//if the users enters no groups then give them the score of all groups
int numGroups = globaldata->Groups.size();
-cout << "NumGroups = " << numGroups << endl;
+
//calculate number of comparsions
int numComp = 0;
for (int r=0; r<numGroups; r++) {
//swap labels in the groups you want to compare
copyTree->assembleRandomUnifracTree(groups[0], groups[1]);
-
+
+ //copyTree->createNewickFile("random"+groupA+toString(count));
- for(int i=t->getNumLeaves();i<t->getNumNodes();i++){
+ for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
- int lc = t->tree[i].getLChild(); //lc = vector index of left child
- int rc = t->tree[i].getRChild(); //rc = vector index of right child
+ 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 = t->tree[i].pcount;
+ 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 ((t->tree[i].getBranchLength() != -1) && (copyIpcount.size() == 1)) { UniqueBL += t->tree[i].getBranchLength(); }
+ 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 ((t->tree[i].getBranchLength() != -1) && (copyIpcount.size() != 0)) {
- totalBL += t->tree[i].getBranchLength();
+ 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 (t->tree[rc].getRChild() == -1) {
+ if (copyTree->tree[rc].getRChild() == -1) {
//if rc is a valid group and rc has a BL
- if ((inUsersGroups(t->tree[rc].getGroup(), groups) == true) && (t->tree[rc].getBranchLength() != -1)) {
- UniqueBL += t->tree[rc].getBranchLength();
- totalBL += t->tree[rc].getBranchLength();
+ if ((inUsersGroups(copyTree->tree[rc].getGroup(), groups) == true) && (copyTree->tree[rc].getBranchLength() != -1)) {
+ UniqueBL += copyTree->tree[rc].getBranchLength();
+ totalBL += copyTree->tree[rc].getBranchLength();
}
}
- if (t->tree[lc].getLChild() == -1) {
+ if (copyTree->tree[lc].getLChild() == -1) {
//if lc is a valid group and lc has a BL
- if ((inUsersGroups(t->tree[lc].getGroup(), groups) == true) && (t->tree[lc].getBranchLength() != -1)) {
- UniqueBL += t->tree[lc].getBranchLength();
- totalBL += t->tree[lc].getBranchLength();
+ if ((inUsersGroups(copyTree->tree[lc].getGroup(), groups) == true) && (copyTree->tree[lc].getBranchLength() != -1)) {
+ UniqueBL += copyTree->tree[lc].getBranchLength();
+ totalBL += copyTree->tree[lc].getBranchLength();
}
}
//swap labels in all the groups you want to compare
copyTree->assembleRandomUnifracTree(groups);
- for(int i=t->getNumLeaves();i<t->getNumNodes();i++){
+ for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
- int lc = t->tree[i].getLChild(); //lc = vector index of left child
- int rc = t->tree[i].getRChild(); //rc = vector index of right child
+ 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 = t->tree[i].pcount;
+ 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 ((t->tree[i].getBranchLength() != -1) && (copyIpcount.size() == 1)) { UniqueBL += t->tree[i].getBranchLength(); }
+ 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 ((t->tree[i].getBranchLength() != -1) && (copyIpcount.size() != 0)) {
- totalBL += t->tree[i].getBranchLength();
+ 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 (t->tree[rc].getRChild() == -1) {
+ if (copyTree->tree[rc].getRChild() == -1) {
//if rc is a valid group and rc has a BL
- if ((inUsersGroups(t->tree[rc].getGroup(), groups) == true) && (t->tree[rc].getBranchLength() != -1)) {
- UniqueBL += t->tree[rc].getBranchLength();
- totalBL += t->tree[rc].getBranchLength();
+ if ((inUsersGroups(copyTree->tree[rc].getGroup(), groups) == true) && (copyTree->tree[rc].getBranchLength() != -1)) {
+ UniqueBL += copyTree->tree[rc].getBranchLength();
+ totalBL += copyTree->tree[rc].getBranchLength();
}
}
- if (t->tree[lc].getLChild() == -1) {
+ if (copyTree->tree[lc].getLChild() == -1) {
//if lc is a valid group and lc has a BL
- if ((inUsersGroups(t->tree[lc].getGroup(), groups) == true) && (t->tree[lc].getBranchLength() != -1)) {
- UniqueBL += t->tree[lc].getBranchLength();
- totalBL += t->tree[lc].getBranchLength();
+ if ((inUsersGroups(copyTree->tree[lc].getGroup(), groups) == true) && (copyTree->tree[lc].getBranchLength() != -1)) {
+ UniqueBL += copyTree->tree[lc].getBranchLength();
+ totalBL += copyTree->tree[lc].getBranchLength();
}
}
projects / mothur.git / blobdiff