try {
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();
- }
+ 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++) {
+ int count = 0;
+ for (int i=0; i<numGroups; i++) {
+ for (int l = i+1; l < numGroups; l++) {
//initialize weighted scores
- if (globaldata->Groups.size() == 0) {
- WScore[tmap->namesOfGroups[i-1]+tmap->namesOfGroups[l]] = 0.0;
- }else {
- WScore[globaldata->Groups[i-1]+globaldata->Groups[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();
- }
-
- //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();
+ 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
+ /********************************************************/
+ //calculate a D value for each group combo
+ for(int v=0;v<t->getNumLeaves();v++){
- if(lc == 0 || rc == 0){
- sum -= t->tree[old_index].getBranchLength();
+ if (m->control_pressed) { return data; }
+
+ 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());
+ }
+
+ //is this sum from a sequence which is in one of the users groups
+ if (m->inUsersGroups(t->tree[v].getGroup(), globaldata->Groups) == true) {
+ //is this sum from a sequence which is in this groupCombo
+ 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;
+ }
}
}
- }
-
- if(t->tree[i].getGroup() != ""){
- sum /= (double)tmap->seqsPerGroup[t->tree[i].getGroup()];
- D += sum;
+ /*********************************************************/
+ count++;
}
}
-
+
+ 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;
- //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();
+ for (int b=0; b<numGroups; b++) {
+ for (int l = b+1; l < numGroups; l++) {
+
+ if (m->control_pressed) { return data; }
- //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]];
- }
+ //calculate a u value for each combo
+ double u;
+ //does this node have descendants from group b-1
+ it = t->tree[i].pcount.find(globaldata->Groups[b]);
+ //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]] / (double) tmap->seqsPerGroup[globaldata->Groups[b]];
+ }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();
+ u = abs(u * t->tree[i].getBranchLength());
- //save groupcombs u value
- WScore[globaldata->Groups[b-1]+globaldata->Groups[l]] += u;
- }
+ //save groupcombs u value
+ WScore[globaldata->Groups[b]+globaldata->Groups[l]] += u;
+ /*********************************************************/
}
- n++;
}
}
//calculate weighted score for each group combination
double UN;
- n = 1;
- 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);
- }else {//they have entered specific groups
- UN = (WScore[globaldata->Groups[i-1]+globaldata->Groups[l]] / D);
- }
+ count = 0;
+ for (int i=0; i<numGroups; i++) {
+ for (int l = i+1; l < numGroups; l++) {
+ UN = (WScore[globaldata->Groups[i]+globaldata->Groups[l]] / D[count]);
+
if (isnan(UN) || isinf(UN)) { UN = 0; }
data.push_back(UN);
+ count++;
}
}
-
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";
+}
+
+/**************************************************************************************************/
+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;
+
+ vector<string> groups; groups.push_back(groupA); groups.push_back(groupB);
+
+ /********************************************************/
+ //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;
+
+ //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->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);
+ //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) {
+ m->errorOut(e, "Weighted", "getValues");
exit(1);
}
-
}
-/**************************************************************************************************/
\ No newline at end of file
+
+
+
+
+
+
+
+
projects / mothur.git / blobdiff