void print_lav_job_header
(FILE* f,
char* _programName,
char* _name1,
char* _name2,
char* _args,
scoreset* scoring,
sthresh* hspThreshold,
sthresh* gappedThreshold,
u8 dynamicMasking)
{
char* programName = _programName;
char* name1 = _name1;
char* name2 = _name2;
char* args = _args;
if (programName == NULL) programName = "(no name)";
if (name1 == NULL) name1 = "(no name)";
if (name2 == NULL) name2 = "(no name)";
if (args == NULL) args = "";
fprintf (f, "#:lav\n");
fprintf (f, "d {\n");
fprintf (f, " \"%s %s %s %s\n", programName, name1, name2, args);
print_score_matrix (f, scoring, false);
fprintf (f, " O = " scoreFmtSimple
", E = " scoreFmtSimple
", K = %s"
", L = %s"
", M = %d\"\n",
scoring->gapOpen, scoring->gapExtend,
score_thresh_to_string (hspThreshold),
score_thresh_to_string (gappedThreshold),
dynamicMasking);
fprintf (f, "}\n");
}
int main(int argc,char *argv[]) {
char alphabet[21] = "acdefghiklmnpqrstvwy";
char *seq1;
char *seq2;
if (argc < 3) {
printf("You need 2 arguments\n");
return 0 ;
} else {
seq1 = argv[1] ;
seq2 = argv[2] ;
}
printf("seq1 = %s\n", seq1);
printf("seq2 = %s\n", seq2);
int seq1_length = 0 ;
int seq2_length = 0;
while (seq1[seq1_length] != '\0') {
seq1_length++;
}
printf("seq1_length = %d\n", seq1_length );
while (seq2[seq2_length] != '\0') {
seq2_length++;
}
printf("seq2_length = %d\n", seq2_length );
// char *seq1 = "ppeaiccc";
// char *seq2 = "ggeaicgg";
int seq1_arr[seq1_length], seq2_arr[seq2_length] ;
int i, j;
int score_matrix[seq2_length+1][seq1_length+1] ;
int direction_matrix[seq2_length+1][seq1_length+1] ;
int max_i=-1, max_j=-1, max_score=-1 ;
int diagonal_score, left_score, up_score ;
int letter1, letter2;
/* Convert residue characters to indices */
printf("STRLEN = %d\n", STRLEN);
printf("d_loc = %d\n", STRLEN);
printf("seq1 = %s\n", seq1);
printf("seq2 = %s\n", seq2);
for (i=0; i < seq1_length; i++)
for (j=0; j<20; j++)
if (seq1[i] == alphabet[j])
seq1_arr[i] = j;
for (i=0; i < seq2_length; i++)
for (j=0; j<20; j++)
if (seq2[i] == alphabet[j])
seq2_arr[i] = j;
for (j=0; j <= seq1_length; j++) {
score_matrix[0][j] = 0;
direction_matrix[0][j] = DIRECTION_NONE;
}
printf("rows = seq1_length = %d\n", seq1_length);
for (i=0; i <= seq2_length; i++ ) {
score_matrix[i][0] = 0;
direction_matrix[i][0] = DIRECTION_NONE;
}
printf("cols = seq2_length = %d\n", seq2_length);
for (i=1; i <= seq2_length; i++) {
for (j=1; j <= seq1_length; j++) {
diagonal_score=0;
left_score=0;
up_score=0;
letter1 = seq1_arr[i-1];
letter2 = seq2_arr[j-1];
// calculate match score
if (letter1 == letter2) {
diagonal_score = score_matrix[i-1][j-1] + MATCH;
}
else {
diagonal_score = score_matrix[i-1][j-1] + MISMATCH;
}
// calculate gap scores
up_score = score_matrix[i-1][j] + GAP;
left_score = score_matrix[i][j-1] + GAP;
// if (i==1 && j==1) {
// printf("[%d,%d] diagonal_score: %d, up_score: %d, left_score: %d, letter1=%d, letter2=%d \n", i, j, diagonal_score, up_score, left_score, letter1, letter2 );
// printf("%d [%d,%d] diagonal_score: %d, up_score: %d, left_score: %d,letter1=%d, letter2=%d \n", ARRAY_OFFSET(i,j,ncols), i, j, diagonal_score,
// up_score, left_score, letter1, letter2 );
// }
if ((diagonal_score <= 0) && (up_score <= 0) && (left_score <= 0)) {
score_matrix[i][j] = 0;
// printf("[%d,%d] diagonal_score: %d, up_score: %d, left_score: %d, score_matrix:%d \n", i, j, diagonal_score, up_score, left_score, score_matrix[i][j]);
direction_matrix[i][j] = DIRECTION_NONE;
continue;
}
// choose best score
if (diagonal_score >= up_score) {
if (diagonal_score >= left_score) {
score_matrix[i][j] = diagonal_score;
direction_matrix[i][j] = DIRECTION_DIAGONAL;
//$matrix[$i][$j]{pointer} = "diagonal";
}
else {
score_matrix[i][j] = left_score;
direction_matrix[i][j] = DIRECTION_LEFT;
//$matrix[$i][$j]{pointer} = "left";
}
} else {
if (up_score >= left_score) {
score_matrix[i][j] = up_score;
direction_matrix[i][j] = DIRECTION_UP;
//$matrix[$i][$j]{pointer} = "up";
}
else {
score_matrix[i][j] = left_score;
direction_matrix[i][j] = DIRECTION_LEFT;
//$matrix[$i][$j]{pointer} = "left";
}
}
// printf("[%d,%d] diagonal_score: %d, up_score: %d, left_score: %d, score_matrix:%d \n", i, j, diagonal_score, up_score, left_score, score_matrix[i][j]);
// set maximum score
if (score_matrix[i][j] > max_score) {
max_i = i;
max_j = j;
max_score = score_matrix[i][j];
}
}
}
printf("max_i = %d\n", max_i);
printf("max_j = %d\n", max_j);
printf("max_score = %d\n", max_score);
// for (i=0; i <= seq2_length; i++) {
// for (j=0; j <= seq1_length; j++) {
//// printf("score_matrix[%d][%d] %d\n", i,j, score_matrix[i][j] );
// }
// }
print_score_matrix(&score_matrix[0][0], seq2_length+1, seq1_length+1 );
print_score_matrix(&direction_matrix[0][0], seq2_length+1, seq1_length+1 );
printf("finished printing score matrix= %d\n", max_score);
// trace-back
//char align1[SEQ1_LEN] = "ppeaiccc";
//char align2[SEQ1_LEN] = "ppeaiccc";
int align1_arr[seq1_length], align2_arr[seq2_length] ;
//align1 = "";
//align2 = "";
j = max_j;
i = max_i;
int align1_index=0;
int align2_index=0;
while (1) {
if (direction_matrix[i][j] == DIRECTION_NONE)
break ;
if (direction_matrix[i][j] == DIRECTION_DIAGONAL ) {
align1_arr[align1_index] = seq1_arr[j-1] ;
align2_arr[align2_index] = seq2_arr[i-1] ;
// $align1 .= substr($seq1, $j-1, 1);
// $align2 .= substr($seq2, $i-1, 1);
i--;
j--;
}
else if (direction_matrix[i][j] == DIRECTION_LEFT ) {
align1_arr[align1_index] = seq1_arr[j-1] ;
align2_arr[align2_index] = -1 ;
// $align1 .= substr($seq1, $j-1, 1);
// $align2 .= "-";
j--;
}
else if (direction_matrix[i][j] == DIRECTION_UP ) {
align1_arr[align1_index] = -1;
align2_arr[align2_index] = seq2_arr[i-1] ;
// align1 .= "-";
// align2 .= substr($seq2, $i-1, 1);
i--;
}
align1_index++;
align2_index++;
}
printf("align1_index = %d, align2_index = %d\n", align1_index, align2_index);
char *align1 ;
char *align2;
align1 = (char *) calloc(seq1_length,sizeof(char) ) ;
align2 = (char *) calloc(seq2_length,sizeof(char) ) ;
for(i=0; i<align1_index; i++) {
align1[align1_index-i-1] = alphabet[align1_arr[i]] ;
}
printf("align1 = %s\n", align1);
printf("align2 = %s\n", align1);
/*
$align1 = reverse $align1;
$align2 = reverse $align2;
print "$align1\n";
print "$align2\n"
*/
return 1;
}
