// Copyright 2013 Calvin Morrison
#include <errno.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>

#include "kmer_total_count.h"

const unsigned char alpha[256] = 
{5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 0, 5, 1, 5, 5, 5, 2, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 0, 5, 1, 5, 5, 5, 2,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5};

const char reverse_alpha[4] = { 'A', 'C', 'G', 'T' };

inline unsigned long long pow_four(unsigned long long x) {
	return (unsigned long long)1 << (x * 2);
}

// convert a string of k-mer size base-4 values  into a
// base-10 index
inline unsigned long num_to_index(const char *str, const int kmer, const long error_pos, size_t *current_position) {

  int i = 0;
  unsigned long out = 0;
  unsigned long multiply = 1;

  for(i = kmer - 1; i >= 0; i--){

		if(str[i] == 5) { 
			current_position += i;
			return error_pos;
		}

    out += str[i] * multiply;
    multiply = multiply << 2;
  }

  return out;
}

// return the number of loaded elements
unsigned long long load_specific_mers_from_file(char *fn, unsigned int kmer, size_t width, size_t *arr) { 
		FILE *fh;
		size_t arr_pos = 0;
		char line[64];

		fh = fopen(fn, "r");
		if(fh == NULL) {
			fprintf(stderr, "Error opening %s - %s\n", fn, strerror(errno));
			exit(EXIT_FAILURE);
		}	

   	while (fgets(line, sizeof(line), fh) != NULL) {
			size_t i;
			size_t len;

			len = strlen(line);
			if(len == 0)
				continue;

			len--;
			line[len] = '\0';


			if(len != kmer)  {
				fprintf(stderr, "SKIPPING: '%s' is not length %u\n", line, kmer);
				continue;
			}
			
			for(i = 0; i < len; i++) {
				line[i] = alpha[(int)line[i]];
			}
				
		 	size_t mer = num_to_index(line, kmer, width, NULL);
			if(mer == width) {
				fprintf(stderr, "SKIPPING: '%s' is a unrecognized mer\n", line);
				continue;
			}
			else {
				arr[arr_pos] = mer;
				arr_pos++;
			}
		}

		fclose(fh);
		return arr_pos;
}

// convert an index back into a kmer string
char *index_to_kmer(unsigned long long index, long kmer)  {

	size_t i = 0;
	size_t j = 0;
	char *num_array = calloc(kmer,  sizeof(char));
	char *ret = calloc(kmer + 1, sizeof(char));
	if(ret == NULL)
		exit(EXIT_FAILURE);
		

	// this is the core of the conversion. modulus 4 for base 4 conversion
	while (index != 0) {
		num_array[i] = index % 4;
		index /= 4;
		i++;
	}
	
	// for our first few nmers, like AAAAA, the output would only be "A" instead
	// of AAAAA so we prepend it
	for(j = 0; j < (kmer - i); j++)
		ret[j] = 'A';

	// our offset for how many chars we prepended
	int offset = j;
	// save i so we can print it
	size_t start = i ;

	// decrement i by 1 to reverse the last i++
	i--;  
	j = 0;

	// reverse the array, as j increases, decrease i
	for(j = 0; j < start; j++, i--) 
		ret[j + offset] = reverse_alpha[(int)num_array[i]];
	
  // set our last character to the null termination byte
	ret[kmer + 1] = '\0';

	free(num_array);
	return ret;
}

// Strip out any character 'c' from char array 's' into a destination dest (you
// need to allocate that) and copy only len characters.
char *strnstrip(const char *s, char *dest, int c, unsigned long long len) {

	unsigned long long i = 0;
	unsigned long long j = 0;

	for(i = 0; i < len; i++) {
		if(s[i] != c) {
			dest[j] = s[i];
			j++;
		}
	}

	dest[j] = '\0';

	return dest;
}

unsigned long long * get_kmer_counts_from_file(const char *fn, const unsigned int kmer) {
	
  char *line = NULL;
  size_t len = 0;
  ssize_t read;

  size_t i = 0;
	size_t position = 0;

  FILE * const fh = fopen(fn, "r");
  if(fh == NULL) {
    fprintf(stderr, "Error opening %s - %s\n", fn, strerror(errno));
    exit(EXIT_FAILURE);
  }

	// width is 4^kmer  
	// there's a sneaky bitshift to avoid pow dependency
	const unsigned long width = pow_four(kmer); 

	// malloc our return array
  unsigned long long * counts = calloc((width+ 1), sizeof(unsigned long long));
  if(counts == NULL)  {
		fprintf(stderr, strerror(errno));
    exit(EXIT_FAILURE);
	}

	char *str = malloc(4096);
	if(str == NULL) { 
		fprintf(stderr, strerror(errno));
		exit(EXIT_FAILURE);
	}

	unsigned long long str_size = 4096;

	while ((read = getdelim(&line, &len, '>', fh)) != -1) {

		// find our first \n, this should be the end of the header
		char *start = strchr(line, '\n');	
		if(start == NULL) 
			continue;

		// point to one past that.
		start = start + 1;

		size_t start_len = strlen(start);


		// if our current str buffer isn't big enough, realloc
		if(start_len + 1 > str_size + 1) { 
			str = realloc(str, start_len + 1);
			if(str == NULL) { 
				exit(EXIT_FAILURE);
				fprintf(stderr, strerror(errno));
			}
		}


		// strip out all other newlines to handle multiline sequences
		str = strnstrip(start, str, '\n',start_len);
		size_t seq_length = strlen(str);

		// relace A, C, G and T with 0, 1, 2, 3 respectively
		// everything else is 5 
		for(i = 0; i < seq_length; i++) {
			str[i] = alpha[(int)str[i]];
		}

		// loop through our string to process each k-mer
		for(position = 0; position < (seq_length - kmer + 1); position++) {
			unsigned long mer = 0;
			unsigned long multiply = 1;

			// for each char in the k-mer check if it is an error char
			for(i = position + kmer - 1; i >= position; i--){
				if(str[i] == 5) { 
					mer = width;
					position = i;
					goto next;
				}

				// multiply this char in the mer by the multiply
				// and bitshift the multiply for the next round
				mer += str[i] * multiply;
				multiply = multiply << 2;
			}
			// use this point to get mer of our loop
			next:
			// bump up the mer value in the counts array
			counts[mer]++;
		}
	} 

  free(line);
	free(str);
	fclose(fh);

	return counts;
}