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	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)
virtual void	set_multi (bool rpl_per, bool gen_per, int rpl_occ, TMatrix *Occ, 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	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 ()

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;
 
  const TMatrix& snp_allele = _FHLinkedTrait->get_diallele_values();
 
  bool _isAsymmetrical = _FHLinkedTrait->get_allele_model() == 2;
 
  unsigned int BIT = _isAsymmetrical;  // read the derived allele value at position 1 in asymmetrical model
  unsigned int loc, rec;
  unsigned int nb_trait = _FHLinkedTrait->get_num_traits();
  unsigned int seqLength = _FHLinkedTrait->get_seq_length();
 
 
  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()));
 
    for(int i = 0; i < patchNbr; i++)
      for(unsigned int k = 0; k < nb_trait; k++) {
        for(unsigned int l = 0, LOCUS; l < _FHLinkedTrait->get_num_locus(k); l++) {
 
          LOCUS = _FHLinkedTrait->get_locus_ID(l,k);
 
          REC<<i+1<<" "<<k+1<<" "<<LOCUS+1<<" "<<snp_allele.get( LOCUS, BIT );  //only '+' or 'A' allele, depends on allele model
 
          _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!
 
#ifdef _DEBUG_
  message("TTQFreqExtractor::compute allele frequencies\n");
#endif
 
  // we are calculating allele frequencies of the whole set of alleles
  // thus also considers cases with pleiotropy
  vector<double> snp_tab(seqLength, 0.0);
 
  rec = 1;
  for(int i = 0; i < patchNbr; i++) {
 
    current_patch = pop->getPatch(i);
 
    snp_tab.assign(seqLength, 0.0);
 
    // cycle through whole population
    for(unsigned int s = 0; s < 2; ++s) {
 
      for(unsigned int j = 0, size = current_patch->size(sex_t(s), ADLTx); j < size; ++j) {
 
        ind = current_patch->get(sex_t(s), ADLTx, j);
 
        trait = dynamic_cast<TTQuanti*>(ind->getTrait(_FHLinkedTraitIndex));
 
        //compute allele freq at all positions, we count allele 1 for 'q' (freq 'p' is for trait-increasing allele 0)
        for(unsigned int i = 0; i < seqLength; ++i) {
          snp_tab[i] +=  trait->get_allele_bit(i, 0) + trait->get_allele_bit(i, 1);
        }
 
      }
    }
 
    double inv2N = 1.0 / double(2*current_patch->size(ADLTx));
 
    //calculate and record frequencies
    for(unsigned int k = 0; k < nb_trait; k++) {
      for(unsigned int l = 0; l < _FHLinkedTrait->get_num_locus(k); l++) {
 
        loc = _FHLinkedTrait->get_locus_seq_pos(l,k);
 
        assert(rec < _records.size());
 
        current = _records[ rec ];
 
        if(_isAsymmetrical)
          _records[ rec ] = _records[ rec ] + " " + tstring::dble2str( snp_tab[loc] * inv2N ); // we report the count of 1's (referred as 'q' above)
        else
          _records[ rec ] = _records[ rec ] + " " + tstring::dble2str(1.0 - (snp_tab[loc] * inv2N) ); // we report the count of 0's, or 'p' = (1-q)
 
        rec++;
      }
    }
  }
 
  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);
    std::ios_base::sync_with_stdio(false); // better for writing performances
 
#ifdef _DEBUG_
  message("TTQFreqExtractor::FHwrite (%s)\n",filename.c_str());
#endif
 
    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();
 
    std::ios_base::sync_with_stdio(true); // reset
  }
}

References TraitFileHandler< TProtoQuanti >::_FHLinkedTrait, TraitFileHandler< TProtoQuanti >::_FHLinkedTraitIndex, _records, ADLTx, Patch::assign(), tstring::dble2str(), fatal(), Patch::get(), TMatrix::get(), TTQuanti::get_allele_bit(), TProtoQuanti::get_allele_model(), TProtoQuanti::get_diallele_values(), FileHandler::get_extension(), TProtoQuanti::get_locus_ID(), TProtoQuanti::get_locus_seq_pos(), TProtoQuanti::get_num_locus(), TProtoQuanti::get_num_traits(), FileHandler::get_path(), FileServices::get_pop_ptr(), TProtoQuanti::get_seq_length(), FileHandler::get_service(), Metapop::getCurrentGeneration(), Metapop::getGenerations(), Metapop::getPatch(), Metapop::getPatchNbr(), FileServices::getReplicateFileName(), Individual::getTrait(), tstring::int2str(), message(), 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