vector<double> D;
numGroups = globaldata->Groups.size();
+
+ vector<double> sums = getBranchLengthSums(t);
+
+ if (m->control_pressed) { return data; }
//calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3;
int count = 0;
//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]);
+
D.push_back(0.0000); //initialize a spot in D for each combination
+
+ //adding the wieghted sums from group i
+ for (int j = 0; j < t->groupNodeInfo[groups[0]].size(); j++) { //the leaf nodes that have seqs from group i
+ map<string, int>::iterator it = t->tree[t->groupNodeInfo[groups[0]][j]].pcount.find(groups[0]);
+ int numSeqsInGroupI = it->second;
+
+ double weightedSum = ((numSeqsInGroupI * sums[t->groupNodeInfo[groups[0]][j]]) / (double)tmap->seqsPerGroup[groups[0]]);
+
+ D[count] += weightedSum;
+ }
- /********************************************************/
+ //adding the wieghted sums from group l
+ for (int j = 0; j < t->groupNodeInfo[groups[1]].size(); j++) { //the leaf nodes that have seqs from group l
+ map<string, int>::iterator it = t->tree[t->groupNodeInfo[groups[1]][j]].pcount.find(groups[1]);
+ int numSeqsInGroupL = it->second;
+
+ double weightedSum = ((numSeqsInGroupL * sums[t->groupNodeInfo[groups[1]][j]]) / (double)tmap->seqsPerGroup[groups[1]]);
+
+ D[count] += weightedSum;
+ }
+
+ /********************************************************
//calculate a D value for each group combo
for(int v=0;v<t->getNumLeaves();v++){
- int index = v;
- double sum = 0.0000;
-
- //while you aren't at root
- while(t->tree[index].getParent() != -1){
-
- //if you have a BL
- if(t->tree[index].getBranchLength() != -1){
- sum += abs(t->tree[index].getBranchLength());
- }
- index = t->tree[index].getParent();
- }
-
- //get last breanch length added
- if(t->tree[index].getBranchLength() != -1){
- sum += abs(t->tree[index].getBranchLength());
- }
-
+
+ if (m->control_pressed) { return data; }
+
//is this sum from a sequence which is in one of the users groups
- if (inUsersGroups(t->tree[v].getGroup(), globaldata->Groups) == true) {
+ if (m->inUsersGroups(t->tree[v].getGroup(), globaldata->Groups) == true) {
//is this sum from a sequence which is in this groupCombo
- if ((t->tree[v].getGroup() == globaldata->Groups[i]) || (t->tree[v].getGroup() == globaldata->Groups[l])) {
- sum /= (double)tmap->seqsPerGroup[t->tree[v].getGroup()];
- D[count] += sum;
+ if (m->inUsersGroups(t->tree[v].getGroup(), groups)) {
+ int numSeqsInGroupI, numSeqsInGroupL;
+
+ map<string, int>::iterator it;
+ it = t->tree[v].pcount.find(groups[0]);
+ if (it != t->tree[v].pcount.end()) { //this leaf node contains seqs from group i
+ numSeqsInGroupI = it->second;
+ }else{ numSeqsInGroupI = 0; }
+
+ it = t->tree[v].pcount.find(groups[1]);
+ if (it != t->tree[v].pcount.end()) { //this leaf node contains seqs from group l
+ numSeqsInGroupL = it->second;
+ }else{ numSeqsInGroupL = 0; }
+
+ double weightedSum = ((numSeqsInGroupI * sum) / (double)tmap->seqsPerGroup[groups[0]]) + ((numSeqsInGroupL * sum) / (double)tmap->seqsPerGroup[groups[1]]);
+
+ //sum /= (double)tmap->seqsPerGroup[t->tree[v].getGroup()];
+
+ D[count] += weightedSum;
}
}
}
//calculate weighted score for each of the group comb i.e. with groups A,B,C = AB, AC, BC.
for (int b=0; b<numGroups; b++) {
for (int l = b+1; l < numGroups; l++) {
+
+ if (m->control_pressed) { return data; }
+
//calculate a u value for each combo
double u;
//does this node have descendants from group b-1
return data;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the Weighted class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "Weighted", "getValues");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the Weighted class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-
}
/**************************************************************************************************/
data.clear(); //clear out old values
+ vector<double> sums = getBranchLengthSums(t);
+
+ if (m->control_pressed) { return data; }
+
//initialize weighted score
WScore[(groupA+groupB)] = 0.0;
- float D = 0.0;
+ double D = 0.0;
-
- /********************************************************/
+ vector<string> groups; groups.push_back(groupA); groups.push_back(groupB);
+
+ //adding the wieghted sums from groupA
+ for (int j = 0; j < t->groupNodeInfo[groupA].size(); j++) { //the leaf nodes that have seqs from group i
+ map<string, int>::iterator it = t->tree[j].pcount.find(groupA);
+ int numSeqsInGroupA = it->second;
+
+ double weightedSum = ((numSeqsInGroupA * sums[j]) / (double)tmap->seqsPerGroup[groupA]);
+
+ D += weightedSum;
+ }
+
+ //adding the wieghted sums from groupB
+ 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[j].pcount.find(groupB);
+ int numSeqsInGroupB = it->second;
+
+ double weightedSum = ((numSeqsInGroupB * sums[j]) / (double)tmap->seqsPerGroup[groupB]);
+
+ D += weightedSum;
+ }
+
+
+ /********************************************************
//calculate a D value for the group combo
for(int v=0;v<t->getNumLeaves();v++){
+ if (m->control_pressed) { return data; }
+
int index = v;
double sum = 0.0000;
sum += abs(t->tree[index].getBranchLength());
}
- if ((t->tree[v].getGroup() == groupA) || (t->tree[v].getGroup() == groupB)) {
- sum /= (double)tmap->seqsPerGroup[t->tree[v].getGroup()];
- D += sum;
+ if (m->inUsersGroups(t->tree[v].getGroup(), groups)) {
+ int numSeqsInGroupI, numSeqsInGroupL;
+
+ map<string, int>::iterator it;
+ it = t->tree[v].pcount.find(groups[0]);
+ if (it != t->tree[v].pcount.end()) { //this leaf node contains seqs from group i
+ numSeqsInGroupI = it->second;
+ }else{ numSeqsInGroupI = 0; }
+
+ it = t->tree[v].pcount.find(groups[1]);
+ if (it != t->tree[v].pcount.end()) { //this leaf node contains seqs from group l
+ numSeqsInGroupL = it->second;
+ }else{ numSeqsInGroupL = 0; }
+
+ double weightedSum = ((numSeqsInGroupI * sum) / (double)tmap->seqsPerGroup[groups[0]]) + ((numSeqsInGroupL * sum) / (double)tmap->seqsPerGroup[groups[1]]);
+
+ //sum /= (double)tmap->seqsPerGroup[t->tree[v].getGroup()];
+
+ D += weightedSum;
}
}
/********************************************************/
//calculate u for the group comb
for(int i=0;i<t->getNumNodes();i++){
+
+ if (m->control_pressed) { return data; }
+
double u;
//does this node have descendants from groupA
it = t->tree[i].pcount.find(groupA);
return data;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the Weighted class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "Weighted", "getValues");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the Weighted class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+/**************************************************************************************************/
+vector<double> Weighted::getBranchLengthSums(Tree* t) {
+ try {
+
+ vector<double> sums;
+
+ for(int v=0;v<t->getNumLeaves();v++){
+
+ if (m->control_pressed) { return sums; }
+
+ int index = v;
+ double sum = 0.0000;
+
+ //while you aren't at root
+ while(t->tree[index].getParent() != -1){
+
+ //if you have a BL
+ if(t->tree[index].getBranchLength() != -1){
+ sum += abs(t->tree[index].getBranchLength());
+ }
+ index = t->tree[index].getParent();
+ }
+
+ //get last breanch length added
+ if(t->tree[index].getBranchLength() != -1){
+ sum += abs(t->tree[index].getBranchLength());
+ }
+
+ sums.push_back(sum);
+ }
+
+ return sums;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Weighted", "getBranchLengthSums");
exit(1);
}
-
}
-
-
-
-
-
-
+/**************************************************************************************************/
projects / mothur.git / blobdiff