//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;
+ float UniqueBL=0.0000; //a branch length is unique if it's chidren are from the same group
+ float totalBL = 0.00; //all branch lengths
+ float 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();
- }
- }
-
- //for each non-leaf node
+ map<string, int>::iterator it; //iterator to traverse pgroups
+ map<string, int> copyLCpcount;
+ map<string, int> copyRCpcount;
+ map<string, int> copyIpcount;
+
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);
+ /**********************************************************************/
+ //This section adds in all lengths that are non leaf
+
+ //copy left childs pGroups and remove groups that the user doesn't want
+ 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{
- penalty.push_back(penalty[t->tree[rc].getIndex()]+penalty[t->tree[lc].getIndex()]);
+
+ //copy left childs pGroups and remove groups that the user doesn't want
+ copyLCpcount = t->tree[lc].pcount;
+ for (it = copyLCpcount.begin(); it != copyLCpcount.end(); it++) {
+ if (inUsersGroups(it->first, globaldata->Groups) != true) { copyLCpcount.erase(it->first); }
}
- //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;
+ //copy right childs pGroups and remove groups that the user doesn't want
+ copyRCpcount = t->tree[rc].pcount;
+ for (it = copyRCpcount.begin(); it != copyRCpcount.end(); it++) {
+ if (inUsersGroups(it->first, globaldata->Groups) != true) { copyRCpcount.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 and i has a BL then add i's length to unique
+ //if copyRCpcount.size() = 0 && copyLCpcount.size() = 0 they are from a branch that is entirely from a group the user doesn't want
+ if ((copyRCpcount.size() == 0) && (copyLCpcount.size() == 0)) { }
+ else {
+ if ((copyRCpcount == copyLCpcount) && (t->tree[i].getBranchLength() != -1)) { UniqueBL += t->tree[i].getBranchLength(); }
+ //if either childs groups = 0 then all of there groups were not valid making the parent unique
+ else if (((copyRCpcount.size() == 0) || (copyLCpcount.size() == 0)) && (t->tree[i].getBranchLength() != -1)) { UniqueBL += t->tree[i].getBranchLength(); }
}
- else if( t->tree[i].pGroups.size() != 0){
- unique[t->tree[i].pGroups.begin()->first] += 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();
}
- }
-
- map<string,double>::iterator pos;
- for(pos=unique.begin();pos!=unique.end();pos++){
- if((pos->first!="xxx") && (inUsersGroups(pos->first))){
- UW += unique[pos->first];
+
+ /**********************************************************************/
+ //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();
+ }
+ }
+
+ 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; }
}
-/**************************************************************************************************/
-bool Unweighted::inUsersGroups(string groupname) {
- try {
- for (int i = 0; i < globaldata->Groups.size(); i++) {
- if (groupname == globaldata->Groups[i]) { return true; }
- }
- return false;
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the Unweighted class Function inUsersGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the Unweighted class function inUsersGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-}
\ No newline at end of file
projects / mothur.git / blobdiff