X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sharedsobs.cpp;h=f9b5eddcd919acdd409c9b0792294034dbcb7391;hp=14f5bf59d6552303d664e275e7c4173643a36179;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05

diff --git a/sharedsobs.cpp b/sharedsobs.cpp
index 14f5bf5..f9b5edd 100644
--- a/sharedsobs.cpp
+++ b/sharedsobs.cpp
@@ -13,29 +13,25 @@
 //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){
+EstOutput SharedSobs::getValues(vector<SharedRAbundVector*> shared){
 	try {
 		data.resize(1,0);
-		int observed = 0;;
+		double observed = 0;
 
 		//loop through the species in each group
-		for (int k = 0; k < shared1->size(); k++) {
+		for (int k = 0; k < shared[0]->getNumBins(); 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++; }
+			if (shared[0]->getAbundance(k) != 0) { observed++; } 
+			else if ((shared[0]->getAbundance(k) == 0) && (shared[1]->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";
+		m->errorOut(e, "SharedSobs", "getValues");
 		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);
-	}	
 }
 
 /***********************************************************************/