+
+ //numComp+1 for AB, AC, BC, ABC
+ data.resize(numComp+1,0);
+
+ int count = 0;
+ for (int a=0; a<numGroups; a++) {
+ for (int l = a+1; l < numGroups; l++) {
+ UniqueBL=0.0000; //a branch length is unique if it's chidren are from the same group
+ totalBL = 0.00; //all branch lengths
+ UW = 0.00; //Unweighted Value = UniqueBL / totalBL;
+ copyIpcount.clear();
+
+ //copy random tree passed in
+ copyTree->getCopy(t);
+
+ //groups in this combo
+ groups.push_back(globaldata->Groups[a]); groups.push_back(globaldata->Groups[l]);
+
+ //swap labels in the groups you want to compare
+ copyTree->assembleRandomUnifracTree(groups[0], groups[1]);
+
+ //copyTree->createNewickFile("random"+groupA+toString(count));
+
+ for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
+
+ int lc = copyTree->tree[i].getLChild(); //lc = vector index of left child
+ int rc = copyTree->tree[i].getRChild(); //rc = vector index of right child
+
+ /**********************************************************************/
+ //This section adds in all lengths that are non leaf
+
+ copyIpcount = copyTree->tree[i].pcount;
+ for (it = copyIpcount.begin(); it != copyIpcount.end(); it++) {
+ if (inUsersGroups(it->first, groups) != true) { copyIpcount.erase(it->first); }
+ }
+
+ //if i's children are from the same group then i's pcount size will be 1
+ //if copyIpcount.size() = 0 they are from a branch that is entirely from a group the user doesn't want
+ if (copyIpcount.size() == 0) { }
+ else if ((copyTree->tree[i].getBranchLength() != -1) && (copyIpcount.size() == 1)) { UniqueBL += copyTree->tree[i].getBranchLength(); }
+
+ //add i's BL to total if it is from the groups the user wants
+ if ((copyTree->tree[i].getBranchLength() != -1) && (copyIpcount.size() != 0)) {
+ totalBL += copyTree->tree[i].getBranchLength();
+ }
+
+ /**********************************************************************/
+ //This section adds in all lengths that are leaf
+
+ //if i's chidren are leaves
+ if (copyTree->tree[rc].getRChild() == -1) {
+ //if rc is a valid group and rc has a BL
+ if ((inUsersGroups(copyTree->tree[rc].getGroup(), groups) == true) && (copyTree->tree[rc].getBranchLength() != -1)) {
+ UniqueBL += copyTree->tree[rc].getBranchLength();
+ totalBL += copyTree->tree[rc].getBranchLength();
+ }
+ }
+
+ if (copyTree->tree[lc].getLChild() == -1) {
+ //if lc is a valid group and lc has a BL
+ if ((inUsersGroups(copyTree->tree[lc].getGroup(), groups) == true) && (copyTree->tree[lc].getBranchLength() != -1)) {
+ UniqueBL += copyTree->tree[lc].getBranchLength();
+ totalBL += copyTree->tree[lc].getBranchLength();
+ }
+ }
+
+ /**********************************************************************/
+ }
+
+ UW = (UniqueBL / totalBL);
+
+ if (isnan(UW) || isinf(UW)) { UW = 0; }
+
+ data[count] = UW;
+ count++;
+ groups.clear();