canberra.cpp

   1 /*
   2  *  canberra.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 12/14/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "canberra.h"
  11
  12 /***********************************************************************/
  13
  14 EstOutput Canberra::getValues(vector<SharedRAbundVector*> shared) {
  15         try {
  16                 data.resize(1,0);
  17
  18                 int numSharedOTUS = 0;
  19
  20                 double sum = 0.0;
  21
  22                 for (int i = 0; i < shared[0]->getNumBins(); i++) {
  23
  24                         int Aij = shared[0]->getAbundance(i);
  25                         int Bij = shared[1]->getAbundance(i);
  26
  27                         //is this otu shared
  28                         if ((Aij != 0) && (Bij != 0)) { numSharedOTUS++; }
  29
  30                         if ((Aij + Bij) != 0) {
  31                                 sum += ((abs(Aij - Bij)) / (float) (Aij + Bij));
  32                         }
  33                 }
  34
  35                 data[0] = (1 / (float) shared[0]->getNumBins()) * sum;
  36
  37                 if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
  38
  39                 return data;
  40         }
  41         catch(exception& e) {
  42                 m->errorOut(e, "Canberra", "getValues");
  43                 exit(1);
  44         }
  45 }
  46
  47 /***********************************************************************/