EstOutput Unweighted::getValues(Tree* t) {
try {
-
+ globaldata = GlobalData::getInstance();
+
//clear out old values
data.resize(1,0);
- penalty.resize(t->getNumLeaves(), 0);
- map<string,double> unique; //group, total of all branch lengths of nodes with that group.
- double shared = 0.0000;
- double UW=0.0000;
+ double UniqueBL=0.0000; //a branch length is unique if it's chidren are from the same group
+ double totalBL = 0.00; //all branch lengths
+ double UW = 0.00; //Unweighted Value = UniqueBL / totalBL;
- //add up the branch lengths for each group.
- for(int i=0;i<t->getNumLeaves();i++){
- if(t->tree[i].pGroups.size() > 0){
- unique[t->tree[i].pGroups.begin()->first] += t->tree[i].getBranchLength();
- }
- }
+ map<string, int>::iterator it; //iterator to traverse pgroups
+ map<string, int> copyIpcount;
- //for each non-leaf node
for(int i=t->getNumLeaves();i<t->getNumNodes();i++){
int lc = t->tree[i].getLChild(); //lc = vector index of left child
int rc = t->tree[i].getRChild(); //rc = vector index of right child
- //get penalty values
- if(t->tree[rc].pGroups.size() == 0 || t->tree[lc].pGroups.size() == 0){
- penalty.push_back(penalty[t->tree[rc].getIndex()]+penalty[t->tree[lc].getIndex()]);
- }
- else if(t->tree[i].pGroups.size() > t->tree[rc].pGroups.size() || t->tree[i].pGroups.size() > t->tree[lc].pGroups.size()){
- penalty.push_back(penalty[t->tree[rc].getIndex()]+penalty[t->tree[lc].getIndex()]+1);
- }
- else{
- penalty.push_back(penalty[t->tree[rc].getIndex()]+penalty[t->tree[lc].getIndex()]);
- }
-
- //not sure when this would ever be true??? if your parent is root could be, but pGroups.size() should never be 0.
- if(t->tree[i].getParent() == -1 && (t->tree[lc].pGroups.size() == 0 || t->tree[rc].pGroups.size() == 0)){
- shared -= 1;
+ /**********************************************************************/
+ //This section adds in all lengths that are non leaf
+
+ copyIpcount = t->tree[i].pcount;
+ for (it = copyIpcount.begin(); it != copyIpcount.end(); it++) {
+ if (inUsersGroups(it->first, globaldata->Groups) != true) { copyIpcount.erase(it->first); }
}
- else if(penalty[i] != 0 && t->tree[i].pGroups.size() != 0){
- shared += t->tree[i].getBranchLength();
+
+ //if i's children are from the same group then i's pcount size will be 1
+ //if copyIpcount.size() = 0 they are from a branch that is entirely from a group the user doesn't want
+ if (copyIpcount.size() == 0) { }
+ else if ((t->tree[i].getBranchLength() != -1) && (copyIpcount.size() == 1)) { UniqueBL += t->tree[i].getBranchLength(); }
+
+ //add i's BL to total if it is from the groups the user wants
+ if ((t->tree[i].getBranchLength() != -1) && (copyIpcount.size() != 0)) {
+ totalBL += t->tree[i].getBranchLength();
}
- else if( t->tree[i].pGroups.size() != 0){
- unique[t->tree[i].pGroups.begin()->first] += t->tree[i].getBranchLength();
+
+ /**********************************************************************/
+ //This section adds in all lengths that are leaf
+
+ //if i's chidren are leaves
+ if (t->tree[rc].getRChild() == -1) {
+ //if rc is a valid group and rc has a BL
+ if ((inUsersGroups(t->tree[rc].getGroup(), globaldata->Groups) == true) && (t->tree[rc].getBranchLength() != -1)) {
+ UniqueBL += t->tree[rc].getBranchLength();
+ totalBL += t->tree[rc].getBranchLength();
+ }
}
- }
-
- map<string,double>::iterator pos;
- for(pos=unique.begin();pos!=unique.end();pos++){
- if(pos->first!="xxx"){
- UW += unique[pos->first];
+
+ if (t->tree[lc].getLChild() == -1) {
+ //if lc is a valid group and lc has a BL
+ if ((inUsersGroups(t->tree[lc].getGroup(), globaldata->Groups) == true) && (t->tree[lc].getBranchLength() != -1)) {
+ UniqueBL += t->tree[lc].getBranchLength();
+ totalBL += t->tree[lc].getBranchLength();
+ }
}
+
+ /**********************************************************************/
}
-
- UW /= (UW + shared);
+
+ UW = (UniqueBL / totalBL);
if (isnan(UW) || isinf(UW)) { UW = 0; }
}
-/**************************************************************************************************/
\ No newline at end of file