Report_manager.cpp

#include "Report_manager.hpp"

Report_manager::Report_manager(std::string database_location, bool clean_ends, std::string marked_motifs_filename, float database_sample, float database_modif)
{
  database = Database(database_location, clean_ends, marked_motifs_filename, database_sample, database_modif);
  mdp_toolbox = Mdp_toolbox(database);
  statistical_toolbox = Statistical_toolbox(mdp_toolbox);
}

std::stringstream Report_manager::number_of_aminoacids_per_coordinate(void)
{
  std::stringstream output;
  for(auto motif : mdp_toolbox.database.get_motif_database())
    {
      output<< motif.get_name();
      for(auto sequence : motif.get_sequence())
	{
	  output << separator << sequence.size();
	}
      output << std::endl;
    }
  return output;
}

std::stringstream Report_manager::aminoacids_per_coordinate(void)
{
  std::stringstream output;
  for(auto motif: mdp_toolbox.database.get_motif_database())
    {
      output << motif.get_name();
      for(auto sequence: motif.get_sequence())
	output << separator << sequence;
      output << std::endl;
    }
  return output;
}

std::stringstream Report_manager::number_k_discriminant_motifs(int k)
{
  std::stringstream output;
  for(auto motif: mdp_toolbox.database.get_motif_database())
    {
      std::vector<Motif_class> k_discriminant_motifs = mdp_toolbox.get_k_discriminant_motifs(motif, k);
      output << motif.get_name() << separator << k_discriminant_motifs.size() << std::endl;
    }
  return output;
}

std::stringstream Report_manager::k_discriminant_motifs_pair(int k)
{
  std::stringstream output;
  for(std::pair<Motif_pair, int> element : mdp_toolbox.get_mdp_database())
    {
      if(element.second == k)
	output << element.first.get_short_motif().get_name() << separator << element.first.get_long_motif().get_name() << std::endl;
    }
  return output;
}


std::stringstream Report_manager::motif_discriminant_positions_alignval(void)
{
  std::stringstream output;

  //Header
  output << "Long motif";
  output <<separator<< "Short motif";
  output <<separator<< "Alignval";
  output <<separator<< "Partial discriminant position";
  output <<separator<< "Effective discriminant position"<< std::endl;
  
  for(std::pair<Motif_pair ,int> element: mdp_toolbox.get_mdp_database())
    {
      Motif_class long_motif = element.first.get_long_motif();
      Motif_class short_motif = element.first.get_short_motif();

      output << long_motif.get_name() << separator;
      output << separator << separator << separator;
      for(auto sequence : long_motif.get_sequence())
	output << separator << sequence;
      output << std::endl;
      
      int length_difference = long_motif.get_sequence().size()-short_motif.get_sequence().size()+1;
      int motif_discriminating_positions = 99;

      forn(i,length_difference)
	{

	  output << separator << short_motif.get_name();
	  
	  std::vector<std::string> sequence;
	  forn(j, short_motif.get_sequence().size())
	    sequence.push_back(long_motif.get_sequence()[i + j]);
	  
	  Motif_class submotif(long_motif.get_name(), sequence);
	  
	  int align_val = mdp_toolbox.alignval(short_motif, submotif);
	  int partial_motif_discriminating_positions = mdp_toolbox.simple_motif_discriminating_positions(short_motif, submotif);
	  if(partial_motif_discriminating_positions < motif_discriminating_positions && align_val > 0)
	    motif_discriminating_positions = partial_motif_discriminating_positions;

	  output << separator << align_val ;
	  output << separator << partial_motif_discriminating_positions;
	  output << separator << mdp_toolbox.get_mdp_database()[element.first];

	  //aligning
	  forn(j,i)
	    output << separator;
	  
	  for(auto sequence: short_motif.get_sequence())
	    output << separator << sequence;
	  output << std::endl;
	} 
    }
  return output;
}

std::stringstream Report_manager::number_pairs_motifs_with_k_discriminant_positions(void)
{
  std::stringstream output;
  output << "k\t #pairs with k discriminant positions\t #pairs with k discriminant positions/total"<<std::endl;
  int total_number_pairs = mdp_toolbox.get_mdp_database().size();
  
  forn(k,20)
    {
      int number_pairs_k_discriminant = mdp_toolbox.get_pairs_k_discriminant_positions(k).size();
      output << k << separator<< number_pairs_k_discriminant << separator <<1.0*number_pairs_k_discriminant/total_number_pairs << std::endl;
    }
  return output;
}

std::stringstream Report_manager::empiric_motif_probabilities()
{
  std::stringstream output;

  //output << "Structure" << separator << "Probability" << std::endl;
  for(std::pair<std::vector<int>, float> element: statistical_toolbox.get_empiric_motif_probabilities())
    output << element.first << separator << statistical_toolbox.compute_empiric_based_probability(element.first)<< separator << element.second << std::endl;

  return output;
}

std::stringstream Report_manager::all_lenghts_accumulated_probabilities()
{
  std::stringstream output;

  //output << "Structure" << separator << "Probability" << std::endl;
  for(std::pair<std::vector<int>, float> element : statistical_toolbox.get_theoretic_motif_probabilities())
    output << element.first << separator << element.second << std::endl;

  return output;
}