sharedsorclass.cpp

   1 /*
   2  *  sharedsorclass.cpp
   3  *  Dotur
   4  *
   5  *  Created by Sarah Westcott on 1/8/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "sharedsorclass.h"
  11
  12 /***********************************************************************/
  13
  14 EstOutput SorClass::getValues(vector<SharedRAbundVector*> shared) {
  15         try {
  16                 double S1, S2, S12, tempA, tempB;
  17                 S1 = 0; S2 = 0; S12 = 0; tempA = 0; tempB = 0;
  18
  19                 /*S1, S2 = number of OTUs observed or estimated in A and B
  20                 S12=number of OTUs shared between A and B */
  21
  22                 data.resize(1,0);
  23
  24                 for (int i = 0; i < shared[0]->getNumBins(); i++) {
  25                         //store in temps to avoid multiple repetitive function calls
  26                         tempA = shared[0]->getAbundance(i);
  27                         tempB = shared[1]->getAbundance(i);
  28
  29                         //find number of bins in shared1 and shared2
  30                         if (tempA != 0) { S1++; }
  31                         if (tempB != 0) { S2++; }
  32
  33                         //they are shared
  34                         if ((tempA != 0) && (tempB != 0)) {     S12++; }
  35                 }
  36
  37                 data[0] = 1.0-(2 * S12) / (float)(S1 + S2);
  38
  39                 if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
  40
  41                 return data;
  42         }
  43         catch(exception& e) {
  44                 m->errorOut(e, "SorClass", "getValues");
  45                 exit(1);
  46         }
  47 }
  48
  49 /***********************************************************************/