unweighted.cpp

   1 /*
   2  *  unweighted.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 2/9/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "unweighted.h"
  11
  12 /**************************************************************************************************/
  13
  14 EstOutput Unweighted::getValues(Tree* t) {
  15         try {
  16                 globaldata = GlobalData::getInstance();
  17
  18                 //clear out old values
  19                 data.resize(1,0);
  20                 penalty.resize(t->getNumLeaves(), 0);
  21
  22                 map<string,double> unique;  //group, total of all branch lengths of nodes with that group.
  23                 double shared = 0.0000;
  24                 double UW=0.0000;
  25
  26                 //add up the branch lengths for each group.
  27                 for(int i=0;i<t->getNumLeaves();i++){
  28                         if(t->tree[i].pGroups.size() > 0){
  29                                 unique[t->tree[i].pGroups.begin()->first] += t->tree[i].getBranchLength();
  30                         }
  31                 }
  32
  33                 //for each non-leaf node
  34                 for(int i=t->getNumLeaves();i<t->getNumNodes();i++){
  35
  36                         int lc = t->tree[i].getLChild();  //lc = vector index of left child
  37                         int rc = t->tree[i].getRChild();  //rc = vector index of right child
  38
  39                         //get penalty values
  40                         if(t->tree[rc].pGroups.size() == 0 || t->tree[lc].pGroups.size() == 0){
  41                                 penalty.push_back(penalty[t->tree[rc].getIndex()]+penalty[t->tree[lc].getIndex()]);
  42                         }
  43                         else if(t->tree[i].pGroups.size() > t->tree[rc].pGroups.size() || t->tree[i].pGroups.size() > t->tree[lc].pGroups.size()){
  44                                 penalty.push_back(penalty[t->tree[rc].getIndex()]+penalty[t->tree[lc].getIndex()]+1);
  45                         }
  46                         else{
  47                                 penalty.push_back(penalty[t->tree[rc].getIndex()]+penalty[t->tree[lc].getIndex()]);
  48                         }
  49
  50                         //not sure when this would ever be true??? if your parent is root could be, but pGroups.size() should never be 0.
  51                         if(t->tree[i].getParent() == -1 && (t->tree[lc].pGroups.size() == 0 || t->tree[rc].pGroups.size() == 0)){
  52                                 shared -= 1;
  53                         }
  54                         else if(penalty[i] != 0 && t->tree[i].pGroups.size() != 0){
  55                                 shared += t->tree[i].getBranchLength();
  56                         }
  57                         else if( t->tree[i].pGroups.size() != 0){
  58                                 unique[t->tree[i].pGroups.begin()->first] += t->tree[i].getBranchLength();
  59                         }
  60                 }
  61
  62                 map<string,double>::iterator pos;
  63                 for(pos=unique.begin();pos!=unique.end();pos++){
  64                         if((pos->first!="xxx") && (inUsersGroups(pos->first))){
  65                                 UW += unique[pos->first];
  66                         }
  67                 }
  68
  69                 UW /= (UW + shared);
  70
  71                 if (isnan(UW) || isinf(UW)) { UW = 0; }
  72
  73                 data[0] = UW;
  74
  75                 return data;
  76
  77         }
  78         catch(exception& e) {
  79                 cout << "Standard Error: " << e.what() << " has occurred in the Unweighted class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  80                 exit(1);
  81         }
  82         catch(...) {
  83                 cout << "An unknown error has occurred in the Unweighted class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  84                 exit(1);
  85         }
  86
  87 }
  88
  89 /**************************************************************************************************/
  90 bool Unweighted::inUsersGroups(string groupname) {
  91         try {
  92                 for (int i = 0; i < globaldata->Groups.size(); i++) {
  93                         if (groupname == globaldata->Groups[i]) { return true; }
  94                 }
  95                 return false;
  96         }
  97         catch(exception& e) {
  98                 cout << "Standard Error: " << e.what() << " has occurred in the Unweighted class Function inUsersGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  99                 exit(1);
 100         }
 101         catch(...) {
 102                 cout << "An unknown error has occurred in the Unweighted class function inUsersGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 103                 exit(1);
 104         }
 105 }