// 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);
}
}
}
}
// Return a new tree rooted a given distance above the given node.
stTree *stTree_reRoot(stTree *node, double distanceAbove) {
if(stTree_getParent(node) == NULL) {
// This node is already the root.
stTree *newRoot = stTree_clone(node);
stTree_clearClientData(newRoot, true);
return newRoot;
}
assert(stTree_getBranchLength(node) >= distanceAbove);
stTree *newRoot = stTree_construct();
// This node and its children (if any) are fine already.
stTree *clonedNode = stTree_clone(node);
stTree_setParent(clonedNode, newRoot);
stTree_setBranchLength(clonedNode, distanceAbove);
tree_cloneFlippedTree(stTree_getParent(node), node, newRoot,
stTree_getBranchLength(node) - distanceAbove);
// Having the same client data can be a problem
stTree_clearClientData(newRoot, true);
return newRoot;
}
/* clone a mafTree */
mafTree *mafTree_clone(mafTree *srcMTree, struct malnBlk *destBlk) {
mafTree *mTree = mafTree_construct(srcMTree->genomes, stTree_clone(srcMTree->tree));
fillNodeCompLinks(mTree, destBlk);
return mTree;
}
