TTDeletMutBitstrFH Class Reference

The FileHandler associated with the TTDeletMutations_bitstring trait. More...

#include <ttdeletmutations_bitstring.h>

Inheritance diagram for TTDeletMutBitstrFH:

Collaboration diagram for TTDeletMutBitstrFH:

Public Member Functions
	TTDeletMutBitstrFH (TProtoDeletMutations_bitstring *TP)
virtual	~TTDeletMutBitstrFH ()
virtual void	FHwrite ()
virtual void	FHread (string &filename)
Public Member Functions inherited from TraitFileHandler< TProtoDeletMutations_bitstring >
	TraitFileHandler (TProtoDeletMutations_bitstring *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, TProtoDeletMutations_bitstring *trait_proto)
virtual void	set_multi (bool rpl_per, bool gen_per, int rpl_occ, TMatrix *Occ, string path, TProtoDeletMutations_bitstring *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< TProtoDeletMutations_bitstring >
TProtoDeletMutations_bitstring *	_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

The FileHandler associated with the TTDeletMutations_bitstring trait.

Used to save genotypes in a text file.

Constructor & Destructor Documentation

TTDeletMutBitstrFH()

TTDeletMutBitstrFH::TTDeletMutBitstrFH ( TProtoDeletMutations_bitstring *  TP )

inline

  : TraitFileHandler<TProtoDeletMutations_bitstring> (TP,".del") { }

~TTDeletMutBitstrFH()

virtual TTDeletMutBitstrFH::~TTDeletMutBitstrFH ( )

inlinevirtual

{ }

Member Function Documentation

FHread()

void TTDeletMutBitstrFH::FHread ( string &  filename )

virtual

Implements FileHandler.

{
  unsigned int nb_locus = _FHLinkedTrait->get_nb_locus();
  unsigned int patchNbr = _pop->getPatchNbr();
  TTDeletMutations_bitstring* trait;
  
  ifstream FILE(filename.c_str(),ios::in);
  
  if(!FILE) fatal("could not open DELET input file \"%s\"\n",filename.c_str());
  
  unsigned int genot, age, sex, ped, origin, xline = 0;
  unsigned long ID;
  int pop;
  age_idx agex;
  Individual *ind;
  unsigned char all0, all1;
  bitstring *seq[2];  
  seq[0] = new bitstring(nb_locus);
  seq[1] = new bitstring(nb_locus);
  
  double* effects[2];
  int lnbr = 3;
  
  effects[0] = new double [nb_locus];
  effects[1] = new double [nb_locus];
  
  string str;  // swallow header line, read pop + num locus + 5 info fields
  for (unsigned int i = 0; i < nb_locus + 6; ++i) {
    FILE>>str;
  }
 
  if(!FILE)
    fatal("reading delet genotypes from \"%s\" failed (expecting %i elements per line)\n",
        filename.c_str(), nb_locus + 6);
 
 
  // read until EOF
  xline = 0;
  while(FILE>>pop) {
 
    if(pop > (int)patchNbr)
      fatal("Patch number found in file exceeds number of patches in the population.\n");
    
    if(pop == -1) { // this is a special row used to store mutation effects
      // copy the mutation effects from the input file
      // effects are recorded on two lines max, first is for 's', the second for 'hs'
        
      assert(xline <= 1);
      
      for(unsigned int i = 0; i < nb_locus; ++i) {
        FILE>>effects[xline][i];
      }
      // read last five columns, unused (set to -1 in the file)
      for(unsigned int i = 0; i < 5; ++i)
        FILE>>str;
 
      if(!FILE)
        fatal("reading delet genotypes from \"%s\" failed (expecting %i elements per line)\n",
            filename.c_str(), nb_locus + 6);
 
      xline++;
    }
    else {
      
      for(unsigned int i = 0; i < nb_locus; ++i) {
        
        FILE>>genot;
        
        all0 = (unsigned char) genot/10;
        all1 = (unsigned char) genot%10;
        
        if(all0 <= 1) {
        
          if(all0) seq[0]->set(i);
        
        } else {
          error("in DELET input file at line %i, locus %i : \
                first allele value %d is greater than 1!\n", lnbr, i+1, all0);
          fatal("Please check the input file.\n");
        }
        
        if(all1 <= 1){
          
          if(all1) seq[1]->set(i);
        
        } else {
          error("in DELET input file at line %i, locus %i : \
                second allele value %i is greater than 1!\n", lnbr, i+1, all1);
          fatal("Please check the input file.\n");
        }
      }
      
      FILE >> age >> sex >> ped >> origin >> ID;
 
      if(!FILE)
        fatal("reading delet genotypes from \"%s\" failed (expecting %i elements per line)\n",
            filename.c_str(), nb_locus + 6);
 
      agex = (age == ADULTS ? ADLTx : OFFSx);
      
      ind = _pop->makeNewIndividual(0, 0, sex_t(sex), origin);
      ind->setPedigreeClass((unsigned char)ped);
      ind->setAge(age);
      ind->setHome(origin);
      trait = dynamic_cast<TTDeletMutations_bitstring*> (ind->getTrait(_FHLinkedTraitIndex));
      trait->set_sequence(seq);   //copy the sequence
      trait->set_value();         //sets the hetero- and homozygosity counters
 
      _pop->getPatch(pop-1)->add(sex_t(sex), agex, ind);
 
      seq[0]->reset();
      seq[1]->reset();
 
    }
 
    lnbr++;
    
  }
 
  FILE.close();
  
  // set the mutation effects from the input file, but only if they have been read:
  if(xline == 2) {
      TProtoDeletMutations_bitstring* proto = dynamic_cast<TProtoDeletMutations_bitstring*>( _FHLinkedTrait );
      
      for(unsigned int i = 0; i < nb_locus; ++i) {
          proto->set_effect(1, i, effects[0][i]);  // the order is swapt in the proto, hs first, then s
          proto->set_effect(0, i, effects[1][i]);
      }
  }
  delete seq[0];
  delete seq[1];
  delete [] effects[0];
  delete [] effects[1];
}

References TraitFileHandler< TProtoDeletMutations_bitstring >::_FHLinkedTrait, TraitFileHandler< TProtoDeletMutations_bitstring >::_FHLinkedTraitIndex, FileHandler::_pop, Patch::add(), ADLTx, ADULTS, error(), fatal(), TProtoDeletMutations_bitstring::get_nb_locus(), Metapop::getPatch(), Metapop::getPatchNbr(), Individual::getTrait(), IndFactory::makeNewIndividual(), OFFSx, bitstring::reset(), bitstring::set(), TProtoDeletMutations_bitstring::set_effect(), TTDeletMutations_bitstring::set_sequence(), TTDeletMutations_bitstring::set_value(), Individual::setAge(), Individual::setHome(), and Individual::setPedigreeClass().

FHwrite()

void TTDeletMutBitstrFH::FHwrite ( )

virtual

Implements TraitFileHandler< TProtoDeletMutations_bitstring >.

{
  if(!get_pop_ptr()->isAlive()) return;
  
  // sets the pop ptr to a sub sampled pop, if sub sampling happened
  _pop = get_service()->getSampledPop();
 
  int nb_locus = this->_FHLinkedTrait->get_nb_locus();
  int patchNbr = _pop->getPatchNbr();
  sex_t SEX;
  bitstring** seq;
  Patch* current_patch;
  Individual *ind;
  
  std::string filename = get_path() + this->get_service()->getGenerationReplicateFileName() + get_extension();
  
#ifdef _DEBUG_
  message("TTNeutralGenesFH::FHwrite (%s)\n",filename.c_str());
#endif
  
  ofstream FILE (filename.c_str(), ios::out);
  
  if(!FILE) fatal("could not open DELET output file!!\n");
  
  //FILE<<patchNbr<<" "<<nb_locus<<" "<<2<<" "<<1<<"\n";
  
  FILE<<"pop ";
  
  for(int i = 0; i < nb_locus; i++)
    FILE<<"loc"<<i+1<<" ";
  
  FILE<<"age sex home ped isMigrant father mother ID\n";
 
  if(_FHLinkedTrait->get_iscontinuous()){
 
    float *s = _FHLinkedTrait->get_s_continous();
 
    float *hs = _FHLinkedTrait->get_hs_continous();
 
    FILE<<"-1 ";                  //'pop'
 
    for(int i = 0; i < nb_locus; i++)
      FILE<< s[i] << " " ;
 
    FILE<<"-1 -1 -1 -1 -1 -1 -1 -1"<< endl; //age sex home ped isMigrant father mother ID
 
    FILE<<"-1 ";
 
    for(int i = 0; i < nb_locus; i++)
      FILE<< hs[i] << " " ;
 
    FILE<<"-1 -1 -1 -1 -1 -1 -1 -1"<< endl;
  }    
 
  for (int i = 0; i < patchNbr; ++i) {
 
    current_patch = _pop->getPatch(i);
 
    for(int s = 1; s >= 0; s-- ) { // always start with females
 
      SEX = sex_t(s);
 
      for (unsigned int j = 0, size = current_patch->size(SEX, OFFSx); j < size; ++j) {
 
 
        FILE<<i+1<<" ";
        ind = current_patch->get(SEX, OFFSx, j);
        seq = (bitstring**)ind->getTrait(_FHLinkedTraitIndex)->get_sequence();
 
        for(int k = 0; k < nb_locus; ++k)
          FILE<<(int)((*seq[0])[k])<<(int)((*seq[1])[k])<<" ";
 
        FILE << OFFSx<<" "<<ind->getSex()<<" "<<ind->getHome()+1<<" "<<ind->getPedigreeClass()<<" "
            << (ind->getFather() && ind->getMother() ?
                (ind->getFather()->getHome()!= current_patch->getID() ) + (ind->getMother()->getHome()!= current_patch->getID() ) : 0)
                <<" "<<ind->getFatherID()<<" "<<ind->getMotherID()<<" "<<ind->getID()<<std::endl;
      }
    }
 
 
    for(int s = 1; s >= 0; s-- ) {
 
      SEX = sex_t(s);
 
      for (unsigned int j = 0, size = current_patch->size(SEX, ADLTx); j < size; ++j) {
 
 
        FILE<<i+1<<" ";
        ind = current_patch->get(SEX, ADLTx, j);
        seq = (bitstring**)ind->getTrait(_FHLinkedTraitIndex)->get_sequence();
 
        for(int k = 0; k < nb_locus; ++k)
          FILE<<(int)((*seq[0])[k])<<(int)((*seq[1])[k])<<" ";
 
        FILE << ADLTx <<" "<<ind->getSex()<<" "<<ind->getHome()+1<<" "<<ind->getPedigreeClass()<<" "
            << (ind->getFather() && ind->getMother() ?
                (ind->getFather()->getHome()!= current_patch->getID() ) + (ind->getMother()->getHome()!= current_patch->getID() ) : 0)
                <<" "<<ind->getFatherID()<<" "<<ind->getMotherID()<<" "<<ind->getID()<<std::endl;
      }
    }
 
  }
  
  FILE.close();
  
  // reset to pop ptr to main pop:
  _pop = get_service()->get_pop_ptr();
}

References TraitFileHandler< TProtoDeletMutations_bitstring >::_FHLinkedTrait, TraitFileHandler< TProtoDeletMutations_bitstring >::_FHLinkedTraitIndex, FileHandler::_pop, ADLTx, fatal(), Patch::get(), FileHandler::get_extension(), TProtoDeletMutations_bitstring::get_hs_continous(), TProtoDeletMutations_bitstring::get_iscontinuous(), TProtoDeletMutations_bitstring::get_nb_locus(), FileHandler::get_path(), FileHandler::get_pop_ptr(), FileServices::get_pop_ptr(), TProtoDeletMutations_bitstring::get_s_continous(), TTrait::get_sequence(), FileHandler::get_service(), Individual::getFather(), Individual::getFatherID(), FileServices::getGenerationReplicateFileName(), Individual::getHome(), Individual::getID(), Patch::getID(), Individual::getMother(), Individual::getMotherID(), Metapop::getPatch(), Metapop::getPatchNbr(), Individual::getPedigreeClass(), FileServices::getSampledPop(), Individual::getSex(), Individual::getTrait(), message(), OFFSx, and Patch::size().

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

• ttdeletmutations_bitstring.h
• ttdeletmutations_bitstring.cc