EstOutput Weighted::getValues(Tree* t) {
try {
-
- int numGroups = tmap->getNumGroups();
+ globaldata = GlobalData::getInstance();
+ int numGroups;
+ vector<double> D;
+
+ //if the user has not entered specific groups to analyze then do them all
+ if (globaldata->Groups.size() == 0) {
+ numGroups = tmap->getNumGroups();
+ }else {
+ numGroups = globaldata->Groups.size();
+ }
//calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3;
int n = 1;
for (int i=1; i<numGroups; i++) {
for (int l = n; l < numGroups; l++) {
//initialize weighted scores
- WScore[tmap->namesOfGroups[i-1]+tmap->namesOfGroups[l]] = 0.0;
- }
- }
-
- data.clear(); //clear out old values
-
- double D = 0.0000;
-
- for(int i=0;i<t->getNumLeaves();i++){
- int index = i;
- double sum = 0.0000;
-
- //while you aren't at root
- while(t->tree[index].getParent() != -1){
-
- if(t->tree[index].pGroups.size() != 0){
- sum += t->tree[index].getBranchLength();
+ 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
}
-
- //old_index = you
- int old_index = index;
- //index = your parent
- index = t->tree[index].getParent();
-
- //if you grandparent is the root
- if(t->tree[index].getParent() == -1 && t->tree[old_index].pGroups.size() != 0){
- int lc = t->tree[t->tree[index].getLChild()].pGroups.size();
- int rc = t->tree[t->tree[index].getRChild()].pGroups.size();
-
-
- if(lc == 0 || rc == 0){
- sum -= t->tree[old_index].getBranchLength();
- }
- }
- }
-
- if(t->tree[i].getGroup() != ""){
- sum /= (double)tmap->seqsPerGroup[t->tree[i].getGroup()];
- D += sum;
}
}
-
+
+ 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++) {
- double u;
- //does this node have descendants from group b-1
- it = t->tree[i].pcount.find(tmap->namesOfGroups[b-1]);
- //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[tmap->namesOfGroups[b-1]] / (double) tmap->seqsPerGroup[tmap->namesOfGroups[b-1]];
- }else { u = 0.00; }
+
+ /********************************************************/
+ //calculate a D value for each group combo
+ for(int v=0;v<t->getNumLeaves();v++){
+ int index = v;
+ double sum = 0.0000;
- //does this node have descendants from group l
- it = t->tree[i].pcount.find(tmap->namesOfGroups[l]);
- //if it does subtract their percentage from u
- if (it != t->tree[i].pcount.end()) {
- u -= (double) t->tree[i].pcount[tmap->namesOfGroups[l]] / (double) tmap->seqsPerGroup[tmap->namesOfGroups[l]];
+ //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 (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;
+ }
+ }
+ }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;
+ }
+ }
+ }
}
+ /*********************************************************/
+ //calculate a u value for each combo
+ double u;
+ //the user has not entered specific groups
+ if (globaldata->Groups.size() == 0) {
+ //does this node have descendants from group b-1
+ it = t->tree[i].pcount.find(tmap->namesOfGroups[b-1]);
+ //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[tmap->namesOfGroups[b-1]] / (double) tmap->seqsPerGroup[tmap->namesOfGroups[b-1]];
+ }else { u = 0.00; }
+
+ //does this node have descendants from group l
+ it = t->tree[i].pcount.find(tmap->namesOfGroups[l]);
+ //if it does subtract their percentage from u
+ if (it != t->tree[i].pcount.end()) {
+ u -= (double) t->tree[i].pcount[tmap->namesOfGroups[l]] / (double) tmap->seqsPerGroup[tmap->namesOfGroups[l]];
+ }
- u = abs(u) * t->tree[i].getBranchLength();
+ u = abs(u) * t->tree[i].getBranchLength();
- //save groupcombs u value
- WScore[tmap->namesOfGroups[b-1]+tmap->namesOfGroups[l]] += u;
-
+ //save groupcombs u value
+ WScore[tmap->namesOfGroups[b-1]+tmap->namesOfGroups[l]] += u;
+
+ //the user has entered specific groups
+ }else {
+ //does this node have descendants from group b-1
+ it = t->tree[i].pcount.find(globaldata->Groups[b-1]);
+ //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[globaldata->Groups[b-1]] / (double) tmap->seqsPerGroup[globaldata->Groups[b-1]];
+ }else { u = 0.00; }
+
+ //does this node have descendants from group l
+ it = t->tree[i].pcount.find(globaldata->Groups[l]);
+ //if it does subtract their percentage from u
+ if (it != t->tree[i].pcount.end()) {
+ u -= (double) t->tree[i].pcount[globaldata->Groups[l]] / (double) tmap->seqsPerGroup[globaldata->Groups[l]];
+ }
+
+ u = abs(u) * t->tree[i].getBranchLength();
+
+ //save groupcombs u value
+ WScore[globaldata->Groups[b-1]+globaldata->Groups[l]] += u;
+ }
+ /*********************************************************/
}
n++;
}
n = 1;
for (int i=1; i<numGroups; i++) {
for (int l = n; l < numGroups; l++) {
- UN = (WScore[tmap->namesOfGroups[i-1]+tmap->namesOfGroups[l]] / D);
+ //the user has not entered specific groups
+ if (globaldata->Groups.size() == 0) {
+ UN = (WScore[tmap->namesOfGroups[i-1]+tmap->namesOfGroups[l]] / D[n-1]);
+ }else {//they have entered specific groups
+ UN = (WScore[globaldata->Groups[i-1]+globaldata->Groups[l]] / D[n-1]);
+ }
if (isnan(UN) || isinf(UN)) { UN = 0; }
data.push_back(UN);
}
projects / mothur.git / blobdiff