102 #define h(i,j) (H[((i)*(size[1]+1))+(j)])
107 #define xback(i,j) (xTraceback[((i)*(size[1]+1))+(j)])
108 #define yback(i,j) (yTraceback[((i)*(size[1]+1))+(j)])
134 int main(
int argc,
char * argv[]){
154 double time_comp_read = 0;
155 double time_comp_hmatrix = 0;
156 double time_comp_back = 0;
174 p1 = malloc(
sizeof(
aa_t)*((
size_t)(
size[0]+1)));
175 p2 = malloc(
sizeof(
aa_t)*((
size_t)(
size[1]+1)));
180 H = malloc(
sizeof(
h_t)*(
size_t)((
size[0]+1)*(
size[1]+1)));
209 printf(
"=== Iteration: %d/%d ===\n\n",iter,iterations);
218 time_comp_read += (time_phaseE-time_phaseS);
226 time_comp_hmatrix += (time_phaseE-time_phaseS);
234 time_comp_back += (time_phaseE-time_phaseS);
247 printf(
"=== Result ===\n");
248 printf(
"Init time: %f\n",time_initE-time_initS);
249 printf(
"Comp time: %f\n",time_compE-time_compS);
250 printf(
" Read: %f\n",time_comp_read);
251 printf(
" H matrix: %f\n",time_comp_hmatrix);
252 printf(
" Backtracking: %f\n\n",time_comp_back);
268 printf(
"\nInputset too big to print to stdout\n");
272 printf(
"\nSmall inputset, it has been rewinded:\n"
323 for (i=0;i<=
size[0];i++){
329 for (j=0;j<=
size[1];j++){
342 for(i=1; i<
size[0]+1; i++){
343 for(j=1; j<size[1]+1; j++){
352 h_t max = MAX4(diag,down,right,0,&idx);
359 }
else if ( idx == 1 ) {
362 }
else if ( idx == 2 ) {
385 for (j=0;j<=size[1];j++){
389 printf(
"%6c",AA2char(
p2[j]));
392 for (i=0;i<=size[0];i++){
397 printf(
"%c |",AA2char(
p1[i]));
399 for (j=0;j<=size[1];j++){
400 printf(
"%6.1f",(
double)
h(i,j));
411 for (j=0;j<=size[1];j++){
415 printf(
"%8c",AA2char(
p2[j]));
418 for (i=0;i<=size[0];i++){
423 printf(
"%c |",AA2char(
p1[i]));
425 for (j=0;j<=size[1];j++){
445 int pos=size[0]+size[1]+1;
448 while (i>0 && j>0 &&
h(i,j) > 0){
450 int movex = (i>
xback(i,j));
451 int movey = (j>
yback(i,j));
456 if (movex && movey) {
470 i=
xback(tempi,tempj);
471 j=
yback(tempi,tempj);
void printProteinMatch(HitTile_aa_t p, int begin, int end)
void closeProtein(ProteinFile *fprotein)
void readProtein(ProteinFile *fprotein, HitTile_aa_t *protein, int psize)
#define CHECK_NULL(check)
void openProtein(ProteinFile *fprotein, char *filename)
void input_parameters(int argc, char *argv[])
HitTile_trace_t yTraceback
void initPAM(char *filename)
void printProtein(HitTile_aa_t p, int offset, int psize)
HitTile_trace_t xTraceback
int main(int argc, char *argv[])
void phase_read_sequences()
void phase_comp_hmatrix()