MAl_addon.h

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#ifndef MAL_ADDON_H
#define MAL_ADDON_H

#include "mal.h"
#include <map>
#include <vector>

class MAl_addon
{
public:
  MAl_addon( MAl* m );
  ~MAl_addon();
  
  int get_min_col();
  int get_max_col();  
  int get_num_rows();
  char get_most_freq_base_on_col( int col );
  int get_num_bases_on_col(int col, char base);
  size_t get_num_DNPs_on_col(int col);
  char get_entry( int row, int col );  
  int get_qual( int row, int col );  
  void set_DNP(int row, int col, bool status, int dnpID, int type);
  bool is_DNP(int row, int col);
  int get_row_start(int row);
  int get_row_end(int row);
  

private:
  struct cons_struct
  {
    cons_struct()
    {
      for( int i = 0; i < 8; i++ ) {
        num.push_back( 0 );
      }
      num_DNPs = 0;
    }
    
    char cons;
    vector<int> num;
    size_t num_DNPs;
  };
  

  MAl* mal;
  size_t min_col;
  size_t max_col;
  map<char, int> base_index;
  vector<char> index_base;
  vector<cons_struct> consensus;
};

#endif //MAL_ADDON_H

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