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sw.c
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sw.c
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//Bergamini Federico 845646
#include "sw.h"
#define BUZZ_SIZE 1024
//#define DEBUG
void to_upper_case(char * string){
do_to_upper_case(string, 0);
}
void do_to_upper_case(char * string, uint64_t i){
if (i == strlen(string))
{
return;
}
string[i] = toupper(string[i]);
do_to_upper_case(string, ++i);
}
void reverse(char * string){
do_reverse(string, 0, strlen(string) - 1);
}
void do_reverse(char * string, int begin, int end){
char c;
if (begin >= end)
{
return;
}
c = string[begin];
string[begin] = string[end];
string[end] = c;
return do_reverse(string, ++begin, --end);
}
void read_text(char * s1, char * s2) {
printf("Inserisci la stringa s1 : ");
scanf("%s", s1);
printf("Inserisci la stringa s2 : ");
scanf("%s", s2);
#ifdef DEBUG
printf("s1 : %s\n", s1);
printf("s2 : %s\n", s2);
#endif
}
int score(char c1, char c2){
#ifdef DEBUG
printf("c1 : %c, c2: %c\n", c1, c2);
#endif
if (c1 == c2 == '*')
{
return 1;
}
if (c1 == '*' || c2 == '*')
{
return -LGP;
}
if (c1 == c2)
{
for (uint64_t i = 0; i < SCORING_LEN; i++)
{
if (scoring_lookup[i] == c1)
{
return scoring_matrix[i][i];
}
}
}
unsigned int i_c1, i_c2;
for (uint64_t i = 0; i < SCORING_LEN; i++)
{
if (scoring_lookup[i] == c1)
{
i_c1 = i;
}
}
for (uint64_t i = 0; i < SCORING_LEN; i++)
{
if (scoring_lookup[i] == c2)
{
i_c2 = i;
}
}
return scoring_matrix[i_c1][i_c2];
}
bool string_analizer(char * string){
return do_string_analizer(string, 0);
}
bool do_string_analizer(char * string, uint64_t i){
if (i == strlen(string))
{
return true;
}
#ifdef DEBUG
printf("i : %ld, string[i] : %c\n", i, string[i]);
#endif
for (size_t j = 0; j < SCORING_LEN; ++j)
{
if (string[i] == scoring_lookup[j])
{
return do_string_analizer(string, ++i);
}
}
return false;
}
int max(int match, int indel_s1, int indel_s2){
int max;
if (match > indel_s1)
{
if (match > indel_s2)
{
max = match;
}
else //indel_s2 >= match
{
max = indel_s2;
}
}
else //indel_s1 >= match
{
if (indel_s1 > indel_s2)
{
max = indel_s1;
}
else //indel_s2 >= indel_s1
{
max = indel_s2;
}
}
#ifdef DEBUG
printf("max: %d\n", max);
#endif
return max;
}
range_s range(band_s band, uint64_t y) {
range_s r = {0, 0};
r.sx = y - band.extra;
if (y < band.extra)
r.sx = 0;
r.dx = y + (band.base - 1) + band.extra;
if (r.dx > band.l2)
r.dx = band.l2;
return r;
}
uint64_t conv(band_s band, uint64_t x, uint64_t y) {
assert(y <= band.l1);
assert(x >= y || y - x <= band.extra);
assert(x <= y || x - y <= band.base + band.extra);
uint64_t width = band.base + 2 * band.extra;
return (width * y) + (x - y + band.extra);
}
static int band_align(uint64_t base, uint64_t extra, char* s1, char* s2, char * allignment_s1, char * allignment_s2) {
uint64_t l1 = strlen(s1);
uint64_t l2 = strlen(s2);
uint64_t band = base + 2 * extra;
int match, indel_s1, indel_s2;
cell_s* m = (cell_s*)malloc(band * (l1 + 1) * sizeof(cell_s));
assert(m != NULL && "Cannot allocate matrix\n");
band_s b = {
.l1 = l1,
.l2 = l2,
.base = base,
.extra = extra
};
for (uint64_t y = 1; y <= l1; y++) {
range_s r = range(b, y);
{ //Inizializzo lower bound e upper bound della banda
cell_s* tp = m + conv(b, r.sx, y);
if (l1 != l2)
{
tp->cell = INT16_MIN;
}
else
{
tp->cell = INT16_MAX;
}
tp->prev_x = 0;
tp->prev_y = 0;
tp = m + conv(b, r.dx, y);
tp->cell = 0;
tp->prev_x = 0;
tp->prev_y = 0;
}
#ifdef DEBUG
printf("r.sx : %ld, r.dx : %ld\n", r.sx, r.dx);
#endif
for (uint64_t x = r.sx + 1; x <= r.dx; x++) {
#ifdef DEBUG
printf("\nStepB: %ld, %ld\n", x, y);
#endif
cell_s* tp = m + conv(b, x, y);
//Programmazione dinamica
if ((x - 1) == 0 && (y - 1) == 0) //Condizione a contorno
{
#ifdef DEBUG
printf("(x - 1) == (y - 1) == 0\n");
#endif
match = 0;
indel_s1 = -LGP;
indel_s2 = -LGP;
}
else if ((x - 1) == 0) //Condizione a contorno
{
#ifdef DEBUG
printf("(x - 1) == 0\n");
#endif
match = -LGP * (y - 1);
indel_s1 = m[conv(b, x, y - 1)].cell;
indel_s2 = -LGP * y;
}
else if ((y - 1) == 0) //Condizione a contorno
{
#ifdef DEBUG
printf("(y - 1) == 0\n");
#endif
match = -LGP * (x - 1);
indel_s1 = -LGP * x;
indel_s2 = m[conv(b, x - 1, y)].cell;
}
else //Caso generico
{
#ifdef DEBUG
printf("else\n");
#endif
match = m[conv(b, x - 1, y - 1)].cell;
if ((x == r.dx && (r.dx - r.sx + 1) < (b.base + 2 * b.extra)) || (x < r.dx))
{
indel_s1 = m[conv(b, x, y - 1)].cell;
}
else
{
indel_s1 = INT16_MIN;
}
indel_s2 = m[conv(b, x - 1, y)].cell;
}
#ifdef DEBUG
printf("result pre incremento: match : %d, indel_s1 : %d, indel_s2 : %d\n", match, indel_s1, indel_s2);
#endif
//Aggiungo i relativi score
match += score(s1[y - 1], s2[x - 1]);
indel_s1 += score('*', s2[x - 1]);
indel_s2 += score(s1[y - 1], '*');
tp->cell = max(match, indel_s1, indel_s2); //Trovo il massimo
#ifdef DEBUG
printf("result: match : %d, indel_s1 : %d, indel_s2 : %d\n", match, indel_s1, indel_s2);
#endif
//Set predecessore e successore in base al caso in cui mi trovo
if (match == tp->cell)
{
tp->prev_x = x - 1;
tp->prev_y = y - 1;
}
else if (indel_s1 == tp->cell)
{
tp->prev_x = x;
tp->prev_y = y - 1;
}
else //if (indel_s2 == tp->cell)
{
tp->prev_x = x - 1;
tp->prev_y = y;
}
#ifdef DEBUG
printf("result: %d, %ld, %ld\n", m[conv(b, x, y)].cell, m[conv(b, x, y)].prev_x, m[conv(b, x, y)].prev_y);
#endif
}
}
uint64_t x = l2;
uint64_t y = l1;
#ifdef DEBUG
printf("StepC: Reconstruction\n");
#endif
//Controllo di non essere sul "bordo" dala banda
for (cell_s c = m[conv(b, x, y)]; x != 0 && y != 0; x = c.prev_x, y = c.prev_y, c = m[conv(b, x, y)])
{
#ifdef DEBUG
printf("StepC: %ld,%ld,%d,%ld,%ld=%c%c\n", x, y, c.cell, c.prev_x, c.prev_y, s1[y-1], s2[x-1]);
#endif
range_s r = range(b, y);
if (x == r.sx && r.sx > 0 || x == r.dx && r.dx < l2)
{
printf("Hai raggiunto il confine della banda\n");
free(m);
return -1;
}
}
x = l2;
y = l1;
uint64_t i = 0;
//Costruzione risultato
for (cell_s c = m[conv(b, x, y)]; x != 0 && y != 0; x = c.prev_x, y = c.prev_y, c = m[conv(b, x, y)])
{
#ifdef DEBUG
printf("%ld, %ld\n", x, y);
#endif
if (x != c.prev_x && y != c.prev_y)
{
allignment_s1[i] = s1[y - 1];
allignment_s2[i] = s2[x - 1];
}
else if(y == c.prev_y)
{
allignment_s1[i] = '-';
allignment_s2[i] = s2[x - 1];
}
else
{
allignment_s2[i] = '-';
allignment_s1[i] = s1[y - 1];
}
i++;
}
if (x == 0)
{
while (y != 0)
{
#ifdef DEBUG
printf("%ld, %ld\n", x, y);
#endif
allignment_s2[i] = '-';
allignment_s1[i] = s1[y - 1];
i++;
y--;
}
}
if (y == 0)
{
while (x != 0)
{
#ifdef DEBUG
printf("%ld, %ld\n", x, y);
#endif
allignment_s1[i] = '-';
allignment_s2[i] = s2[x - 1];
i++;
x--;
}
}
allignment_s1[i] = '\0';
allignment_s2[i] = '\0';
int tot_score = m[conv(b, l2, l1)].cell;
reverse(allignment_s1);
reverse(allignment_s2);
free(m);
return tot_score;
}
void swap(char *str1, char *str2)
{
char temp[BUZZ_SIZE];
strcpy(temp, str1);
strcpy(str1, str2);
strcpy(str2, temp);
}
int main(int argc, char const *argv[])
{
char s1[BUZZ_SIZE];
char s2[BUZZ_SIZE];
char allignment_s1[2 * BUZZ_SIZE] = "\0";
char allignment_s2[2 * BUZZ_SIZE] = "\0";
read_text(s1, s2);
to_upper_case(s1);
to_upper_case(s2);
assert(string_analizer(s1) && "La striga s1 assume valori non concessi");
assert(string_analizer(s2) && "La striga s2 assume valori non concessi");
if (strlen(s2) < strlen(s1))
{
swap(s1, s2);
#ifdef DEBUG
printf("len1, len2 : %ld %ld\n", strlen(s1), strlen(s2));
printf("s1, s2: %s,%s\n", s1, s2);
#endif
}
uint64_t l1 = strlen(s1);
uint64_t l2 = strlen(s2);
uint64_t base = l2 - l1 + 1;
uint64_t extra = 1;
#ifdef DEBUG
printf("Instance lengths: %ld,%ld\n", l1, l2);
#endif
int ret_val = -1;
int p_ret_val = band_align(base, 0, s1, s2, allignment_s1, allignment_s2);
//Allineamento con banda
for(;base + 2 * extra <= l2 + 1 && (ret_val != p_ret_val || ret_val == -1); extra *= 2)
{
printf("\n\nStep:\nbase : %ld, extra : %ld, LGP : %d, width : %ld\n", base, extra, LGP, base + 2 * extra);
p_ret_val = ret_val;
ret_val = band_align(base, extra, s1, s2, allignment_s1, allignment_s2);
}
if (ret_val == -1) //Provo con banda massima
{
printf("\n\nStep max:\nbase : %ld, extra : %ld, LGP : %d, width : %ld\n", base, l1, LGP, base + 2 * l1);
ret_val = band_align(base, l1, s1, s2, allignment_s1, allignment_s2);
}
printf("\nRicostruzione avvenuta\n\n");
printf("%s\n", allignment_s1);
printf("%s\n", allignment_s2);
printf("score : %d\n", ret_val);
return 0;
}