//calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3;
int n = 1;
+ int count = 0;
for (int i=1; i<numGroups; i++) {
- for (int l = n; l < numGroups; l++) {
+ for (int l = n; l < numGroups; l++) {
//initialize weighted scores
if (globaldata->Groups.size() == 0) {
WScore[tmap->namesOfGroups[i-1]+tmap->namesOfGroups[l]] = 0.0;
- D.push_back(0.0000); //initialize a spot in D for each combination
}else {
WScore[globaldata->Groups[i-1]+globaldata->Groups[l]] = 0.0;
- D.push_back(0.0000); //initialize a spot in D for each combination
}
- }
- }
-
- data.clear(); //clear out old values
-
- for(int i=0;i<t->getNumNodes();i++){
- //calculate weighted score for each of the group comb i.e. with groups A,B,C = AB, AC, BC.
- n = 1;
- for (int b=1; b<numGroups; b++) {
- for (int l = n; l < numGroups; l++) {
+
+ D.push_back(0.0000); //initialize a spot in D for each combination
/********************************************************/
//calculate a D value for each group combo
- for(int v=0;v<t->getNumLeaves();v++){
- int index = v;
- double sum = 0.0000;
+ 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){
+ //while you aren't at root
+ while(t->tree[index].getParent() != -1){
- //if you have a BL
- if(t->tree[index].getBranchLength() != -1){
- sum += t->tree[index].getBranchLength();
- }
-
- index = t->tree[index].getParent();
- }
-
- //get last breanch length added
+ //if you have a BL
if(t->tree[index].getBranchLength() != -1){
- sum += t->tree[index].getBranchLength();
+ sum += t->tree[index].getBranchLength();
}
+ index = t->tree[index].getParent();
+ }
- if (globaldata->Groups.size() == 0) {
- //is this sum from a sequence which is in one of the users groups
- if (inUsersGroups(t->tree[v].getGroup(), tmap->namesOfGroups) == true) {
- //is this sum from a sequence which is in this groupCombo
- if ((t->tree[v].getGroup() == tmap->namesOfGroups[b-1]) || (t->tree[v].getGroup() == tmap->namesOfGroups[l])) {
- sum /= (double)tmap->seqsPerGroup[t->tree[v].getGroup()];
- D[n-1] += sum;
- }
+ //get last breanch length added
+ if(t->tree[index].getBranchLength() != -1){
+ sum += t->tree[index].getBranchLength();
+ }
+
+ if (globaldata->Groups.size() == 0) {
+ //is this sum from a sequence which is in one of the users groups
+ if (inUsersGroups(t->tree[v].getGroup(), tmap->namesOfGroups) == true) {
+ //is this sum from a sequence which is in this groupCombo
+ if ((t->tree[v].getGroup() == tmap->namesOfGroups[i-1]) || (t->tree[v].getGroup() == tmap->namesOfGroups[l])) {
+ sum /= (double)tmap->seqsPerGroup[t->tree[v].getGroup()];
+ D[count] += sum;
}
- }else {
- //is this sum from a sequence which is in one of the users groups
- if (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[b-1]) || (t->tree[v].getGroup() == globaldata->Groups[l])) {
- sum /= (double)tmap->seqsPerGroup[t->tree[v].getGroup()];
- D[n-1] += sum;
- }
+ }
+ }else {
+ //is this sum from a sequence which is in one of the users groups
+ if (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-1]) || (t->tree[v].getGroup() == globaldata->Groups[l])) {
+ sum /= (double)tmap->seqsPerGroup[t->tree[v].getGroup()];
+ D[count] += sum;
}
}
}
+ }
/*********************************************************/
- //calculate a u value for each combo
+ count++;
+ }
+ n++;
+ }
+
+ data.clear(); //clear out old values
+
+ for(int i=0;i<t->getNumNodes();i++){
+ //calculate weighted score for each of the group comb i.e. with groups A,B,C = AB, AC, BC.
+ n = 1;
+ for (int b=1; b<numGroups; b++) {
+ for (int l = n; l < numGroups; l++) {
+ //calculate a u value for each combo
double u;
//the user has not entered specific groups
if (globaldata->Groups.size() == 0) {
//calculate weighted score for each group combination
double UN;
n = 1;
+ count = 0;
for (int i=1; i<numGroups; i++) {
for (int l = n; l < numGroups; l++) {
//the user has not entered specific groups
if (globaldata->Groups.size() == 0) {
- UN = (WScore[tmap->namesOfGroups[i-1]+tmap->namesOfGroups[l]] / D[n-1]);
+ UN = (WScore[tmap->namesOfGroups[i-1]+tmap->namesOfGroups[l]] / D[count]);
}else {//they have entered specific groups
- UN = (WScore[globaldata->Groups[i-1]+globaldata->Groups[l]] / D[n-1]);
+ UN = (WScore[globaldata->Groups[i-1]+globaldata->Groups[l]] / D[count]);
}
if (isnan(UN) || isinf(UN)) { UN = 0; }
data.push_back(UN);
+ count++;
}
+ n++;
}
-
return data;
}
catch(exception& e) {
}
-/**************************************************************************************************/
\ No newline at end of file
+/**************************************************************************************************/
+EstOutput Weighted::getValues(Tree* t, string groupA, string groupB) {
+ try {
+ globaldata = GlobalData::getInstance();
+
+ data.clear(); //clear out old values
+
+ //initialize weighted score
+ WScore[(groupA+groupB)] = 0.0;
+ float D = 0.0;
+
+
+ /********************************************************/
+ //calculate a D value for the 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 += t->tree[index].getBranchLength();
+ }
+ index = t->tree[index].getParent();
+ }
+
+ //get last breanch length added
+ if(t->tree[index].getBranchLength() != -1){
+ sum += 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;
+ }
+ }
+ /********************************************************/
+
+ //calculate u for the group comb
+ for(int i=0;i<t->getNumNodes();i++){
+ double u;
+ //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];
+ }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];
+ }
+
+ u = abs(u) * t->tree[i].getBranchLength();
+
+ //save groupcombs u value
+ WScore[(groupA+groupB)] += u;
+ }
+
+ /********************************************************/
+
+ //calculate weighted score for the group combination
+ double UN;
+ UN = (WScore[(groupA+groupB)] / D);
+
+ if (isnan(UN) || isinf(UN)) { UN = 0; }
+ data.push_back(UN);
+
+ 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";
+ 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);
+ }
+
+}
+
+
+
+
+
+
+
+
+
projects / mothur.git / blobdiff