int pairalign_seq(int istart, int iend, int jstart, int jend)
{
int i, n, m, si, sj;
int len1, len2, maxres;
double gg, mm_score;
int *mat_xref, *matptr;
matptr = gon250mt;
mat_xref = def_aa_xref;
maxres = get_matrix(matptr, mat_xref, 10);
if (maxres == 0) return(-1);
for (si = 0; si < nseqs; si++) {
if ((n = seqlen_array[si+1]) != 0){
for (i = 1, len1 = 0; i <= n; i++) {
char c = seq_array[si+1][i];
if ((c != gap_pos1) && (c != gap_pos2)) len1++;
}
for (sj = si + 1; sj < nseqs; sj++) {
if ((m = seqlen_array[sj+1]) != 0){
int se1, se2, sb1, sb2, maxscore, seq1, seq2, g, gh;
int displ[2*MAX_ALN_LENGTH+1];
int print_ptr, last_print;
for (i = 1, len2 = 0; i <= m; i++) {
char c = seq_array[sj+1][i];
if ((c != gap_pos1) && (c != gap_pos2)) len2++;
}
gh = 10 * pw_ge_penalty;
gg = pw_go_penalty + log((double) MIN(n, m));
g = (mat_avscore <= 0) ? 20 * gg : 2 * mat_avscore * gg;
seq1 = si + 1;
seq2 = sj + 1;
forward_pass(&seq_array[seq1][0], &seq_array[seq2][0], n, m, &se1, &se2, &maxscore, g, gh);
reverse_pass(&seq_array[seq1][0], &seq_array[seq2][0], se1, se2, &sb1, &sb2, maxscore, g, gh);
print_ptr = 1;
last_print = 0;
diff(sb1-1, sb2-1, se1-sb1+1, se2-sb2+1, 0, 0, &print_ptr, &last_print, displ, seq1, seq2, g, gh);
mm_score = tracepath(sb1, sb2, &print_ptr, &last_print, displ, seq1, seq2);
if (len1 == 0 || len2 == 0) mm_score = 0.0;
else mm_score /= (double) MIN(len1,len2);
seq_output[si*nseqs+sj] = mm_score;
}
}
}
}
return 0;
}
sint pairalign(sint istart, sint iend, sint jstart, sint jend)
{
short *mat_xref;
static sint si, sj, i;
static sint n,m,len1,len2;
static sint maxres;
static short *matptr;
static char c;
static float gscale,ghscale;
displ = (sint *)ckalloc((2*max_aln_length+1) * sizeof(sint));
HH = (pwint *)ckalloc((max_aln_length) * sizeof(pwint));
DD = (pwint *)ckalloc((max_aln_length) * sizeof(pwint));
RR = (pwint *)ckalloc((max_aln_length) * sizeof(pwint));
SS = (pwint *)ckalloc((max_aln_length) * sizeof(pwint));
#ifdef MAC
int_scale = 10;
#else
int_scale = 100;
#endif
gscale=ghscale=1.0;
if (dnaflag)
{
if (debug>1) fprintf(stdout,"matrix %s\n",pw_dnamtrxname);
if (strcmp(pw_dnamtrxname, "iub") == 0)
{
matptr = swgapdnamt;
mat_xref = def_dna_xref;
}
else if (strcmp(pw_dnamtrxname, "clustalw") == 0)
{
matptr = clustalvdnamt;
mat_xref = def_dna_xref;
gscale=0.6667;
ghscale=0.751;
}
else
{
matptr = pw_userdnamat;
mat_xref = pw_dna_xref;
}
maxres = get_matrix(matptr, mat_xref, matrix, TRUE, int_scale);
if (maxres == 0) return((sint)-1);
matrix[0][4]=transition_weight*matrix[0][0];
matrix[4][0]=transition_weight*matrix[0][0];
matrix[2][11]=transition_weight*matrix[0][0];
matrix[11][2]=transition_weight*matrix[0][0];
matrix[2][12]=transition_weight*matrix[0][0];
matrix[12][2]=transition_weight*matrix[0][0];
}
else
{
if (debug>1) fprintf(stdout,"matrix %s\n",pw_mtrxname);
if (strcmp(pw_mtrxname, "blosum") == 0)
{
matptr = blosum30mt;
mat_xref = def_aa_xref;
}
else if (strcmp(pw_mtrxname, "pam") == 0)
{
matptr = pam350mt;
mat_xref = def_aa_xref;
}
else if (strcmp(pw_mtrxname, "gonnet") == 0)
{
matptr = gon250mt;
int_scale /= 10;
mat_xref = def_aa_xref;
}
else if (strcmp(pw_mtrxname, "id") == 0)
{
matptr = idmat;
mat_xref = def_aa_xref;
}
else
{
matptr = pw_usermat;
mat_xref = pw_aa_xref;
}
maxres = get_matrix(matptr, mat_xref, matrix, TRUE, int_scale);
if (maxres == 0) return((sint)-1);
}
for (si=MAX(0,istart);si<nseqs && si<iend;si++)
{
n = seqlen_array[si+1];
len1 = 0;
for (i=1;i<=n;i++) {
c = seq_array[si+1][i];
if ((c!=gap_pos1) && (c != gap_pos2)) len1++;
}
for (sj=MAX(si+1,jstart+1);sj<nseqs && sj<jend;sj++)
{
m = seqlen_array[sj+1];
if(n==0 || m==0) {
tmat[si+1][sj+1]=1.0;
tmat[sj+1][si+1]=1.0;
continue;
}
len2 = 0;
for (i=1;i<=m;i++) {
c = seq_array[sj+1][i];
if ((c!=gap_pos1) && (c != gap_pos2)) len2++;
}
if (dnaflag) {
g = 2 * (float)pw_go_penalty * int_scale*gscale;
gh = pw_ge_penalty * int_scale*ghscale;
}
else {
if (mat_avscore <= 0)
g = 2 * (float)(pw_go_penalty + log((double)(MIN(n,m))))*int_scale;
else
g = 2 * mat_avscore * (float)(pw_go_penalty +
log((double)(MIN(n,m))))*gscale;
gh = pw_ge_penalty * int_scale;
}
if (debug>1) fprintf(stdout,"go %d ge %d\n",(pint)g,(pint)gh);
/*
align the sequences
*/
seq1 = si+1;
seq2 = sj+1;
forward_pass(&seq_array[seq1][0], &seq_array[seq2][0],
n, m);
reverse_pass(&seq_array[seq1][0], &seq_array[seq2][0]);
last_print = 0;
print_ptr = 1;
/*
sb1 = sb2 = 1;
se1 = n-1;
se2 = m-1;
*/
/* use Myers and Miller to align two sequences */
maxscore = diff(sb1-1, sb2-1, se1-sb1+1, se2-sb2+1,
(sint)0, (sint)0);
/* calculate percentage residue identity */
mm_score = tracepath(sb1,sb2);
if(len1==0 || len2==0) mm_score=0;
else
mm_score /= (float)MIN(len1,len2);
tmat[si+1][sj+1] = ((float)100.0 - mm_score)/(float)100.0;
tmat[sj+1][si+1] = ((float)100.0 - mm_score)/(float)100.0;
if (debug>1)
{
fprintf(stdout,"Sequences (%d:%d) Aligned. Score: %d CompScore: %d\n",
(pint)si+1,(pint)sj+1,
(pint)mm_score,
(pint)maxscore/(MIN(len1,len2)*100));
}
else
{
info("Sequences (%d:%d) Aligned. Score: %d",
(pint)si+1,(pint)sj+1,
(pint)mm_score);
}
}
}
displ=ckfree((void *)displ);
HH=ckfree((void *)HH);
DD=ckfree((void *)DD);
RR=ckfree((void *)RR);
SS=ckfree((void *)SS);
return((sint)1);
}
int pairalign(int istart, int iend, int jstart, int jend)
{
int i, n, m, si, sj;
int len1, len2, maxres;
double gg, mm_score;
int *mat_xref, *matptr;
matptr = gon250mt;
mat_xref = def_aa_xref;
maxres = get_matrix(matptr, mat_xref, 10);
if (maxres == 0) return(-1);
bots_message("Start aligning ");
#pragma omp parallel
{
#pragma omp single private(i,n,si,sj,len1,m)
for (si = 0; si < nseqs; si++) {
if ((n = seqlen_array[si+1]) != 0){
for (i = 1, len1 = 0; i <= n; i++) {
char c = seq_array[si+1][i];
if ((c != gap_pos1) && (c != gap_pos2)) len1++;
}
for (sj = si + 1; sj < nseqs; sj++)
{
if ((m = seqlen_array[sj+1]) != 0)
{
#pragma omp task untied \
private(i,gg,len2,mm_score) firstprivate(m,n,si,sj,len1) \
shared(nseqs, bench_output,seqlen_array,seq_array,gap_pos1,gap_pos2,pw_ge_penalty,pw_go_penalty,mat_avscore)
{
int se1, se2, sb1, sb2, maxscore, seq1, seq2, g, gh;
int displ[2*MAX_ALN_LENGTH+1];
int print_ptr, last_print;
for (i = 1, len2 = 0; i <= m; i++) {
char c = seq_array[sj+1][i];
if ((c != gap_pos1) && (c != gap_pos2)) len2++;
}
gh = 10 * pw_ge_penalty;
gg = pw_go_penalty + log((double) MIN(n, m));
g = (mat_avscore <= 0) ? 20 * gg : 2 * mat_avscore * gg;
seq1 = si + 1;
seq2 = sj + 1;
forward_pass(&seq_array[seq1][0], &seq_array[seq2][0], n, m, &se1, &se2, &maxscore, g, gh);
reverse_pass(&seq_array[seq1][0], &seq_array[seq2][0], se1, se2, &sb1, &sb2, maxscore, g, gh);
print_ptr = 1;
last_print = 0;
diff(sb1-1, sb2-1, se1-sb1+1, se2-sb2+1, 0, 0, &print_ptr, &last_print, displ, seq1, seq2, g, gh);
mm_score = tracepath(sb1, sb2, &print_ptr, &last_print, displ, seq1, seq2);
if (len1 == 0 || len2 == 0) mm_score = 0.0;
else mm_score /= (double) MIN(len1,len2);
bench_output[si*nseqs+sj] = mm_score;
}
}
}
}
}
}
bots_message(" completed!\n");
return 0;
}
