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
  21                 double UniqueBL=0.0000;  //a branch length is unique if it's chidren are from the same group
  22                 double totalBL = 0.00;  //all branch lengths
  23                 double UW = 0.00;               //Unweighted Value = UniqueBL / totalBL;
  24
  25                 map<string, int>::iterator it;  //iterator to traverse pgroups
  26                 map<string, int> copyIpcount;
  27
  28                 for(int i=t->getNumLeaves();i<t->getNumNodes();i++){
  29
  30                         int lc = t->tree[i].getLChild();  //lc = vector index of left child
  31                         int rc = t->tree[i].getRChild();  //rc = vector index of right child
  32
  33                         /**********************************************************************/
  34                         //This section adds in all lengths that are non leaf
  35
  36                         copyIpcount = t->tree[i].pcount;
  37                         for (it = copyIpcount.begin(); it != copyIpcount.end(); it++) {
  38                                 if (inUsersGroups(it->first, globaldata->Groups) != true) {     copyIpcount.erase(it->first);   }
  39                         }
  40
  41                         //if i's children are from the same group then i's pcount size will be 1
  42                         //if copyIpcount.size() = 0 they are from a branch that is entirely from a group the user doesn't want
  43                         if (copyIpcount.size() == 0) { }
  44                         else if ((t->tree[i].getBranchLength() != -1) && (copyIpcount.size() == 1)) {  UniqueBL += t->tree[i].getBranchLength();        }
  45
  46                         //add i's BL to total if it is from the groups the user wants
  47                         if ((t->tree[i].getBranchLength() != -1) && (copyIpcount.size() != 0)) {
  48                                 totalBL += t->tree[i].getBranchLength();
  49                         }
  50
  51                         /**********************************************************************/
  52                         //This section adds in all lengths that are leaf
  53
  54                         //if i's chidren are leaves
  55                         if (t->tree[rc].getRChild() == -1) {
  56                                 //if rc is a valid group and rc has a BL
  57                                 if ((inUsersGroups(t->tree[rc].getGroup(), globaldata->Groups) == true) && (t->tree[rc].getBranchLength() != -1)) {
  58                                         UniqueBL += t->tree[rc].getBranchLength();
  59                                         totalBL += t->tree[rc].getBranchLength();
  60                                 }
  61                         }
  62
  63                         if (t->tree[lc].getLChild() == -1) {
  64                                 //if lc is a valid group and lc has a BL
  65                                 if ((inUsersGroups(t->tree[lc].getGroup(), globaldata->Groups) == true) && (t->tree[lc].getBranchLength() != -1)) {
  66                                         UniqueBL += t->tree[lc].getBranchLength();
  67                                         totalBL += t->tree[lc].getBranchLength();
  68                                 }
  69                         }
  70
  71                         /**********************************************************************/
  72                 }
  73
  74                 UW = (UniqueBL / totalBL);
  75
  76                 if (isnan(UW) || isinf(UW)) { UW = 0; }
  77
  78                 data[0] = UW;
  79
  80                 return data;
  81
  82         }
  83         catch(exception& e) {
  84                 cout << "Standard Error: " << e.what() << " has occurred in the Unweighted class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  85                 exit(1);
  86         }
  87         catch(...) {
  88                 cout << "An unknown error has occurred in the Unweighted class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  89                 exit(1);
  90         }
  91
  92 }
  93