sharedjest.cpp

   1 /*
   2  *  sharedjest.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 "sharedchao1.h"
  11 #include "chao1.h"
  12 #include "sharedjest.h"
  13
  14
  15 /***********************************************************************/
  16
  17 EstOutput Jest::getValues(vector<SharedRAbundVector*> shared) {
  18         try {
  19                 EstOutput S1, S2, S12;
  20                 S12.resize(1,0);
  21                 S1.resize(3,0);
  22                 S2.resize(3,0);
  23
  24                 /*S1, S2 = number of OTUs estimated in A and B using the Chao estimator
  25                 S12 = estimated number of OTUs shared between A and B using the SharedChao estimator*/
  26
  27                 data.resize(1,0);
  28
  29                 SharedChao1* sharedChao = new SharedChao1();
  30                 Chao1* chaoS1 = new Chao1();
  31                 Chao1* chaoS2 = new Chao1();
  32                 SAbundVector* chaoS1Sabund = new SAbundVector();
  33                 SAbundVector* chaoS2Sabund = new SAbundVector();
  34
  35                 *chaoS1Sabund = shared[0]->getSAbundVector();
  36                 *chaoS2Sabund = shared[1]->getSAbundVector();
  37
  38         //chaoS1Sabund->print(cout);
  39         //chaoS2Sabund->print(cout);
  40
  41                 S12 = sharedChao->getValues(shared);
  42                 S1 = chaoS1->getValues(chaoS1Sabund);
  43                 S2 = chaoS2->getValues(chaoS2Sabund);
  44
  45         //cout << S12[0] << '\t' << S1[0] << '\t' << S2[0] << endl;
  46
  47                 data[0] = 1.0 - S12[0] / (float)(S1[0] + S2[0] - S12[0]);
  48         //cout << data[0] << endl;
  49
  50                 if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
  51
  52                 delete sharedChao;
  53                 delete chaoS1;
  54                 delete chaoS2;
  55                 delete chaoS1Sabund;
  56                 delete chaoS2Sabund;
  57
  58                 return data;
  59         }
  60         catch(exception& e) {
  61                 m->errorOut(e, "Jest", "getValues");
  62                 exit(1);
  63         }
  64 }
  65
  66 /***********************************************************************/