/* clone a node, linking in new mafTreeNodeCompLink object */
static stTree *cloneNode(stTree *srcNode, struct malnCompCompMap *srcDestCompMap) {
stTree *destNode = stTree_cloneNode(srcNode);
struct mafTreeNodeCompLink *srcNcLink = getNodeCompLink(srcNode);
struct malnComp *destComp = malnCompCompMap_get(srcDestCompMap, srcNcLink->comp);
mafTreeNodeCompLink_construct(-1, destNode, destComp);
return destNode;
}
// clone this node, make its supertree a child, and clone all children
// other than oldNode, leaving this node as a child of nodeToAddTo
static void tree_cloneFlippedTree(stTree *node, stTree *oldNode,
stTree *nodeToAddTo,
double branchLength) {
if(stTree_getParent(node) != NULL) {
// This node isn't the root
stTree *clonedNode = stTree_cloneNode(node);
stTree_setParent(clonedNode, nodeToAddTo);
stTree_setBranchLength(clonedNode, branchLength);
// Clone its children (other than oldNode) and their subtrees
for(int64_t i = 0; i < stTree_getChildNumber(node); i++) {
stTree *child = stTree_getChild(node, i);
if(child != oldNode) {
stTree *clonedChild = stTree_clone(child);
stTree_setParent(clonedChild, clonedNode);
}
}
// Recurse on the parent of this node.
tree_cloneFlippedTree(stTree_getParent(node), node,
clonedNode, stTree_getBranchLength(node));
} else {
// We have to treat the root specially, because we're going to
// eliminate it. Just add all the other children of the root
// as children of nodeToAddTo.
for(int64_t i = 0; i < stTree_getChildNumber(node); i++) {
stTree *child = stTree_getChild(node, i);
if(child != oldNode) {
stTree *clonedChild = stTree_clone(child);
stTree_setParent(clonedChild, nodeToAddTo);
stTree_setBranchLength(clonedChild, stTree_getBranchLength(child) + branchLength);
}
}
}
}
/* recursively clone a tree */
static stTree *tree_clonetree(stTree *node, stTree *parent2) {
stTree *node2 = stTree_cloneNode(node);
stTree_setParent(node2, parent2);
for (int i = 0; i < stTree_getChildNumber(node); i++) {
tree_clonetree(stTree_getChild(node, i), node2);
}
return node2;
}