//build_kmer_tree specification

#include <fstream>
#include <iostream>
#include <string>
#include <stdio.h>

using namespace std;

#include "mx_node.h"

//In this version, gRNA is the barcode and the stgRNAs are the ones that we are interested in 
//extracting


void build_kmer_tree(mx_node* master_node, const string& kmers_filename, const int& bc_length)
{
	ifstream gRNA_file;

	string ipt_line;
	string gRNA;
	int gRNA_len;
	char curr_char;
	string curr_kmer;
	string stgRNA = "";
	int curr_depth;
	bool end_of_gRNA;
        int curr_counter = 0;

        gRNA_file.open(kmers_filename);

	size_t gRNA_end;

	mx_node* iter_node;
	mx_node* parent_node_p;

	while (getline(gRNA_file, ipt_line))
	{

		gRNA_end = ipt_line.find(" ");
		gRNA = ipt_line.substr(0, bc_length);
	  	gRNA_len = gRNA.length();

		
		while(gRNA.length() == bc_length)
		{

		iter_node = master_node;
		end_of_gRNA = 0;

	    for (int i = 1; i<=gRNA_len; i++)
		   {
		    curr_char = gRNA.back();
		    gRNA.pop_back();
		    curr_kmer = iter_node->get_kmer();
		    curr_depth = iter_node->get_depth();
         	
		    if (i==gRNA_len)
			   end_of_gRNA = 1; 

		    if (curr_char == 'M')
			{
				if(iter_node->is_pointer_M()) {
					parent_node_p = iter_node;
					iter_node = iter_node->get_pointer_M(end_of_gRNA, stgRNA);
				}
				else {
					parent_node_p = iter_node;
					iter_node = iter_node->set_pointer_M(curr_kmer, curr_depth, end_of_gRNA, stgRNA);
					curr_counter++;
				}
			}
			else if (curr_char == 'X')
			{
				if(iter_node->is_pointer_X()) {
					parent_node_p = iter_node;
					iter_node = iter_node->get_pointer_X(end_of_gRNA, stgRNA);
				}
				else {
					parent_node_p = iter_node;
					iter_node = iter_node->set_pointer_X(curr_kmer, curr_depth, end_of_gRNA, stgRNA);
					curr_counter++;
				}
			}
			else if (curr_char == 'I')
			{
				if(iter_node->is_pointer_I()) {
					parent_node_p = iter_node;
					iter_node = iter_node->get_pointer_I(end_of_gRNA, stgRNA);
				}
				else {
					parent_node_p = iter_node;
					iter_node = iter_node->set_pointer_I(curr_kmer, curr_depth, end_of_gRNA, stgRNA);
					curr_counter++;
				}
			}
			else if (curr_char == 'D')
			{
				if(iter_node->is_pointer_D()) {
					parent_node_p = iter_node;
					iter_node = iter_node->get_pointer_D(end_of_gRNA, stgRNA);
				}
				else {
					parent_node_p = iter_node;
					iter_node = iter_node->set_pointer_D(curr_kmer, curr_depth, end_of_gRNA, stgRNA);
					curr_counter++;
				}
			}
			else if (curr_char)
			{
				if(iter_node->is_pointer_M()) {
					parent_node_p = iter_node;
					iter_node = iter_node->get_pointer_M(end_of_gRNA, stgRNA);
				}
				else {
					parent_node_p = iter_node;
					iter_node = iter_node->set_pointer_M(curr_kmer, curr_depth, end_of_gRNA, stgRNA);
					curr_counter++;
				}
			}
		   }
		
		}
	}

}