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->Groups.size();
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->Groups[i]); groups.push_back(m->Groups[l]);
namesOfGroupCombos.push_back(groups);
}
}
m->gobble(in);
}
in.close();
- remove(s.c_str());
+ m->mothurRemove(s);
}
m->mothurOut("DONE."); m->mothurOutEndLine(); m->mothurOutEndLine();
D[count] += weightedSum;
}
-
+
//adding the wieghted sums from group l
for (int j = 0; j < t->groupNodeInfo[groupB].size(); j++) { //the leaf nodes that have seqs from group l
map<string, int>::iterator it = t->tree[t->groupNodeInfo[groupB][j]].pcount.find(groupB);
D[count] += weightedSum;
}
-
count++;
}
-
+
//calculate u for the group comb
-
for (int h = start; h < (start+num); h++) {
//report progress
- m->mothurOut("Processing combo: " + toString(h)); m->mothurOutEndLine();
+ //m->mothurOut("Processing combo: " + toString(h)); m->mothurOutEndLine();
string groupA = namesOfGroupCombos[h][0];
string groupB = namesOfGroupCombos[h][1];
//does this node have descendants from group l
it = t->tree[i].pcount.find(groupB);
+
//if it does subtract their percentage from u
if (it != t->tree[i].pcount.end()) {
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) {
- u = abs(u * t->tree[i].getBranchLength());
- WScore[(groupA+groupB)] += u;
+ 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;
+ }
+ }
}
-
}
+
}
/********************************************************/
count = 0;
for (int h = start; h < (start+num); h++) {
UN = (WScore[namesOfGroupCombos[h][0]+namesOfGroupCombos[h][1]] / D[count]);
-
if (isnan(UN) || isinf(UN)) { UN = 0; }
results.push_back(UN);
count++;
/**************************************************************************************************/
EstOutput Weighted::getValues(Tree* t, string groupA, string groupB) {
try {
- globaldata = GlobalData::getInstance();
data.clear(); //clear out old values
D += weightedSum;
}
-
- int numLeaves = t->getNumLeaves();
-
+
//calculate u for the group comb
for(int i=0;i<t->getNumNodes();i++){
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) {
- u = abs(u * t->tree[i].getBranchLength());
- WScore[(groupA+groupB)] += u;
+ 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;
+ }
+ }
}
}
/********************************************************/
-
+
//calculate weighted score for the group combination
double UN;
UN = (WScore[(groupA+groupB)] / D);
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; }
+ int parent = t->tree[index].getParent();
- 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());
+ }
}
}
//get all nodes above the root to add so we don't add their u values above
index = *(rootForGrouping[grouping].begin());
+
while(t->tree[index].getParent() != -1){
int parent = t->tree[index].getParent();
rootForGrouping[grouping].insert(parent);
index = parent;
}
-
return sum;
}
catch(exception& e) {
projects / mothur.git / blobdiff