memchord.cpp

   1 /*
   2  *  memchord.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 12/17/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "memchord.h"
  11
  12 /***********************************************************************/
  13 EstOutput MemChord::getValues(vector<SharedRAbundVector*> shared) {
  14         try {
  15                 data.resize(1,0);
  16
  17                 double nonZeroA = 0;
  18                 double nonZeroB = 0;
  19
  20                 //for each otu
  21                 for (int i = 0; i < shared[0]->getNumBins(); i++) {
  22                         if (shared[0]->getAbundance(i) != 0) { nonZeroA++; }
  23                         if (shared[1]->getAbundance(i) != 0) { nonZeroB++; }
  24                 }
  25
  26                 nonZeroA = sqrt(nonZeroA);
  27                 nonZeroB = sqrt(nonZeroB);
  28
  29                 double sum = 0.0;
  30                 for (int i = 0; i < shared[0]->getNumBins(); i++) {
  31                         int A = shared[0]->getAbundance(i);
  32                         int B = shared[1]->getAbundance(i);
  33
  34                         if (A > 0) { A = 1; }
  35                         if (B > 0) { B = 1; }
  36
  37                         double Aterm = A / nonZeroA;
  38                         double Bterm = B / nonZeroB;
  39
  40                         sum += ((Aterm-Bterm)*(Aterm-Bterm));
  41                 }
  42
  43                 data[0] = sqrt(sum);
  44
  45                 if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
  46
  47                 return data;
  48         }
  49         catch(exception& e) {
  50                 m->errorOut(e, "MemChord", "getValues");
  51                 exit(1);
  52         }
  53 }
  54 /***********************************************************************/
  55