out.close();
exit(0);
- }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
+ }else {
+ m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
+ for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+ exit(0);
+ }
}
results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num);
EstOutput results; results.resize(num);
int count = 0;
+ int numLeaves = t->getNumLeaves();
int total = num;
int twentyPercent = (total * 0.20);
if (twentyPercent == 0) { twentyPercent = 1; }
- for (int h = start; h < (start+num); h++) {
+ for (int h = start; h < (start+num); h++) {
+ //cout << namesOfGroupCombos[h][0] << '\t' << namesOfGroupCombos[h][1] << endl;
if (m->control_pressed) { return results; }
double UniqueBL=0.0000; //a branch length is unique if it's chidren are from the same group
double totalBL = 0.00; //all branch lengths
double UW = 0.00; //Unweighted Value = UniqueBL / totalBL;
+ map<int, double> tempTotals; //maps node to total Branch Length
+ map<int, int> nodePcountSize; //maps node to pcountSize
+ map<int, int>::iterator itCount;
for(int i=0;i<t->getNumNodes();i++){
map<string, int>::iterator itGroup = t->tree[i].pcount.find(namesOfGroupCombos[h][j]);
if (itGroup != t->tree[i].pcount.end()) { pcountSize++; if (pcountSize > 1) { break; } }
}
+
+ nodePcountSize[i] = pcountSize;
+ //cout << i << '\t' << t->tree[i].getName() << " br = " << abs(t->tree[i].getBranchLength()) << '\t';
if (pcountSize == 0) { }
- else if ((t->tree[i].getBranchLength() != -1) && (pcountSize == 1)) { UniqueBL += abs(t->tree[i].getBranchLength()); }
+ else if ((t->tree[i].getBranchLength() != -1) && (pcountSize == 1)) { UniqueBL += abs(t->tree[i].getBranchLength()); }
+
+ //if you are a leaf from a users group add to total
+ if (i < numLeaves) {
+ if ((t->tree[i].getBranchLength() != -1) && pcountSize != 0) {
+ //cout << "added to total" << endl;
+ totalBL += abs(t->tree[i].getBranchLength());
+ }
+ tempTotals[i] = 0.0; //we don't care about you, or we have already added you
+ }else{ //if you are not a leaf
+ //do both your chidren have have descendants from the users groups?
+ int lc = t->tree[i].getLChild();
+ int rc = t->tree[i].getRChild();
- if ((t->tree[i].getBranchLength() != -1) && (pcountSize != 0)) {
- totalBL += abs(t->tree[i].getBranchLength());
+ //if yes, add your childrens tempTotals
+ if ((nodePcountSize[lc] != 0) && (nodePcountSize[rc] != 0)) {
+ totalBL += tempTotals[lc] + tempTotals[rc];
+ //cout << "added to total " << tempTotals[lc] << '\t' << tempTotals[rc] << endl;
+ if (t->tree[i].getBranchLength() != -1) {
+ tempTotals[i] = abs(t->tree[i].getBranchLength());
+ }else {
+ tempTotals[i] = 0.0;
+ }
+ }else if ((nodePcountSize[lc] == 0) && (nodePcountSize[rc] == 0)) { tempTotals[i] = 0.0; //we don't care about you
+ }else { //if no, your tempTotal is your childrens temp totals + your branch length
+ tempTotals[i] = tempTotals[lc] + tempTotals[rc] + abs(t->tree[i].getBranchLength());
+ }
+ //cout << "temptotal = "<< tempTotals[i] << endl;
}
+
}
-
+ //cout << UniqueBL << '\t' << totalBL << endl;
UW = (UniqueBL / totalBL);
if (isnan(UW) || isinf(UW)) { UW = 0; }
out.close();
exit(0);
- }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
+ }else {
+ m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
+ for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+ exit(0);
+ }
}
results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, usingGroups);
int count = 0;
int total = num;
int twentyPercent = (total * 0.20);
+ int numLeaves = t->getNumLeaves();
Tree* copyTree = new Tree;
double UniqueBL=0.0000; //a branch length is unique if it's chidren are from the same group
double totalBL = 0.00; //all branch lengths
double UW = 0.00; //Unweighted Value = UniqueBL / totalBL;
+ map<int, double> tempTotals; //maps node to total Branch Length
+ map<int, int> nodePcountSize; //maps node to pcountSize
- for(int i=0;i<t->getNumNodes();i++){
+ for(int i=0;i<copyTree->getNumNodes();i++){
if (m->control_pressed) { return data; }
int pcountSize = 0;
for (int j = 0; j < namesOfGroupCombos[h].size(); j++) {
- map<string, int>::iterator itGroup = t->tree[i].pcount.find(namesOfGroupCombos[h][j]);
- if (itGroup != t->tree[i].pcount.end()) { pcountSize++; if (pcountSize > 1) { break; } }
+ map<string, int>::iterator itGroup = copyTree->tree[i].pcount.find(namesOfGroupCombos[h][j]);
+ if (itGroup != copyTree->tree[i].pcount.end()) { pcountSize++; if (pcountSize > 1) { break; } }
}
+ nodePcountSize[i] = pcountSize;
+
if (pcountSize == 0) { }
- else if ((t->tree[i].getBranchLength() != -1) && (pcountSize == 1)) { UniqueBL += abs(t->tree[i].getBranchLength()); }
+ else if ((copyTree->tree[i].getBranchLength() != -1) && (pcountSize == 1)) { UniqueBL += abs(copyTree->tree[i].getBranchLength()); }
+
+ //if you are a leaf from a users group add to total
+ if (i < numLeaves) {
+ if ((copyTree->tree[i].getBranchLength() != -1) && pcountSize != 0) {
+ totalBL += abs(copyTree->tree[i].getBranchLength());
+ }
+ tempTotals[i] = 0.0; //we don't care about you, or we have already added you
+ }else{ //if you are not a leaf
+ //do both your chidren have have descendants from the users groups?
+ int lc = copyTree->tree[i].getLChild();
+ int rc = copyTree->tree[i].getRChild();
+
+ //if yes, add your childrens tempTotals
+ if ((nodePcountSize[lc] != 0) && (nodePcountSize[rc] != 0)) {
+ totalBL += tempTotals[lc] + tempTotals[rc];
+
+ if (copyTree->tree[i].getBranchLength() != -1) {
+ tempTotals[i] = abs(copyTree->tree[i].getBranchLength());
+ }else {
+ tempTotals[i] = 0.0;
+ }
+ }else if ((nodePcountSize[lc] == 0) && (nodePcountSize[rc] == 0)) { tempTotals[i] = 0.0; //we don't care about you
+ }else { //if no, your tempTotal is your childrens temp totals + your branch length
+ tempTotals[i] = tempTotals[lc] + tempTotals[rc] + abs(copyTree->tree[i].getBranchLength());
+ }
- if ((t->tree[i].getBranchLength() != -1) && (pcountSize != 0)) {
- totalBL += abs(t->tree[i].getBranchLength());
}
+
}
UW = (UniqueBL / totalBL);