#ifndef PROTEIN_H
#define PROTEIN_H

#include <iostream>
#include <vector>
#include <cstdlib>

using namespace std;

class protein
{
 private:
  string sequence;
  string info_line;
  int id;
  int gnums;
  int gene_ids;
  bool deleter;
  bool manually_include; //beats deleter.

 public:
  protein();
  void mark_keeper();
  void add_gnums(int i);
  void add_gis(int i);
  void mark_for_deletion();
  void print_protein_info();
  void reset_deleters();
  bool ginclude();
  void minclude();  

  //setters
  void set_sequence(string s);
  void set_info_line(string il);
  void set_id(int i);  

  //getters
  string get_sequence();
  string get_info_line();
  int get_gnums();
  int get_geneids();
  bool get_deleter();
  double get_ratio();
  int get_id();
  bool get_mi();
};

protein::protein()
{
  deleter=false;
  manually_include=false;
  gnums=0;
  gene_ids=0;
}

void protein::set_sequence(string s)
{
  sequence = s;
}

void protein::mark_keeper()
{
  manually_include=true;
}

void protein::set_info_line(string il)
{
  info_line = il;
}

void protein::set_id(int i)
{
  id = i;
}

string protein::get_sequence()
{
  return sequence;
}

string protein::get_info_line()
{
  return info_line;
}

void protein::add_gnums(int i)
{
  gnums+=i;
}

void protein::add_gis(int i)
{
  gene_ids+=i;
}

void protein::mark_for_deletion()
{
  deleter=true;
}

int protein::get_gnums()
{
  return gnums;
}

int protein::get_geneids()
{
  return gene_ids;
}

void protein::print_protein_info()
{
  cout<<info_line<<endl<<sequence<<endl<<gnums<<endl<<gene_ids<<endl;
}

double protein::get_ratio()
{
  return (double)gene_ids/(double)gnums;
}

void protein::reset_deleters()
{
  if(deleter)
    {
      print_protein_info();
      gnums=0;
    }
}


bool protein::get_deleter()
{
  return deleter;
}

void protein::minclude()
{
  manually_include=true;
}

bool protein::ginclude()
{
  return manually_include;
}

int protein::get_id()
{
  return id;
}

bool protein::get_mi()
{
  return manually_include;
}

#endif