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++;
}
m->mothurOut("Processing combo: " + toString(h)); m->mothurOutEndLine();
int numLeaves = t->getNumLeaves();
- map<int, double> tempTotals; //maps node to total Branch Length
- map<int, int> nodePcountSize; //maps node to pcountSize
string groupA = namesOfGroupCombos[h][0];
string groupB = namesOfGroupCombos[h][1];
if (m->control_pressed) { return data; }
double u;
- int pcountSize = 0;
+ //int pcountSize = 0;
//does this node have descendants from groupA
it = t->tree[i].pcount.find(groupA);
//if it does u = # of its descendants with a certain group / total number in tree with a certain group
if (it != t->tree[i].pcount.end()) {
u = (double) t->tree[i].pcount[groupA] / (double) tmap->seqsPerGroup[groupA];
- pcountSize++;
}else { u = 0.00; }
//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];
- pcountSize++;
}
- u = abs(u * t->tree[i].getBranchLength());
-
- nodePcountSize[i] = pcountSize;
-
- //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;
- WScore[(groupA+groupB)] += u;
- }
- 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 yes, add your childrens tempTotals
- if ((nodePcountSize[lc] != 0) && (nodePcountSize[rc] != 0)) {
- WScore[(groupA+groupB)] += tempTotals[lc] + tempTotals[rc];
- //cout << "added to total " << tempTotals[lc] << '\t' << tempTotals[rc] << endl;
- if (t->tree[i].getBranchLength() != -1) {
- tempTotals[i] = u;
- }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] + u;
- }
- //cout << "temptotal = "<< tempTotals[i] << endl;
+ //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;
}
+
}
}
}
int numLeaves = t->getNumLeaves();
- map<int, double> tempTotals; //maps node to total Branch Length
- map<int, int> nodePcountSize; //maps node to pcountSize
//calculate u for the group comb
for(int i=0;i<t->getNumNodes();i++){
-
+
if (m->control_pressed) { return data; }
double u;
- int pcountSize = 0;
+ //int pcountSize = 0;
//does this node have descendants from groupA
it = t->tree[i].pcount.find(groupA);
//if it does u = # of its descendants with a certain group / total number in tree with a certain group
if (it != t->tree[i].pcount.end()) {
u = (double) t->tree[i].pcount[groupA] / (double) tmap->seqsPerGroup[groupA];
- pcountSize++;
}else { u = 0.00; }
-
-
+
+
//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];
- pcountSize++;
}
-
- u = abs(u * t->tree[i].getBranchLength());
- nodePcountSize[i] = pcountSize;
-
- //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;
- WScore[(groupA+groupB)] += u;
- }
- 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 yes, add your childrens tempTotals
- if ((nodePcountSize[lc] != 0) && (nodePcountSize[rc] != 0)) {
- WScore[(groupA+groupB)] += tempTotals[lc] + tempTotals[rc];
- //cout << "added to total " << tempTotals[lc] << '\t' << tempTotals[rc] << endl;
- if (t->tree[i].getBranchLength() != -1) {
- tempTotals[i] = u;
- }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] + u;
- }
- //cout << "temptotal = "<< tempTotals[i] << endl;
+ //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;
}
- }
-
+ }
/********************************************************/
//calculate weighted score for the group combination
try {
double sum = 0.0;
- map<int, double> tempTotals; //maps node to total Branch Length
- map<int, int> nodePcountSize; //maps node to pcountSize
- map<int, int>::iterator itCount;
-
int index = v;
//you are a leaf
if(t->tree[index].getBranchLength() != -1){ sum += abs(t->tree[index].getBranchLength()); }
- tempTotals[index] = 0.0;
+ double tempTotal = 0.0;
index = t->tree[index].getParent();
+
+ vector<string> grouping; grouping.push_back(groupA); grouping.push_back(groupB);
+
+ rootForGrouping[grouping].insert(index);
//while you aren't at root
while(t->tree[index].getParent() != -1){
if (m->control_pressed) { return sum; }
- int pcountSize = 0;
- map<string, int>::iterator itGroup = t->tree[index].pcount.find(groupA);
- if (itGroup != t->tree[index].pcount.end()) { pcountSize++; }
- itGroup = t->tree[index].pcount.find(groupB);
- if (itGroup != t->tree[index].pcount.end()) { pcountSize++; }
-
- nodePcountSize[index] = pcountSize;
-
- //do both your chidren have have descendants from the users groups?
- int lc = t->tree[index].getLChild();
- int rc = t->tree[index].getRChild();
+ //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();
- itCount = nodePcountSize.find(lc);
- if (itCount == nodePcountSize.end()) {
- int LpcountSize = 0;
- itGroup = t->tree[lc].pcount.find(groupA);
- if (itGroup != t->tree[lc].pcount.end()) { LpcountSize++; }
- itGroup = t->tree[lc].pcount.find(groupB);
- if (itGroup != t->tree[lc].pcount.end()) { LpcountSize++; }
- nodePcountSize[lc] = LpcountSize;
- }
+ int sib = lc;
+ if (lc == index) { sib = rc; }
- itCount = nodePcountSize.find(rc);
- if (itCount == nodePcountSize.end()) {
- int RpcountSize = 0;
- itGroup = t->tree[rc].pcount.find(groupA);
- if (itGroup != t->tree[rc].pcount.end()) { RpcountSize++; }
- itGroup = t->tree[rc].pcount.find(groupB);
- if (itGroup != t->tree[rc].pcount.end()) { RpcountSize++; }
- nodePcountSize[rc] = RpcountSize;
- }
-
- //if yes, add your childrens tempTotals
- if ((nodePcountSize[lc] != 0) && (nodePcountSize[rc] != 0)) {
- sum += tempTotals[lc] + tempTotals[rc];
-
- //cout << "added to total " << tempTotals[lc] << '\t' << tempTotals[rc] << endl;
+ 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) {
- tempTotals[index] = abs(t->tree[index].getBranchLength());
+ sum += abs(t->tree[index].getBranchLength()) + tempTotal;
+ tempTotal = 0.0;
}else {
- tempTotals[index] = 0.0;
+ 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());
}
- }else { //if no, your tempTotal is your childrens temp totals + your branch length
- tempTotals[index] = tempTotals[lc] + tempTotals[rc] + abs(t->tree[index].getBranchLength());
}
- //cout << "temptotal = "<< tempTotals[i] << endl;
- index = t->tree[index].getParent();
+ index = parent;
}
-
+
+ //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