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#include <u.h>
#include <libn.h>
#include <libbio.h>
// -----------------------------------------------------------------------
// subtree manipulation methods
// NOTE: As of now these don't update nnode & nleaf stats.
// It is the caller's responsibility to refresh counts.
error
phylo·addchild(bio·Node* parent, bio·Node* child)
{
bio·Node *it, *sibling;
if (!parent->nchild) {
parent->child = child;
goto SUCCESS;
}
for (it = parent->child, sibling = it; it != nil; it = it->sibling) {
sibling = it;
}
sibling->sibling = child;
SUCCESS:
child->parent = parent;
parent->nchild++;
return 0;
}
error
phylo·rmchild(bio·Node *parent, bio·Node *child)
{
bio·Node *it, *prev;
enum {
error·nil,
error·notfound,
error·nochildren,
};
prev = nil;
for (it = parent->child; it != nil; it = it->sibling) {
if (it == child) goto FOUND;
prev = it;
}
return error·notfound;
FOUND:
if (prev == nil) {
parent->child = child->sibling;
} else {
prev->sibling = child->sibling;
}
return error·nil;
}
// -----------------------------------------------------------------------
// subtree statistics
error
phylo·countnodes(bio·Node *node, int *n)
{
int m;
error err;
bio·Node *child;
m = *n;
for (child = node->child; child != nil; child = child->sibling) {
if (err = phylo·countnodes(child, n), err) {
errorf("node count: failure at '%s'", child->name);
return 1;
}
}
node->nnode = *n - m;
*n += 1;
return 0;
}
error
phylo·countleafs(bio·Node *node, int *n)
{
error err;
bio·Node *child;
if (!node->nchild) {
*n += 1;
}
for (child = node->child; child != nil; child = child->sibling) {
if (err = phylo·countleafs(child, n), err) {
errorf("leaf count: failure at '%s'", child->name);
return 1;
}
}
return 0;
}
// -----------------------------------------------------------------------
// tree editing
static
void
sortnodelist(bio·Node **head, bio·Node *next)
{
bio·Node tmp, *it;
it = &tmp;
tmp.sibling = *head;
while (it->sibling != nil && it->sibling->nnode < next->nnode) {
it = it->sibling;
}
next->sibling = it->sibling;
it->sibling = next;
*head = tmp.sibling;
}
error
phylo·ladderize(bio·Node *root)
{
int i;
error err;
bio·Node *child, *sorted, *sibling;
if (!root->nchild) return 0;
// ladderize below
for (child = root->child; child != nil; child = child->sibling) {
if (err = phylo·ladderize(child), err) {
errorf("ladderize: failure at '%s'", child->name);
return 1;
}
}
// ladderize yourself
sorted = nil;
child = root->child;
while (child != nil) {
sibling = child->sibling;
sortnodelist(&sorted, child);
child = sibling;
}
root->child = sorted;
return 0;
}
static
error
rotateparent(bio·Node *node, bio·Node *to)
{
error err;
bio·Node *it, *prev;
if (node->parent == to) {
return 0;
}
prev = nil;
for (it = node->child; it != nil; it = it->sibling) {
if (it == to) goto FOUND;
prev = it;
}
errorf("inconsistent topology: attempting to rotate to non-child");
return 1;
FOUND:
if (err = rotateparent(node->parent, node), err) {
errorf("failure: broken tree");
return err;
}
if (!prev) {
node->child = node->parent;
} else {
prev->sibling = node->parent;
}
node->parent->sibling = it->sibling;
node->parent = to;
return 0;
}
#define FLOAT_PREC .00000001
error
phylo·reroot(bio·Tree *tree, bio·Node *node, double d)
{
bio·Node *old;
bio·Node *new;
// TODO: should check that node is part of this tree?
old = tree->root;
if (fabs(d) < FLOAT_PREC) new = node;
if (fabs(d-node->dist) < FLOAT_PREC) new = node->parent;
else {
new = tree->heap.alloc(tree->h, 1, sizeof(*new));
memset(new, 0, sizeof(*new));
}
// TODO: Use rotateparent() to perform necessary flips
tree->root = new;
return 0;
}
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