void NWK_roothandl(char *nwktr, int nwklen, int ntax, int numnodes,
tree *newtree, bool isRooted)
{
int ctr = 0;
int *ctrp;
ctrp = &ctr;
newtree->trnodes[ntax] = cpyfromNWK(nwktr, nwklen, ntax, numnodes, ctrp,
newtree->trnodes, isRooted);
newtree->root = newtree->trnodes[ntax];
if (!isRooted) {
mfl_unroot(ntax, newtree);
}
/* debugging print */
/*dbg_printf("[&");
if (newtree->root)
{
dbg_printf("R] = ");
printNewick(newtree->root);
}
else
{
dbg_printf("U] = ");
printNewick(newtree->trnodes[0]);
}
dbg_printf("\n");*/
/* end debugging print */
}
void mfl_nni_traversal(node *n, tree *swapingon, tree **savedtrees, int ntax,
int nchar, int numnodes, long int *current,
charstate *tipdata, bool *undertreelimit,
int *currentbesttree, bool *foundbettertree)
{
int trlength = 0;
node *p;
if (n->start) {
mfl_nni_traversal(n->edge, swapingon, savedtrees, ntax, nchar, numnodes,
current, tipdata, undertreelimit, currentbesttree,
foundbettertree);
return;
}
if (n->tip || !(*undertreelimit)) {
return;
}
if (!n->edge->tip)
{
/* Nearly identical steps are conducted twice because all nearest-
* neighbor interchanges produce two distinct tree topologies */
if (*current + 1 <= TREELIMIT) {
mfl_bswap(n->next->edge, n->edge->next->edge);
mfl_root_tree(swapingon, 1, ntax);
trlength = mfl_get_treelen(swapingon, ntax, nchar, currentbesttree);
mfl_unroot(ntax, swapingon);
if (trlength < *currentbesttree) {
*foundbettertree = true;
*currentbesttree = trlength;
swapingon->length = trlength;
mfl_reinit_treebuffer(savedtrees, swapingon, current, numnodes);
trlength = 0;
*current = *current + 1;
return;
}
if (trlength == *currentbesttree) {
*foundbettertree = false;
savedtrees[*current] = mfl_copytree(swapingon, ntax, numnodes);
savedtrees[*current]->index = *current;
savedtrees[*current]->length = trlength;
trlength = 0;
*current = *current + 1;
}
mfl_bswap(n->next->edge, n->edge->next->edge);
if (*current + 1 <= TREELIMIT){
mfl_bswap(n->next->next->edge, n->edge->next->edge);
mfl_root_tree(swapingon, 1, ntax);
trlength = mfl_get_treelen(swapingon, ntax, nchar, currentbesttree);
mfl_unroot(ntax, swapingon);
if (trlength < *currentbesttree) {
*foundbettertree = true;
*currentbesttree = trlength;
swapingon->length = trlength;
mfl_reinit_treebuffer(savedtrees, swapingon, current, numnodes);
trlength = 0;
*current = *current + 1;
return;
}
if (trlength == *currentbesttree) {
*foundbettertree = false;
savedtrees[*current] = mfl_copytree(swapingon, ntax, numnodes);
savedtrees[*current]->index = *current;
savedtrees[*current]->length = trlength;
trlength = 0;
*current = *current + 1;
}
mfl_bswap(n->next->next->edge, n->edge->next->edge);
}
}
else {
dbg_printf("Hit tree limit\n");
*undertreelimit = false;
return;
}
}
p = n->next;
while (p != n) {
mfl_nni_traversal(p->edge, swapingon, savedtrees, ntax, nchar, numnodes,
current, tipdata, undertreelimit, currentbesttree,
foundbettertree);
p = p->next;
}
}
