cf2_skip.cpp

#define NEW_SIGMA 16

#include "common.h"

void cf2_skip (const uchar *P, const int m, const uchar *T, const int n, const int sigma, const int k) {
	int *hp = (int*)malloc(sizeof(int)*sigma);
	int *ht = (int*)malloc(sizeof(int)*sigma);
	int sum = 0;
	for ( int i = 0; i < sigma; ++i) {
		hp[ i ] = ht[ i ] = 0;
	}

	for ( int i = 0; i < m; ++i) {
		++hp[ map[P[i]] ];	// pattern
		++ht[ map[T[i]] ];	// initial window
	}

	for(int i = m; i < n; ) {
		sum = 0;
		for(int j = 0; j < sigma; j++) {
			sum += abs(hp[j] - ht[j]);
		}

		if ( sum <= k*2 ) {
			++v_count;
		}
		for(int j = 1; j < sum/2 - k; j++) {
			--ht[ map[T[i-m] ]];	
			++ht[ map[T[i] ]];	
			i++;
		}
		--ht[ map[T[i-m] ]];	
		++ht[ map[T[i] ]];	
		i++;
	}
	free(hp);
	free(ht);
}


/* MAIN */

int main(int argc, char *argv[]) {
	if ( argc < 4 ) return EXIT_FAILURE;
	t_timemes t_data_acc = {0}, t_pre = {0}, t_run = {0};
	t_init(t_data_acc); t_init(t_pre); t_init(t_run);
	t_start(t_pre);
	
	const char *patterns_filename = argv[1], *patt_size_pch = argv[2], *filename = argv[3];

	unsigned int patt_size = atoi(patt_size_pch), text_size = 0;
	uchar *text = NULL, *pattern = NULL;
	FILE * file = NULL;

	text_size = read_file_content<uchar>(&text, filename);
	if (text == NULL) return EXIT_FAILURE;

	pattern = (uchar*)calloc (patt_size+1, CH_SIZE);
	if (pattern == NULL) { printf("Error: Can't allocate memory for pattern."); free(text); return EXIT_FAILURE; }

	file = fopen (patterns_filename, "rb");
	if (!file) { printf("Error: Can't open patterns file."); free(text); free(pattern); return EXIT_FAILURE; }
	
	indexes = (bool*)calloc(text_size, BOOL_SIZE);

	int sigma = CreateMapByHistogramBinPack<uchar>(text, text_size);
	
	while (fread (pattern, CH_SIZE, patt_size, file)==patt_size) {
		t_start(t_run);
		cf2_skip(pattern, patt_size, text, text_size, sigma, K_DIFF);
		t_stop(t_run);
	}

	for(unsigned long l = 0; l < text_size; ++l) if( indexes[l] ) ++counter;
	print_resultn(t_get_seconds(t_run), v_count, counter, sigma, Q_GRAM, K_DIFF);
	free(text);
	free(pattern);
	free(indexes);
	fclose(file);
	return EXIT_SUCCESS;
}