obj rs_save_image_file( obj root, obj ref_vec, obj ref_names,
obj rplc, obj out_info )
{
int i;
obj *save, result, output_id;
char *outfile_name = NULL;
FILE *outfile_strm = NULL;
/* Phase 1 --- Setup */
if (STRING_P(out_info))
{
outfile_name = string_text(out_info);
outfile_strm = fopen( outfile_name, "wb" );
if (!outfile_strm)
{
scheme_error( "~a: error opening image output", 1, out_info );
}
}
for (i=0; i<NUM_CLASS_MODES; i++)
hi_init_queue( &image_modes[i].queue );
hi_init_queue( &used_refs );
if (OBJ_ISA_PTR(rplc))
setup_replacement_objects( rplc );
save = setup_reference_objects( ref_vec );
/* Phase 2 --- Traversal */
spot_object( root );
traverse_all();
/* Phase 3 --- Name Assignment */
output_id = OBJ(POINTER_TAG);
output_id = assign_ref_queue_names( &used_refs, output_id );
for (i=0; i<NUM_CLASS_MODES; i++)
output_id = assign_queue_names( &image_modes[i].queue, output_id );
#if DEBUG_SAVE
printf( "%u objects named in output\n", VAL(output_id)>>PRIMARY_TAG_SIZE );
#endif
/* Phase 4 --- Output */
if (outfile_strm)
{
#if DEBUG_SAVE
printf( "writing image to file: \"%s\"\n", outfile_name );
#endif
do_file_output( outfile_strm, ref_vec, ref_names, root );
}
/* Phase 5 --- Cleanup */
for (i=0; i<NUM_CLASS_MODES; i++)
cleanup_queued_objects( &image_modes[i].queue );
cleanup_reference_objects( ref_vec, save );
cleanup_queued_objects( &rplc_queue );
if (EQ(out_info,TRUE_OBJ))
result = do_vector_output();
else
result = TRUE_OBJ;
for (i=0; i<NUM_CLASS_MODES; i++)
hi_free_queue( &image_modes[i].queue );
clear_part_descr_labels( &used_refs );
hi_free_queue( &used_refs );
return result;
}
int neighbor_joining(matrix *distance, tree_s *out_tree) {
size_t matrix_size = distance->size;
if (matrix_size < 3 || !out_tree) return -2;
int check;
check = tree_init(out_tree, matrix_size);
if (check) return check;
tree_node *node_pool = out_tree->pool;
tree_node *empty_node_ptr = &node_pool[matrix_size];
tree_node **unjoined_nodes = malloc(matrix_size * sizeof(tree_node *));
CHECK_MALLOC(unjoined_nodes);
size_t n = matrix_size;
size_t i, j;
for (i = 0; i < n; i++) {
node_pool[i] = LEAF(i);
unjoined_nodes[i] = &node_pool[i];
}
double r[matrix_size];
matrix local_copy;
check = matrix_copy(&local_copy, distance);
assert(check == 0);
assert(local_copy.size == distance->size);
assert(memcmp(local_copy.data, distance->data,
matrix_size * matrix_size * sizeof(double)) == 0);
#define M(I, J) (MATRIX_CELL(local_copy, I, J))
while (n > 3) {
for (i = 0; i < n; i++) {
double rr = 0.0;
for (j = 0; j < n; j++) {
if (i == j) assert(M(i, j) == 0.0);
assert(M(i, j) == M(j, i));
rr += M(i, j);
}
r[i] = rr / (double)(n - 2);
}
size_t min_i = 0, min_j = 1;
double min_value = M(0, 1) - r[0] - r[1];
for (i = 0; i < n; i++) {
for (j = 0; j < n; j++) {
if (i == j) continue;
double value = M(i, j) - r[i] - r[j];
if (value < min_value) {
min_i = i;
min_j = j;
min_value = value;
}
}
}
// force i < j
if (min_j < min_i) {
size_t temp = min_i;
min_i = min_j;
min_j = temp;
}
tree_node branch = {
.left_branch = unjoined_nodes[min_i],
.right_branch = unjoined_nodes[min_j],
.left_dist = (M(min_i, min_j) + r[min_i] - r[min_j]) / 2.0,
.right_dist = (M(min_i, min_j) - r[min_i] + r[min_j]) / 2.0,
.index = -1};
*empty_node_ptr++ = branch;
unjoined_nodes[min_i] = empty_node_ptr - 1;
unjoined_nodes[min_j] = unjoined_nodes[n - 1];
double row_k[matrix_size];
double M_ij = M(min_i, min_j);
for (size_t m = 0; m < n; m++) {
if (m == min_i || m == min_j) continue;
row_k[m] = (M(min_i, m) + M(min_j, m) - M_ij) / 2.0;
// if( row_k[m] < 0) row_k[m] = 0;
}
// row_k[min_i] and row_k[min_j] are undefined!
row_k[min_i] = 0.0;
row_k[min_j] = row_k[n - 1];
memmove(&M(min_i, 0), row_k, matrix_size * sizeof(double));
memmove(&M(min_j, 0), &M((n - 1), 0), matrix_size * sizeof(double));
M(min_i, min_i) = M(min_j, min_j) = 0.0;
for (i = 0; i < n; i++) {
M(i, min_i) = M(min_i, i);
}
for (i = 0; i < n; i++) {
M(i, min_j) = M(min_j, i);
}
n--;
}
// join three remaining nodes
tree_root root = {.left_branch = unjoined_nodes[0],
.right_branch = unjoined_nodes[1],
.extra_branch = unjoined_nodes[2],
.left_dist = (M(0, 1) + M(0, 2) - M(1, 2)) / 2.0,
.right_dist = (M(0, 1) + M(1, 2) - M(0, 2)) / 2.0,
.extra_dist = (M(0, 2) + M(1, 2) - M(0, 1)) / 2.0};
//*empty_node_ptr++ = root;
out_tree->root = root;
free(unjoined_nodes);
matrix_free(&local_copy);
return 0;
}
void traverse_all(tree_node *current, visitor_ctx *v, void *context) {
if (v->pre) {
v->pre(current, context);
}
if (current->left_branch) {
traverse_all(current->left_branch, v, context);
}
if (v->process) {
v->process(current, context);
}
if (current->right_branch) {
traverse_all(current->right_branch, v, context);
}
if (v->post) {
v->post(current, context);
}
}
void newick_sv_pre(tree_node *current, void *ctx) {
if (current->left_branch) {
printf("(");
}
}
void newick_sv_process(tree_node *current, void *ctx) {
if (current->left_branch) {
if (current->left_branch->left_branch) {
printf("%d:%lf,", (int)(current->left_support * 100),
current->left_dist);
} else {
printf(":%lf,", current->left_dist);
}
} else {
printf("%s", ((char **)ctx)[current->index]);
}
}
void newick_sv_post(tree_node *current, void *ctx) {
if (!current->right_branch) return;
if (current->right_branch->right_branch) {
printf("%d:%lf)", (int)(current->right_support * 100),
current->right_dist);
} else {
printf(":%lf)", current->right_dist);
}
}
void newick_sv(tree_root *root, char **names) {
visitor_ctx v = {.pre = newick_sv_pre,
.process = newick_sv_process,
.post = newick_sv_post};
printf("(");
traverse_all(root->left_branch, &v, names);
newick_sv_process(&root->as_tree_node, names);
traverse_all(root->right_branch, &v, names);
if (root->right_branch && root->right_branch->right_branch) {
printf("%d:%lf,", (int)(root->right_support * 100), root->right_dist);
} else {
printf(":%lf,", root->right_dist);
}
traverse_all(root->extra_branch, &v, names);
if (root->extra_branch && root->extra_branch->left_branch) {
printf("%d:%lf)", (int)(root->extra_support * 100), root->extra_dist);
} else {
printf(":%lf)", root->extra_dist);
}
printf(";\n");
}