X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=unweighted.cpp;h=1a2573b6d5738055ddd7d69448a321369d72bb53;hb=d97b619c4297b1274c754d73a64792ba656b0a79;hp=4416e79afd680059b8958cab6c28e035b3633d1c;hpb=bfbc55964f1977da72c2cea984288a427d370a59;p=mothur.git diff --git a/unweighted.cpp b/unweighted.cpp index 4416e79..1a2573b 100644 --- a/unweighted.cpp +++ b/unweighted.cpp @@ -17,56 +17,81 @@ EstOutput Unweighted::getValues(Tree* t) { //clear out old values data.resize(1,0); - penalty.resize(t->getNumLeaves(), 0); - map 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;igetNumLeaves();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::iterator it; //iterator to traverse pgroups + map copyLCpcount; + map copyRCpcount; + map copyIpcount; + for(int i=t->getNumLeaves();igetNumNodes();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::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; } @@ -86,20 +111,3 @@ EstOutput Unweighted::getValues(Tree* t) { } -/**************************************************************************************************/ -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