sharedbraycurtis.cpp

   1 /*
   2  *  sharedbraycurtis.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 3/24/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "sharedbraycurtis.h"
  11
  12 /***********************************************************************/
  13 //This is used by SharedJAbund and SharedSorAbund
  14 EstOutput BrayCurtis::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2) {
  15         try {
  16                 EstOutput data;
  17                 data.resize(1,0);
  18
  19                 int sumSharedA, sumSharedB, sumSharedAB, tempA, tempB;
  20                 sumSharedA = 0; sumSharedB = 0; sumSharedAB = 0;
  21
  22                 /*Xi, Yi = abundance of the ith shared OTU in A and B
  23                 sumSharedA = the sum of all shared otus in A
  24                 sumSharedB = the sum of all shared otus in B
  25                 sumSharedAB = the sum of the minimum otus int all shared otus in AB.
  26                 */
  27
  28                 for (int i = 0; i < shared1->size(); i++) {
  29                         //store in temps to avoid multiple repetitive function calls
  30                         tempA = shared1->getAbundance(i);
  31                         tempB = shared2->getAbundance(i);
  32
  33
  34                         if ((tempA != 0) && (tempB != 0)) {//they are shared
  35                                 sumSharedA += tempA;
  36                                 sumSharedB += tempB;
  37
  38                                 //sum the min of tempA and tempB
  39                                 if (tempA < tempB) { sumSharedAB += tempA; }
  40                                 else  { sumSharedAB += tempB; }
  41                         }
  42                 }
  43
  44                 data[0] = (2 * sumSharedAB) / (float)( sumSharedA + sumSharedB);
  45
  46                 if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
  47
  48                 return data;
  49         }
  50         catch(exception& e) {
  51                 cout << "Standard Error: " << e.what() << " has occurred in the BrayCurtis class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  52                 exit(1);
  53         }
  54         catch(...) {
  55                 cout << "An unknown error has occurred in the BrayCurtis class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  56                 exit(1);
  57         }
  58
  59
  60 }
  61
  62 /***********************************************************************/