EstOutput Weighted::getValues(Tree* t, int p, string o) {
try {
- globaldata = GlobalData::getInstance();
-
data.clear(); //clear out old values
int numGroups;
vector<double> D;
processors = p;
outputDir = o;
- numGroups = globaldata->Groups.size();
+ numGroups = m->getNumGroups();
if (m->control_pressed) { return data; }
for (int l = 0; l < i; l++) {
//initialize weighted scores
//WScore[globaldata->Groups[i]+globaldata->Groups[l]] = 0.0;
- vector<string> groups; groups.push_back(globaldata->Groups[i]); groups.push_back(globaldata->Groups[l]);
+ vector<string> groups; groups.push_back((m->getGroups())[i]); groups.push_back((m->getGroups())[l]);
namesOfGroupCombos.push_back(groups);
}
}
m->gobble(in);
}
in.close();
- remove(s.c_str());
+ m->mothurRemove(s);
}
m->mothurOut("DONE."); m->mothurOutEndLine(); m->mothurOutEndLine();
u -= (double) t->tree[i].pcount[groupB] / (double) tmap->seqsPerGroup[groupB];
}
- //if this is not the root then add it
- if (rootForGrouping[namesOfGroupCombos[h]].count(i) == 0) {
+ if (includeRoot) {
if (t->tree[i].getBranchLength() != -1) {
u = abs(u * t->tree[i].getBranchLength());
WScore[(groupA+groupB)] += u;
}
+ }else {
+ //if this is not the root then add it
+ if (rootForGrouping[namesOfGroupCombos[h]].count(i) == 0) {
+ if (t->tree[i].getBranchLength() != -1) {
+ u = abs(u * t->tree[i].getBranchLength());
+ WScore[(groupA+groupB)] += u;
+ }
+ }
}
}
/**************************************************************************************************/
EstOutput Weighted::getValues(Tree* t, string groupA, string groupB) {
try {
- globaldata = GlobalData::getInstance();
data.clear(); //clear out old values
u -= (double) t->tree[i].pcount[groupB] / (double) tmap->seqsPerGroup[groupB];
}
- //if this is not the root then add it
- if (rootForGrouping[groups].count(i) == 0) {
+ if (includeRoot) {
if (t->tree[i].getBranchLength() != -1) {
u = abs(u * t->tree[i].getBranchLength());
WScore[(groupA+groupB)] += u;
}
+ }else{
+ //if this is not the root then add it
+ if (rootForGrouping[groups].count(i) == 0) {
+ if (t->tree[i].getBranchLength() != -1) {
+ u = abs(u * t->tree[i].getBranchLength());
+ WScore[(groupA+groupB)] += u;
+ }
+ }
}
}
/********************************************************/
while(t->tree[index].getParent() != -1){
if (m->control_pressed) { return sum; }
-
- //am I the root for this grouping? if so I want to stop "early"
- //does my sibling have descendants from the users groups?
+
int parent = t->tree[index].getParent();
- int lc = t->tree[parent].getLChild();
- int rc = t->tree[parent].getRChild();
- int sib = lc;
- if (lc == index) { sib = rc; }
-
- map<string, int>::iterator itGroup;
- int pcountSize = 0;
- itGroup = t->tree[sib].pcount.find(groupA);
- if (itGroup != t->tree[sib].pcount.end()) { pcountSize++; }
- itGroup = t->tree[sib].pcount.find(groupB);
- if (itGroup != t->tree[sib].pcount.end()) { pcountSize++; }
-
- //if yes, I am not the root so add me
- if (pcountSize != 0) {
- if (t->tree[index].getBranchLength() != -1) {
- sum += abs(t->tree[index].getBranchLength()) + tempTotal;
- tempTotal = 0.0;
- }else {
- sum += tempTotal;
- tempTotal = 0.0;
- }
- rootForGrouping[grouping].clear();
- rootForGrouping[grouping].insert(parent);
- }else { //if no, I may be the root so add my br to tempTotal until I am proven innocent
- if (t->tree[index].getBranchLength() != -1) {
- tempTotal += abs(t->tree[index].getBranchLength());
+ if (includeRoot) { //add everyone
+ if(t->tree[index].getBranchLength() != -1){ sum += abs(t->tree[index].getBranchLength()); }
+ }else {
+
+ //am I the root for this grouping? if so I want to stop "early"
+ //does my sibling have descendants from the users groups?
+ int lc = t->tree[parent].getLChild();
+ int rc = t->tree[parent].getRChild();
+
+ int sib = lc;
+ if (lc == index) { sib = rc; }
+
+ map<string, int>::iterator itGroup;
+ int pcountSize = 0;
+ itGroup = t->tree[sib].pcount.find(groupA);
+ if (itGroup != t->tree[sib].pcount.end()) { pcountSize++; }
+ itGroup = t->tree[sib].pcount.find(groupB);
+ if (itGroup != t->tree[sib].pcount.end()) { pcountSize++; }
+
+ //if yes, I am not the root so add me
+ if (pcountSize != 0) {
+ if (t->tree[index].getBranchLength() != -1) {
+ sum += abs(t->tree[index].getBranchLength()) + tempTotal;
+ tempTotal = 0.0;
+ }else {
+ sum += tempTotal;
+ tempTotal = 0.0;
+ }
+ rootForGrouping[grouping].clear();
+ rootForGrouping[grouping].insert(parent);
+ }else { //if no, I may be the root so add my br to tempTotal until I am proven innocent
+ if (t->tree[index].getBranchLength() != -1) {
+ tempTotal += abs(t->tree[index].getBranchLength());
+ }
}
}