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[mothur.git] / sharedsobs.cpp

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+/*
+ *  sharedsobs.cpp
+ *  Dotur
+ *
+ *  Created by Sarah Westcott on 1/7/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "sharedsobs.h"
+
+/***********************************************************************/
+//This returns the number of unique species observed in several groups.  
+//The shared vector is each groups sharedrabundvector.
+
+EstOutput SharedSobs::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2){
+       try {
+               data.resize(1,0);
+               int observed = 0;;
+
+               //loop through the species in each group
+               for (int k = 0; k < shared1->size(); k++) {
+                       //if you have found a new species
+                       if (shared1->getAbundance(k) != 0) { observed++; } 
+                       else if ((shared1->getAbundance(k) == 0) && (shared2->getAbundance(k) != 0)) { observed++; }
+               }
+
+               data[0] = observed;
+               return data;
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the SharedSobs class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the SharedSobs class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }       
+}
+
+/***********************************************************************/