phylodiversity.cpp

   1 /*
   2  *  phylodiversity.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 4/30/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "phylodiversity.h"
  11
  12 /**************************************************************************************************
  13 EstOutput PhyloDiversity::getValues(Tree* t, vector<int> treeNodes, vector< vector<float> >& data) {
  14     try {
  15
  16                 map<string, float> DScore;
  17                 float totalLength = 0.0;
  18                 data.clear();
  19
  20                 //initialize Dscore
  21                 for (int i=0; i<globaldata->Groups.size(); i++) {               DScore[globaldata->Groups[i]] = 0.0;    }
  22
  23                 ********************************************************
  24                 //calculate a D value for each group
  25                 for(int v=0;v<treeNodes.size();v++){
  26
  27                         if (m->control_pressed) { return data; }
  28
  29                         //calc the branch length
  30                         //while you aren't at root
  31                         float sum = 0.0;
  32                         int index = treeNodes[v];
  33
  34                         while(t->tree[index].getParent() != -1){
  35
  36                                 //if you have a BL
  37                                 if(t->tree[index].getBranchLength() != -1){
  38                                         sum += abs(t->tree[index].getBranchLength());
  39                                 }
  40                                 index = t->tree[index].getParent();
  41                         }
  42
  43                         //get last breanch length added
  44                         if(t->tree[index].getBranchLength() != -1){
  45                                 sum += abs(t->tree[index].getBranchLength());
  46                         }
  47
  48                         //for each group in the groups update the total branch length accounting for the names file
  49                         vector<string> groups = t->tree[treeNodes[v]].getGroup();
  50                         for (int j = 0; j < groups.size(); j++) {
  51                                 int numSeqsInGroupJ = 0;
  52                                 map<string, int>::iterator it;
  53                                 it = t->tree[treeNodes[v]].pcount.find(groups[j]);
  54                                 if (it != t->tree[treeNodes[v]].pcount.end()) { //this leaf node contains seqs from group j
  55                                         numSeqsInGroupJ = it->second;
  56                                 }
  57
  58                                 //add branch length to total for group
  59                                 DScore[groups[j]] += (numSeqsInGroupJ * sum);
  60                         }
  61
  62                 }
  63
  64
  65                 for (int i=0; i<globaldata->Groups.size(); i++) {
  66                         float percent = DScore[globaldata->Groups[i]];
  67                         data.push_back(percent);
  68
  69                 }
  70
  71                 return data;
  72         }
  73         catch(exception& e) {
  74                 m->errorOut(e, "PhyloDiversity", "getValues");
  75                 exit(1);
  76         }
  77 }
  78 **************************************************************************************************/
  79
  80
  81