void Tree::getCopy(Tree* copy, bool subsample) {
try {
//for each node in the tree copy its info
for (int i = 0; i < numNodes; i++) {
//copy branch length
tree[i].setBranchLength(copy->tree[i].getBranchLength());
//copy parent
tree[i].setParent(copy->tree[i].getParent());
//copy children
tree[i].setChildren(copy->tree[i].getLChild(), copy->tree[i].getRChild());
}
//build the pGroups in non leaf nodes to be used in the parsimony calcs.
for (int i = numLeaves; i < numNodes; i++) {
if (m->control_pressed) { break; }
tree[i].pGroups = (mergeGroups(i));
tree[i].pcount = (mergeGcounts(i));
}
}
catch(exception& e) {
m->errorOut(e, "Tree", "getCopy");
exit(1);
}
}
int Tree::assembleTree() {
try {
//build the pGroups in non leaf nodes to be used in the parsimony calcs.
for (int i = numLeaves; i < numNodes; i++) {
if (m->control_pressed) { return 1; }
tree[i].pGroups = (mergeGroups(i));
tree[i].pcount = (mergeGcounts(i));
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "Tree", "assembleTree");
exit(1);
}
}
void unarySortAdd(vec<Formula>& Xs,vec<Formula>& Ys,vec<Formula>& out_sorter,bool useShortCuts){
vec<Formula> propgationShortCuts;
int XsLen = Xs.size();
int YsLen = Ys.size();
if (YsLen==0) {
if (XsLen>0) {
add(Xs,out_sorter);
safeSortNetwork(out_sorter,propgationShortCuts);
if (useShortCuts) overwrite(out_sorter,propgationShortCuts);
}
}
else if (XsLen==0) add(Ys,out_sorter);
else if (XsLen==1 & YsLen==1) {
add(Xs,out_sorter);
add(Ys,out_sorter);
cmp2(out_sorter, 0);
}
else {
int Ysize; for (Ysize = 2; Ysize < YsLen; Ysize *= 2);
Ys.growTo(Ysize,_0_);
propgationShortCuts.growTo(Ysize*2,_0_);
addShortCuts(Ys,propgationShortCuts);
if (XsLen <= YsLen) {
Xs.growTo(Ysize,_0_);
sortNetwork(Xs,propgationShortCuts);
mergeNetwork(Xs,Ys,out_sorter,propgationShortCuts);
}
else {
vec<vec<Formula> > SubXs;
SubXs.push();
add(Ys,SubXs.last());
splitToGroups(Xs, Ysize, SubXs);
sortGroups(SubXs,propgationShortCuts);
mergeGroups(SubXs, Ysize, out_sorter,propgationShortCuts);
}
out_sorter.shrink(out_sorter.size() - XsLen-YsLen);
if(useShortCuts) overwrite(out_sorter,propgationShortCuts);
}
}