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[mothur.git] / sharedmarczewski.cpp

diff --git a/sharedmarczewski.cpp b/sharedmarczewski.cpp
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+/*
+ *  sharedmarczewski.cpp
+ *  Mothur
+ *
+ *  Created by Thomas Ryabin on 4/8/09.
+ *  Copyright 2009 __MyCompanyName__. All rights reserved.
+ *
+ */
+
+#include "sharedmarczewski.h"
+
+EstOutput SharedMarczewski::getValues(vector<SharedRAbundVector*> vectorShared){
+       try {
+               SharedRAbundVector* shared1 = vectorShared[0];
+               SharedRAbundVector* shared2 = vectorShared[1];
+               
+               data.resize(1,0);
+               
+               double a = 0;
+               double b = 0;
+               double c = 0;
+               for(int i = 1; i < shared1->size(); i++)
+               {
+                       int abund1 = shared1->get(i).abundance;
+                       int abund2 = shared2->get(i).abundance;
+                       
+                       if(abund1 > 0 && abund2 > 0)
+                               a++;
+                       else if(abund1 > 0 && abund2 == 0)
+                               b++;
+                       else if(abund1 == 0 && abund2 > 0)
+                               c++;
+               }
+               data[0] = (b+c)/(a+b+c);
+
+               if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+               
+               return data;
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the SharedMarczewski class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the SharedMarczewski class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }       
+}
+
+/***********************************************************************/