#ifndef DATA_TYPES_H
 #define DATA_TYPES_H
 
 #include <Rcpp.h>
 using namespace Rcpp;
 
 using namespace std;
 
 //
 // definitions of data types
 //
 typedef map<string, vector<unsigned int> > Bins_end_coord; // a map: chr -> a vector of end coordinate of each bin. coordinate is 1-base
 typedef map<string, vector<int> > Bins_index; // a map: chr -> a vector of bin index. Note some bins are void/complementary, so their indexes are 0
 typedef map<string, vector<string> > Bins_info; // a map: chr -> a vector of bins' info. Each bin's info is a string
 
 typedef map<string, map<int,map<int,double> > > Wig_bins_data; // chr -> (bin_internal_index -> (position -> value)). This is a three-layer map
 
 typedef unsigned int GENOME_POSITION;
 
 // Bins2Values: a map for bin_index -> a vector of value. bin_index is always 1-base
 typedef map<int, vector<double> > Bins2Values;
 typedef map<int, vector<unsigned int> > Bins2UnsignedIntegers;
 
 // Bins2PairedValues: a map for bin_index -> two vectors of values. bin_index is always 1-base
 typedef map<int, pair<vector<double>,vector<double> > > Bins2PairedValues;
 
 // Bins2PositionValuePairs: a map for bin_index -> a pair of (position vector, value vector). bin_index is always 1-base
 typedef map<unsigned int, pair<vector<GENOME_POSITION>,vector<double> > > Bins2PositionValuePairs;
 
 // Bins2Value: a map of bin_index -> a value. bin_index is always 1-base
 typedef map<int, double> Bins2Value;
 
 //
 // functions for these data types
 //
 void read_bins_annot_file(string input_bins_annot_file, Bins_end_coord & bins_end_coord,
 	Bins_index & bins_index, Bins_info & bins_info, bool has_header_line);
 int get_num_of_non_void_bins(Bins_index & bins_index, vector<int> & returned_markers_index);
 int find_exact_bin(Bins_end_coord & bins_end_coord, string chr, unsigned int bin_start_coord, unsigned int bin_end_coord);
 int find_bin_of_position(Bins_end_coord & bins_end_coord, string chr, unsigned int position);
 int find_overlap_bin(Bins_end_coord & bins_end_coord, string query_region_chr, unsigned int query_region_start_coord,
 	unsigned int query_region_end_coord, int & overlap_length);
 void print_bins( ostream& os, Bins_end_coord & bins_end_coord, Bins_index & bins_index, Bins_info & bins_info);
 
 void create_Bins2Values(int num_bins, int num_of_values, double init_value, Bins2Values & bins2values);
 void create_Bins2Values(vector<int> markers_index, int num_of_values, double init_value, Bins2Values & bins2values);
 void write_Bins2Values(Bins2Values & bins2values, vector<string> & columns_names, string output_file, bool optional_write=false);
 void print_Bins2Values(Bins2Values & bins2values);
 void print_Bins2UnsignedIntegers(Bins2UnsignedIntegers& bins2values);
 
 void create_Bins2Value(int num_bins, double init_value, Bins2Value & bins2value);
 ostream& operator<<(ostream& out, Bins2Value& bins2value);
 void write_Bins2Value(Bins2Value & bins2value, string output_file);
 
 #endif