sharedsobscollectsummary.cpp

   1 /*
   2  *  sharedsobscollectsummary.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 2/12/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "sharedsobscollectsummary.h"
  11
  12 /***********************************************************************/
  13 //This returns the number of shared species observed in several groups.
  14 //The shared vector is each groups sharedrabundvector.
  15
  16 EstOutput SharedSobsCS::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2){
  17         try {
  18                 data.resize(1,0);
  19                 int observed = 0;
  20                 int tempA, tempB;
  21
  22                 //loop through the species in each group
  23                 for (int k = 0; k < shared1->size(); k++) {
  24                         tempA = shared1->getAbundance(k); //store in temps to avoid calling getAbundance multiple times
  25                         tempB = shared2->getAbundance(k);
  26
  27                         //if you have found a new species
  28                         if ((tempA != 0) && (tempB != 0)) {//they are shared
  29                                 observed++;
  30                         }
  31                 }
  32
  33                 data[0] = observed;
  34                 return data;
  35         }
  36         catch(exception& e) {
  37                 cout << "Standard Error: " << e.what() << " has occurred in the SharedSobsCS class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  38                 exit(1);
  39         }
  40         catch(...) {
  41                 cout << "An unknown error has occurred in the SharedSobsCS class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  42                 exit(1);
  43         }
  44 }
  45
  46 /***********************************************************************/