sharedsorest.cpp

   1 /*
   2  *  sharedsorest.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 "sharedsorest.h"
  11 #include "chao1.h"
  12 #include "sharedchao1.h"
  13
  14 /***********************************************************************/
  15
  16 EstOutput SorEst::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2) {
  17         try {
  18                 EstOutput S1, S2, S12;
  19                 S12.resize(1,0);
  20                 S1.resize(3,0);
  21                 S2.resize(3,0);
  22
  23                 /*S1, S2 = number of OTUs estimated in A and B using the Chao estimator
  24                 S12 = estimated number of OTUs shared between A and B using the SharedChao estimator*/
  25
  26                 data.resize(1,0);
  27
  28                 SharedChao1* sharedChao = new SharedChao1();
  29                 Chao1* chaoS1 = new Chao1();
  30                 Chao1* chaoS2 = new Chao1();
  31                 SAbundVector* chaoS1Sabund = new SAbundVector();
  32                 SAbundVector* chaoS2Sabund = new SAbundVector();
  33
  34                 *chaoS1Sabund = shared1->getSAbundVector();
  35                 *chaoS2Sabund = shared2->getSAbundVector();
  36
  37                 S12 = sharedChao->getValues(shared1, shared2);
  38                 S1 = chaoS1->getValues(chaoS1Sabund);
  39                 S2 = chaoS2->getValues(chaoS2Sabund);
  40
  41                 data[0] = (2 * S12[0]) / (float)(S1[0] + S2[0]);
  42
  43                 if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
  44
  45                 return data;
  46         }
  47         catch(exception& e) {
  48                 cout << "Standard Error: " << e.what() << " has occurred in the SorEst class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  49                 exit(1);
  50         }
  51         catch(...) {
  52                 cout << "An unknown error has occurred in the SorEst class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  53                 exit(1);
  54         }
  55 }
  56
  57 /***********************************************************************/