void nj(double *D, int *N, int *edge1, int *edge2, double *edge_length)
{
double *S, Sdist, Ndist, *new_dist, A, B, smallest_S, x, y;
int n, i, j, k, ij, smallest, OTU1, OTU2, cur_nod, o_l, *otu_label;
S = &Sdist;
new_dist = &Ndist;
otu_label = &o_l;
n = *N;
cur_nod = 2*n - 2;
S = (double*)R_alloc(n + 1, sizeof(double));
new_dist = (double*)R_alloc(n*(n - 1)/2, sizeof(double));
otu_label = (int*)R_alloc(n + 1, sizeof(int));
for (i = 1; i <= n; i++) otu_label[i] = i; /* otu_label[0] is not used */
k = 0;
while (n > 3) {
for (i = 1; i <= n; i++)
S[i] = sum_dist_to_i(n, D, i); /* S[0] is not used */
ij = 0;
smallest_S = 1e50;
B = n - 2;
for (i = 1; i < n; i++) {
for (j = i + 1; j <= n; j++) {
A = B*D[ij] - S[i] - S[j];
if (A < smallest_S) {
OTU1 = i;
OTU2 = j;
smallest_S = A;
smallest = ij;
}
ij++;
}
}
edge2[k] = otu_label[OTU1];
edge2[k + 1] = otu_label[OTU2];
edge1[k] = edge1[k + 1] = cur_nod;
/* get the distances between all OTUs but the 2 selected ones
and the latter:
a) get the sum for both
b) compute the distances for the new OTU */
A = D[smallest];
ij = 0;
for (i = 1; i <= n; i++) {
if (i == OTU1 || i == OTU2) continue;
x = D[give_index(i, OTU1, n)]; /* dist between OTU1 and i */
y = D[give_index(i, OTU2, n)]; /* dist between OTU2 and i */
new_dist[ij] = (x + y - A)/2;
ij++;
}
/* compute the branch lengths */
B = (S[OTU1] - S[OTU2])/B; /* don't need B anymore */
edge_length[k] = (A + B)/2;
edge_length[k + 1] = (A - B)/2;
/* update before the next loop
(we are sure that OTU1 < OTU2) */
if (OTU1 != 1)
for (i = OTU1; i > 1; i--)
otu_label[i] = otu_label[i - 1];
if (OTU2 != n)
for (i = OTU2; i < n; i++)
otu_label[i] = otu_label[i + 1];
otu_label[1] = cur_nod;
for (i = 1; i < n; i++) {
if (i == OTU1 || i == OTU2) continue;
for (j = i + 1; j <= n; j++) {
if (j == OTU1 || j == OTU2) continue;
new_dist[ij] = D[DINDEX(i, j)];
ij++;
}
}
n--;
for (i = 0; i < n*(n - 1)/2; i++) D[i] = new_dist[i];
cur_nod--;
k = k + 2;
}
for (i = 0; i < 3; i++) {
edge1[*N*2 - 4 - i] = cur_nod;
edge2[*N*2 - 4 - i] = otu_label[i + 1];
}
edge_length[*N*2 - 4] = (D[0] + D[1] - D[2])/2;
edge_length[*N*2 - 5] = (D[0] + D[2] - D[1])/2;
edge_length[*N*2 - 6] = (D[2] + D[1] - D[0])/2;
}
void ape_nj(double *D, int *N, int *edge1, int *edge2, double *edge_length)
{
double *S, Sdist, Ndist, *new_dist, A, B, smallest_S, *DI, d_i, x, y;
int n, i, j, k, ij, smallest, OTU1, OTU2, cur_nod, o_l, *otu_label;
OTU1 = 0;
OTU2 = 0;
smallest = 0;
S = &Sdist;
new_dist = &Ndist;
otu_label = &o_l;
DI = &d_i;
n = *N;
cur_nod = 2*n - 2;
/*
S = (double*)R_alloc(n, sizeof(double));
new_dist = (double*)R_alloc(n*(n - 1)/2, sizeof(double));
otu_label = (int*)R_alloc(n, sizeof(int));
DI = (double*)R_alloc(n - 2, sizeof(double));
*/
S = (double*) malloc(n * sizeof(double));
new_dist = (double*) malloc(n*(n - 1)/2 * sizeof(double));
otu_label = (int*) malloc(n * sizeof(int));
DI = (double*) malloc((n - 2) * sizeof(double));
if(S == NULL || new_dist == NULL || otu_label == NULL || DI == NULL){
printf("Memory allocation fails!\n");
exit(1);
}
for (i = 0; i < n; i++) otu_label[i] = i + 1;
k = 0;
while (n > 3) {
for (i = 0; i < n; i++)
S[i] = sum_dist_to_i(n, D, i + 1);
ij = 0;
smallest_S = 1e50;
B = n - 2;
for (i = 0; i < n - 1; i++) {
for (j = i + 1; j < n; j++) {
A = D[ij] - (S[i] + S[j])/B;
if (A < smallest_S) {
OTU1 = i + 1;
OTU2 = j + 1;
smallest_S = A;
smallest = ij;
}
ij++;
}
}
edge2[k] = otu_label[OTU1 - 1];
edge2[k + 1] = otu_label[OTU2 - 1];
edge1[k] = edge1[k + 1] = cur_nod;
/* get the distances between all OTUs but the 2 selected ones
and the latter:
a) get the sum for both
b) compute the distances for the new OTU */
A = B = ij = 0;
for (i = 1; i <= n; i++) {
if (i == OTU1 || i == OTU2) continue;
x = D[give_index(i, OTU1, n)]; /* dist between OTU1 and i */
y = D[give_index(i, OTU2, n)]; /* dist between OTU2 and i */
new_dist[ij] = (x + y)/2;
A += x;
B += y;
ij++;
}
/* compute the branch lengths */
A /= n - 2;
B /= n - 2;
edge_length[k] = (D[smallest] + A - B)/2;
edge_length[k + 1] = (D[smallest] + B - A)/2;
DI[cur_nod - *N - 1] = D[smallest];
/* update before the next loop */
if (OTU1 > OTU2) { /* make sure that OTU1 < OTU2 */
i = OTU1;
OTU1 = OTU2;
OTU2 = i;
}
if (OTU1 != 1)
for (i = OTU1 - 1; i > 0; i--)
otu_label[i] = otu_label[i - 1];
if (OTU2 != n)
for (i = OTU2; i < n; i++)
otu_label[i - 1] = otu_label[i];
otu_label[0] = cur_nod;
for (i = 1; i < n; i++) {
if (i == OTU1 || i == OTU2) continue;
for (j = i + 1; j <= n; j++) {
if (j == OTU1 || j == OTU2) continue;
new_dist[ij] = D[DINDEX(i, j)];
ij++;
}
}
n--;
for (i = 0; i < n*(n - 1)/2; i++) D[i] = new_dist[i];
cur_nod--;
k = k + 2;
}
for (i = 0; i < 3; i++) {
edge1[*N*2 - 4 - i] = cur_nod;
edge2[*N*2 - 4 - i] = otu_label[i];
}
edge_length[*N*2 - 4] = (D[0] + D[1] - D[2])/2;
edge_length[*N*2 - 5] = (D[0] + D[2] - D[1])/2;
edge_length[*N*2 - 6] = (D[2] + D[1] - D[0])/2;
for (i = 0; i < *N*2 - 3; i++) {
if (edge2[i] <= *N) continue;
/* In case there are zero branch lengths: */
if (DI[edge2[i] - *N - 1] == 0) continue;
edge_length[i] -= DI[edge2[i] - *N - 1]/2;
}
free(S);
free(new_dist);
free(otu_label);
free(DI);
} /* End of ape_nj(). */
