/* clone a node */
stTree *stTree_cloneNode(stTree *node) {
stTree *node2 = stTree_construct();
stTree_setBranchLength(node2, stTree_getBranchLength(node));
stTree_setClientData(node2, stTree_getClientData(node));
stTree_setLabel(node2, stTree_getLabel(node));
return node2;
}
// Set client data to NULL (optionally recursively).
static void stTree_clearClientData(stTree *tree, bool recursive) {
stTree_setClientData(tree, NULL);
if (recursive) {
for (int64_t i = 0; i < stTree_getChildNumber(tree); i++) {
stTree_clearClientData(stTree_getChild(tree, i), true);
}
}
}
/* destructor */
static void mafTreeNodeCompLink_destruct(struct mafTreeNodeCompLink *ncLink) {
if (ncLink->node != NULL) {
stTree_setClientData(ncLink->node, NULL);
}
if (ncLink->comp != NULL) {
ncLink->comp->ncLink = NULL;
}
freeMem(ncLink);
}
/* constructor, link with node and comp */
static struct mafTreeNodeCompLink *mafTreeNodeCompLink_construct(int treeOrder, stTree *node, struct malnComp *comp) {
struct mafTreeNodeCompLink *ncLink;
AllocVar(ncLink);
ncLink->treeOrder = treeOrder;
if (node != NULL) {
ncLink->node = node;
stTree_setClientData(node, ncLink);
}
if (comp != NULL) {
ncLink->comp = comp;
ncLink->comp->ncLink = ncLink;
}
return ncLink;
}
/* add genome objects as client data */
static void speciesTreeAddLinks(stTree *speciesNode, struct Genomes *genomes) {
stTree_setClientData(speciesNode, genomesGetGenome(genomes, stTree_getLabel(speciesNode)));
for (int i = 0; i < stTree_getChildNumber(speciesNode); i++) {
speciesTreeAddLinks(stTree_getChild(speciesNode, i), genomes);
}
}
