/* 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;
}
static stTree *eventTree_getStTree_R(Event *event) {
stTree *ret = stTree_construct();
stTree_setLabel(ret, stString_print("%" PRIi64, event_getName(event)));
stTree_setBranchLength(ret, event_getBranchLength(event));
for(int64_t i = 0; i < event_getChildNumber(event); i++) {
Event *child = event_getChild(event, i);
stTree *childStTree = eventTree_getStTree_R(child);
stTree_setParent(childStTree, ret);
}
return ret;
}
// 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;
}
static stTree *tree_parseNewickStringP(char **token, char **newickTreeString) {
stTree *tree = stTree_construct();
if((*token)[0] == '(') {
assert(strlen(*token) == 1);
tree_parseNewickTreeString_getNextToken(token, newickTreeString);
while(1) {
stTree_setParent(tree_parseNewickStringP(token, newickTreeString), tree);
assert(strlen(*token) == 1);
if((*token)[0] == ',') {
tree_parseNewickTreeString_getNextToken(token, newickTreeString);
}
else {
break;
}
}
assert((*token)[0] == ')'); //for every opening bracket we must have a close bracket.
tree_parseNewickTreeString_getNextToken(token, newickTreeString);
}
tree_parseNewickString_getLabel(token, newickTreeString, tree);
tree_parseNewickString_getBranchLength(token, newickTreeString, tree);
assert(**token == ',' || **token == ';' || **token == ')'); //these are the correct termination criteria
return tree;
}
/* construct an ETree node from a malnComp */
static stTree *malnCompToETreeNode(struct malnComp *comp) {
stTree *eTree = stTree_construct();
stTree_setLabel(eTree, comp->seq->orgSeqName);
return eTree;
}