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
  17                 //clear out old values
  18                 data.resize(1,0);
  19                 penalty.resize(t->getNumLeaves(), 0);
  20
  21                 map<string,double> unique;  //group, total of all branch lengths of nodes with that group.
  22                 double shared = 0.0000;
  23                 double UW=0.0000;
  24
  25                 //add up the branch lengths for each group.
  26                 for(int i=0;i<t->getNumLeaves();i++){
  27                         if(t->tree[i].pGroups.size() > 0){
  28                                 unique[t->tree[i].pGroups.begin()->first] += t->tree[i].getBranchLength();
  29                         }
  30                 }
  31
  32                 //for each non-leaf node
  33                 for(int i=t->getNumLeaves();i<t->getNumNodes();i++){
  34
  35                         int lc = t->tree[i].getLChild();  //lc = vector index of left child
  36                         int rc = t->tree[i].getRChild();  //rc = vector index of right child
  37
  38                         //get penalty values
  39                         if(t->tree[rc].pGroups.size() == 0 || t->tree[lc].pGroups.size() == 0){
  40                                 penalty.push_back(penalty[t->tree[rc].getIndex()]+penalty[t->tree[lc].getIndex()]);
  41                         }
  42                         else if(t->tree[i].pGroups.size() > t->tree[rc].pGroups.size() || t->tree[i].pGroups.size() > t->tree[lc].pGroups.size()){
  43                                 penalty.push_back(penalty[t->tree[rc].getIndex()]+penalty[t->tree[lc].getIndex()]+1);
  44                         }
  45                         else{
  46                                 penalty.push_back(penalty[t->tree[rc].getIndex()]+penalty[t->tree[lc].getIndex()]);
  47                         }
  48
  49                         //not sure when this would ever be true??? if your parent is root could be, but pGroups.size() should never be 0.
  50                         if(t->tree[i].getParent() == -1 && (t->tree[lc].pGroups.size() == 0 || t->tree[rc].pGroups.size() == 0)){
  51                                 shared -= 1;
  52                         }
  53                         else if(penalty[i] != 0 && t->tree[i].pGroups.size() != 0){
  54                                 shared += t->tree[i].getBranchLength();
  55                         }
  56                         else if( t->tree[i].pGroups.size() != 0){
  57                                 unique[t->tree[i].pGroups.begin()->first] += t->tree[i].getBranchLength();
  58                         }
  59                 }
  60
  61                 map<string,double>::iterator pos;
  62                 for(pos=unique.begin();pos!=unique.end();pos++){
  63                         if(pos->first!="xxx"){
  64                                 UW += unique[pos->first];
  65                         }
  66                 }
  67
  68                 UW /= (UW + shared);
  69
  70                 if (isnan(UW) || isinf(UW)) { UW = 0; }
  71
  72                 data[0] = UW;
  73
  74                 return data;
  75
  76         }
  77         catch(exception& e) {
  78                 cout << "Standard Error: " << e.what() << " has occurred in the Unweighted class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  79                 exit(1);
  80         }
  81         catch(...) {
  82                 cout << "An unknown error has occurred in the Unweighted class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  83                 exit(1);
  84         }
  85
  86 }
  87
  88 /**************************************************************************************************/