ind->getMother() ?
            (ind->getFather()->getHome()!= patch->getID() ) + (ind->getMother()->getHome()!= patch->getID() ) : 0)
            <<" "<<ind->getFatherID()<<" "<<ind->getMotherID()<<" "<<ind->getID()<<std::endl;
//
//    << (AGE == OFFSx ? OFFSPRG : ADULTS) << " " << SEX << " "
//       << ind->getPedigreeClass() << " " << ind->getHome()+1<<endl;
  }
  
}

References TraitFileHandler< TProtoBDMI >::_FHLinkedTrait, TraitFileHandler< TProtoBDMI >::_FHLinkedTraitIndex, Patch::get(), TT_BDMI::get_genome_sequence(), TProtoBDMI::get_num_locus(), Individual::getFather(), Individual::getFatherID(), Individual::getHome(), Individual::getID(), Patch::getID(), Individual::getMother(), Individual::getMotherID(), Individual::getPedigreeClass(), Individual::getSex(), Individual::getTrait(), TT_BDMI::getValue(), and Patch::size().

Referenced by FHwrite().

write_haplo()

void TTBDMI_FH::write_haplo	(	Patch *	patch,
		sex_t	SEX,
		age_idx	AGE,
		ofstream &	FH
	)

{
  const bitstring* seq;
  Individual *ind;
  TT_BDMI* trait;
 
 for (unsigned int j = 0, size = patch->size(SEX, AGE); j < size; ++j) {
    
    FH<<patch->getID()+1<<" ";
    ind = patch->get(SEX, AGE, j);
    trait = dynamic_cast<TT_BDMI*>(ind->getTrait(_FHLinkedTraitIndex));
    seq = trait->get_genome_sequence();
    
    for(int k = 0; k < _FHLinkedTrait->get_num_locus(); ++k)
      FH<<seq[0][k]<<" ";
    
    FH <<*(double*)trait->getValue()<<" "<<AGE<<" "<<ind->getSex()<<" "<<ind->getHome()+1<<" "<<ind->getPedigreeClass()<<" "
        << (ind->getFather() && ind->getMother() ?
            (ind->getFather()->getHome()!= patch->getID() ) + (ind->getMother()->getHome()!= patch->getID() ) : 0)
            <<" "<<ind->getFatherID()<<" "<<ind->getMotherID()<<" "<<ind->getID()<<std::endl;
 
//    << (AGE == OFFSx ? OFFSPRG : ADULTS) << " " << SEX << " "
//       << ind->getPedigreeClass() << " " << ind->getHome()+1<<endl;
  }
  
}

References TraitFileHandler< TProtoBDMI >::_FHLinkedTrait, TraitFileHandler< TProtoBDMI >::_FHLinkedTraitIndex, Patch::get(), TT_BDMI::get_genome_sequence(), TProtoBDMI::get_num_locus(), Individual::getFather(), Individual::getFatherID(), Individual::getHome(), Individual::getID(), Patch::getID(), Individual::getMother(), Individual::getMotherID(), Individual::getPedigreeClass(), Individual::getSex(), Individual::getTrait(), TT_BDMI::getValue(), and Patch::size().

Referenced by FHwrite().

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

• ttbdmi.h
• ttbdmi.cc