cf1_gram.cpp

#define NEW_SIGMA 16
#define Q_GRAM 2
#include "common.h"

void cf1_gram (const uchar *P, const int m, const uchar *T, const int n, const int k) {
	/* Preprocessing */
	long  count = 0, j = 0;
	char *A = (char*)malloc(CH_SIZE*ASIZE);
	if (A==NULL) { printf("Error: CMP_CountFilter: Can't allocate memory for variable A."); return; }
	for ( int i = 0; i < ASIZE; ++i) A[ i ] = 0;
	for ( int i = 0; i < m - 1; ++i) A[ get_q_gram<Q_GRAM, NEW_SIGMA>(P + i) ]++;
	count = -( ( m-(Q_GRAM-1) ) - k*Q_GRAM );

	for ( j = 0 ; j < m-1 ; j++ )
		if ( A[ get_q_gram<Q_GRAM, NEW_SIGMA>(T+j) ]-- > 0 ) count++;

	while (j <= n-1) {
		if ( count >= 0 ) {
			++v_count;
		}
		if ( ++A[ get_q_gram<Q_GRAM, NEW_SIGMA>(T + j - (m-1)) ] > 0 ) count--;
		if ( A[ get_q_gram<Q_GRAM, NEW_SIGMA>(T + j) ]-- > 0 ) count++;
		j++;
	}
	free(A);
}

/* 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);
		cf1_gram(pattern, patt_size, text, text_size, 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;
}