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                 float UniqueBL=0.0000;  //a branch length is unique if it's chidren are from the same group
  22                 float totalBL = 0.00;   //all branch lengths
  23                 float UW = 0.00;                //Unweighted Value = UniqueBL / totalBL;
  24
  25                 map<string, int>::iterator it;  //iterator to traverse pgroups
  26                 map<string, int> copyLCpcount;
  27                 map<string, int> copyRCpcount;
  28                 map<string, int> copyIpcount;
  29
  30                 for(int i=t->getNumLeaves();i<t->getNumNodes();i++){
  31
  32                         int lc = t->tree[i].getLChild();  //lc = vector index of left child
  33                         int rc = t->tree[i].getRChild();  //rc = vector index of right child
  34
  35                         /**********************************************************************/
  36                         //This section adds in all lengths that are non leaf
  37
  38                         //copy left childs pGroups and remove groups that the user doesn't want
  39                         copyIpcount = t->tree[i].pcount;
  40                         for (it = copyIpcount.begin(); it != copyIpcount.end(); it++) {
  41                                 if (inUsersGroups(it->first, globaldata->Groups) != true) {     copyIpcount.erase(it->first);   }
  42                         }
  43
  44                         //copy left childs pGroups and remove groups that the user doesn't want
  45                         copyLCpcount = t->tree[lc].pcount;
  46                         for (it = copyLCpcount.begin(); it != copyLCpcount.end(); it++) {
  47                                 if (inUsersGroups(it->first, globaldata->Groups) != true) {     copyLCpcount.erase(it->first);  }
  48                         }
  49
  50                         //copy right childs pGroups and remove groups that the user doesn't want
  51                         copyRCpcount = t->tree[rc].pcount;
  52                         for (it = copyRCpcount.begin(); it != copyRCpcount.end(); it++) {
  53                                 if (inUsersGroups(it->first, globaldata->Groups) != true) {     copyRCpcount.erase(it->first);  }
  54                         }
  55
  56                         //if i's children are from the same group and i has a BL then add i's length to unique
  57                         //if copyRCpcount.size() = 0 && copyLCpcount.size() = 0 they are from a branch that is entirely from a group the user doesn't want
  58                         if ((copyRCpcount.size() == 0) && (copyLCpcount.size() == 0)) { }
  59                         else {
  60                                 if ((copyRCpcount == copyLCpcount) && (t->tree[i].getBranchLength() != -1)) {  UniqueBL += t->tree[i].getBranchLength();        }
  61                                 //if either childs groups = 0 then all of there groups were not valid making the parent unique
  62                                 else if (((copyRCpcount.size() == 0) || (copyLCpcount.size() == 0)) && (t->tree[i].getBranchLength() != -1)) {  UniqueBL += t->tree[i].getBranchLength();       }
  63                         }
  64
  65                         //add i's BL to total if it is from the groups the user wants
  66                         if ((t->tree[i].getBranchLength() != -1) && (copyIpcount.size() != 0)) {
  67                                 totalBL += t->tree[i].getBranchLength();
  68                         }
  69
  70                         /**********************************************************************/
  71                         //This section adds in all lengths that are leaf
  72
  73                         //if i's chidren are leaves
  74                         if (t->tree[rc].getRChild() == -1) {
  75                                 //if rc is a valid group and rc has a BL
  76                                 if ((inUsersGroups(t->tree[rc].getGroup(), globaldata->Groups) == true) && (t->tree[rc].getBranchLength() != -1)) {
  77                                         UniqueBL += t->tree[rc].getBranchLength();
  78                                         totalBL += t->tree[rc].getBranchLength();
  79                                 }
  80                         }
  81
  82                         if (t->tree[lc].getLChild() == -1) {
  83                                 //if lc is a valid group and lc has a BL
  84                                 if ((inUsersGroups(t->tree[lc].getGroup(), globaldata->Groups) == true) && (t->tree[lc].getBranchLength() != -1)) {
  85                                         UniqueBL += t->tree[lc].getBranchLength();
  86                                         totalBL += t->tree[lc].getBranchLength();
  87                                 }
  88                         }
  89
  90                         /**********************************************************************/
  91
  92                 }
  93
  94                 UW = (UniqueBL / totalBL);
  95
  96                 if (isnan(UW) || isinf(UW)) { UW = 0; }
  97
  98                 data[0] = UW;
  99
 100                 return data;
 101
 102         }
 103         catch(exception& e) {
 104                 cout << "Standard Error: " << e.what() << " has occurred in the Unweighted class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 105                 exit(1);
 106         }
 107         catch(...) {
 108                 cout << "An unknown error has occurred in the Unweighted class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 109                 exit(1);
 110         }
 111
 112 }
 113