Genetix.cpp

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#include "Genetix.h"
 
using namespace bpp;
using namespace std;
 
Genetix::Genetix() {}
 
Genetix::~Genetix() {}
 
void Genetix::read(istream& is, DataSet& data_set)
{
  if (!is)
    throw IOException("Genetix::read: fail to open stream.");
  // Loci number
  string temp = FileTools::getNextLine(is);
  unsigned int loc_nbr;
  stringstream(temp) >> loc_nbr;
  data_set.initAnalyzedLoci(loc_nbr);
 
  // Groups number
  temp = FileTools::getNextLine(is);
  unsigned int grp_nbr;
  stringstream(temp) >> grp_nbr;
 
  // Loci data
  for (unsigned int i = 0; i < loc_nbr; i++)
  {
    // Locus name
    string name = FileTools::getNextLine(is);
    name = TextTools::removeSurroundingWhiteSpaces(name);
    LocusInfo tmp_loc(name);
    // Alleles
    stringstream values(FileTools::getNextLine(is));
    unsigned int nbr_al;
    values >> nbr_al;
    for (unsigned int j = 0; j < nbr_al; j++)
    {
      string al_id;
      values >> al_id;
      BasicAlleleInfo tmp_al(al_id);
      tmp_loc.addAlleleInfo(tmp_al);
    }
    data_set.setLocusInfo(i, tmp_loc);
  }
 
  // Groups
  for (unsigned int i = 0; i < grp_nbr; i++)
  {
    data_set.addEmptyGroup(i);
    // Group name ... Now used khalid
    temp = FileTools::getNextLine(is);
    data_set.setGroupName(i, temp);
 
    // Number of individuals
    unsigned int ind_nbr;
    temp = FileTools::getNextLine(is);
    stringstream tmp(temp);
    tmp >> ind_nbr;
    for (unsigned int j = 0; j < ind_nbr; j++)
    {
      temp = FileTools::getNextLine(is);
      string ind_name(temp.begin(), temp.begin() + 11);
      temp = string(temp.begin() + 11, temp.end());
      data_set.addEmptyIndividualToGroup(i, TextTools::removeSurroundingWhiteSpaces(ind_name) + string("_") + TextTools::toString(i + 1) + string("_") + TextTools::toString(j + 1));
      data_set.initIndividualGenotypeInGroup(i, j);
      StringTokenizer alleles(temp, string(" "));
      // cout << alleles.numberOfRemainingTokens() << endl;
      for (unsigned int k = 0; k < loc_nbr; k++)
      {
        string tmp_string = alleles.nextToken();
        vector<string> tmp_alleles;
        tmp_alleles.push_back(string(tmp_string.begin(), tmp_string.begin() + 3));
        tmp_alleles.push_back(string(tmp_string.begin() + 3, tmp_string.begin() + 6));
        if (tmp_alleles[0] != string("000") && tmp_alleles[1] != string("000"))
          data_set.setIndividualMonolocusGenotypeByAlleleIdInGroup(i, j, k, tmp_alleles);
      }
    }
  }
}
 
void Genetix::read(const string& path, DataSet& data_set)
{
  AbstractIDataSet::read(path, data_set);
}
 
DataSet* Genetix::read(istream& is)
{
  return AbstractIDataSet::read(is);
}
 
DataSet* Genetix::read(const string& path)
{
  return AbstractIDataSet::read(path);
}