EstOutput Parsimony::getValues(Tree* t) {
try {
globaldata = GlobalData::getInstance();
+ vector<string> groups;
copyTree = new Tree();
//if the users enters no groups then give them the score of all groups
int numGroups = globaldata->Groups.size();
- if (numGroups == 0) {
- numGroups++;
- for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
- globaldata->Groups.push_back(tmap->namesOfGroups[i]);
- }
- }
//calculate number of comparsions
int numComp = 0;
//numComp+1 for AB, AC, BC, ABC
data.resize(numComp+1,0);
- vector<string> groups;
int count = 0;
for (int a=0; a<numGroups; a++) {
- for (int l = a+1; l < numGroups; l++) {
+ for (int l = 0; l < a; l++) {
int score = 0;
//groups in this combo
}
for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
+
+ if (m->control_pressed) { return data; }
+
int lc = copyTree->tree[i].getLChild();
int rc = copyTree->tree[i].getRChild();
}
}
- //get score for all users groups
-
- //copy users tree so that you can redo pgroups
- copyTree->getCopy(t);
- int score = 0;
+ if (numComp != 1) {
+ if (numGroups == 0) {
+ //get score for all users groups
+ for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
+ if (tmap->namesOfGroups[i] != "xxx") {
+ groups.push_back(tmap->namesOfGroups[i]);
+ }
+ }
+ }else {
+ for (int i = 0; i < globaldata->Groups.size(); i++) {
+ groups.push_back(globaldata->Groups[i]);
+ }
+ }
+
+ //copy users tree so that you can redo pgroups
+ copyTree->getCopy(t);
+ int score = 0;
- //create pgroups that reflect the groups the user want to use
- for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
- copyTree->tree[i].pGroups = (copyTree->mergeUserGroups(i, globaldata->Groups));
- }
+ //create pgroups that reflect the groups the user want to use
+ for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
+ copyTree->tree[i].pGroups = (copyTree->mergeUserGroups(i, groups));
+ }
- for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
- int lc = copyTree->tree[i].getLChild();
- int rc = copyTree->tree[i].getRChild();
+// map<string,int>::iterator it;
+
+ for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
+
+ if (m->control_pressed) { return data; }
+
+ int lc = copyTree->tree[i].getLChild();
+ int rc = copyTree->tree[i].getRChild();
- int iSize = copyTree->tree[i].pGroups.size();
- int rcSize = copyTree->tree[rc].pGroups.size();
- int lcSize = copyTree->tree[lc].pGroups.size();
+ int iSize = copyTree->tree[i].pGroups.size();
+ int rcSize = copyTree->tree[rc].pGroups.size();
+ int lcSize = copyTree->tree[lc].pGroups.size();
+
+
+ //if isize are 0 then that branch is to be ignored
+ if (iSize == 0) { }
+ else if ((rcSize == 0) || (lcSize == 0)) { }
+ //if you have more groups than either of your kids then theres been a change.
+ else if(iSize > rcSize || iSize > lcSize){
+ score++;
+ }
+ }
- //if isize are 0 then that branch is to be ignored
- if (iSize == 0) { }
- else if ((rcSize == 0) || (lcSize == 0)) { }
- //if you have more groups than either of your kids then theres been a change.
- else if(iSize > rcSize || iSize > lcSize){
- score++;
- }
- }
+ data[count] = score;
+
+ }
- data[count] = score;
+ delete copyTree;
return data;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the Parsimony class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "Parsimony", "getValues");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the Parsimony class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-
}
/**************************************************************************************************/