TTQFreqExtractor Class Reference

TTQFreqExtractor. More...

#include <ttquanti.h>

Inheritance diagram for TTQFreqExtractor:

Collaboration diagram for TTQFreqExtractor:

Public Member Functions
	TTQFreqExtractor (TProtoQuanti *T)
void	resetTable ()
virtual	~TTQFreqExtractor ()
virtual void	FHwrite ()
virtual void	FHread (string &filename)
Public Member Functions inherited from TraitFileHandler< TProtoQuanti >
	TraitFileHandler (TProtoQuanti *trait_proto, const char *ext)
virtual	~TraitFileHandler ()
virtual void	FHwrite ()=0
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, TProtoQuanti *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	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
vector< string >	_records

Additional Inherited Members
Protected Attributes inherited from TraitFileHandler< TProtoQuanti >
TProtoQuanti *	_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

TTQFreqExtractor.

Constructor & Destructor Documentation

TTQFreqExtractor()

TTQFreqExtractor::TTQFreqExtractor ( TProtoQuanti *  T )

inline

: TraitFileHandler<TProtoQuanti>(T,".qfreq") {}

~TTQFreqExtractor()

virtual TTQFreqExtractor::~TTQFreqExtractor ( )

inlinevirtual

{}

Member Function Documentation

FHread()

virtual void TTQFreqExtractor::FHread ( string &  filename )

inlinevirtual

Implements FileHandler.

{}

FHwrite()

void TTQFreqExtractor::FHwrite ( )

virtual

Implements TraitFileHandler< TProtoQuanti >.

{
  // make sure we don't use a sub-sampled pop
  Metapop* pop = get_service()->get_pop_ptr();
  int patchNbr = pop->getPatchNbr();
  Patch* current_patch;
  Individual* ind;
  //  TTQuanti* trait;
  //  double* Tval;
  double **genes;
  int total_size = 0;
 
  double *snp_tab;
  //  double *snp_tab2;
 
  double **snp_allele = _FHLinkedTrait->get_allele_values();
 
 
  unsigned int loc, rec;
  unsigned int nb_trait = _FHLinkedTrait->get_nb_traits();
  unsigned int nb_locus = _FHLinkedTrait->get_nb_locus();
 
 
  snp_tab = new double [ (nb_trait * nb_locus) ];
 
  //  snp_allele = new double [ (nb_trait * nb_locus)];
 
 
  ostringstream REC;
  string current;
 
  //first generation to record, build the record table;
 
  if(pop->getCurrentGeneration() == this->get_GenerationOccurrence() ||
      pop->getCurrentGeneration() == 1) {
 
    resetTable();
 
    //create header
    _records.push_back("pop trait locus allele g" + tstring::int2str(pop->getCurrentGeneration()));
 
    rec = 1;
    for(int i = 0; i < patchNbr; i++)
      for(unsigned int k = 0; k < nb_trait; k++) {
        for(unsigned int l = 0; l < nb_locus; l++) {
 
          REC<<i+1<<" "<<k+1<<" "<<l+1<<" "<<snp_allele[l][0];  //only '+' or 'A' allele
 
          _records.push_back(REC.str());
 
          REC.str("");
 
        }
      }
 
  } else { //add a 'column' for each generation recorded
 
    current =  _records[0];
 
    _records[0] = current + " g" + tstring::int2str(pop->getCurrentGeneration());
  }
 
 
  //ONLY IMPLEMENTED FOR DIALLELIC LOCI!
 
  rec = 1;
  for(int i = 0; i < patchNbr; i++) {
 
 
    current_patch = pop->getPatch(i);
 
    // fill the SNP_alleles with the first individual's haplotype, for comparison purposes:
    //    ind = current_patch->get(FEM, ADLTx, 0);
    //    genes = (double**)ind->getTrait(_FHLinkedTraitIndex)->get_sequence();
 
    for(unsigned int k = 0; k < nb_trait; k++) {
      for(unsigned int l = 0; l < nb_locus; l++) {
        loc = l * nb_trait + k;
        snp_tab [loc] = 0;
      }
    }
 
    total_size = current_patch->size(FEM, ADLTx) + current_patch->size(MAL, ADLTx);
 
 
    for(unsigned int j = 0, size = current_patch->size(FEM, ADLTx); j < size; j++) {
 
      ind = current_patch->get(FEM, ADLTx, j);
 
      genes = (double**)ind->getTrait(_FHLinkedTraitIndex)->get_sequence();
 
 
      for(unsigned int k = 0; k < nb_trait; k++) {
        for(unsigned int l = 0; l < nb_locus; l++) {
          loc = l * nb_trait + k;
 
          if (genes[0][loc] == snp_allele[l][0]){
            snp_tab [loc] += 1;
          }
 
          if (genes[1][loc] == snp_allele[l][0]){
            snp_tab [loc] += 1;
          }
 
        }
      }
 
 
    }
 
 
    for(unsigned int j = 0, size = current_patch->size(MAL, ADLTx); j < size; j++) {
 
      ind = current_patch->get(MAL, ADLTx, j);
 
      genes = (double**)ind->getTrait(_FHLinkedTraitIndex)->get_sequence();
 
      for(unsigned int k = 0; k < nb_trait; k++) {
        for(unsigned int l = 0; l < nb_locus; l++) {
          loc = l * nb_trait + k;
 
          if (genes[0][loc] == snp_allele[l][0]){
            snp_tab [loc] += 1;
          }
          if (genes[1][loc] == snp_allele[l][0]){
            snp_tab [loc] += 1;
          }
        }
      }
 
 
    }
 
    //calculate and record frequencies
    for(unsigned int k = 0; k < nb_trait; k++) {
      for(unsigned int l = 0; l < nb_locus; l++) {
 
        loc = l * nb_trait + k;
        //rec = i*nb_trait*nb_locus + k*nb_locus + l;
 
        assert(rec < _records.size());
 
        current = _records[ rec ];
 
        _records[ rec ] = _records[ rec ] + " " + tstring::dble2str( (snp_tab[loc] / (2 * total_size)) );
 
        rec++;
      }
    }    
  }
 
 
  delete [] snp_tab;
 
  if(pop->getCurrentGeneration() == pop->getGenerations() ) { //have we reached the last generation?
 
    std::string filename = get_path() + get_service()->getReplicateFileName() + get_extension();
    std::ofstream FILE ;
 
    //open for writing
    FILE.open(filename.c_str(), ios::out);
 
    if(!FILE) fatal("Trait quanti could not open output file: \"%s\"\n",filename.c_str());
 
    for(unsigned int i = 0; i < _records.size(); ++i)
      FILE<<_records[i]<<endl;
 
    FILE.close();
  }
}

References TraitFileHandler< TProtoQuanti >::_FHLinkedTrait, TraitFileHandler< TProtoQuanti >::_FHLinkedTraitIndex, _records, ADLTx, tstring::dble2str(), fatal(), FEM, Patch::get(), TProtoQuanti::get_allele_values(), FileHandler::get_extension(), FileHandler::get_GenerationOccurrence(), TProtoQuanti::get_nb_locus(), TProtoQuanti::get_nb_traits(), FileHandler::get_path(), FileServices::get_pop_ptr(), TTrait::get_sequence(), FileHandler::get_service(), Metapop::getCurrentGeneration(), Metapop::getGenerations(), Metapop::getPatch(), Metapop::getPatchNbr(), FileServices::getReplicateFileName(), Individual::getTrait(), tstring::int2str(), MAL, resetTable(), and Patch::size().

resetTable()

void TTQFreqExtractor::resetTable

(

)

{
  if(_records.size() != 0) _records.clear();
}

References _records.

Referenced by FHwrite(), and TProtoQuanti::loadFileServices().

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Member Data Documentation

_records

vector< string > TTQFreqExtractor::_records

private

Referenced by FHwrite(), and resetTable().

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

• ttquanti.h
• ttquanti.cc