X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sharedsobscollectsummary.cpp;h=b53b09afc0091e91baf6609aa9c8d5b0ab528b63;hp=6815d875fa6d0bf5f1ad88f0fa7e26aeda20568b;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=50ed3b6104d5821d6184f882e1e1423d47dcbf10

diff --git a/sharedsobscollectsummary.cpp b/sharedsobscollectsummary.cpp
index 6815d87..b53b09a 100644
--- a/sharedsobscollectsummary.cpp
+++ b/sharedsobscollectsummary.cpp
@@ -16,10 +16,10 @@
 EstOutput SharedSobsCS::getValues(vector<SharedRAbundVector*> shared){
 	try {
 		data.resize(1,0);
-		int observed = 0;
+		double observed = 0;
 		int numGroups = shared.size();
 
-		for (int i = 0; i < shared[0]->size(); i++) {
+		for (int i = 0; i < shared[0]->getNumBins(); i++) {
 			//get bin values and set sharedByAll 
 			bool sharedByAll = true;
 			for (int j = 0; j < numGroups; j++) {
@@ -34,13 +34,39 @@ EstOutput SharedSobsCS::getValues(vector<SharedRAbundVector*> shared){
 		return data;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SharedSobsCS class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SharedSobsCS", "getValues");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SharedSobsCS class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+/***********************************************************************/
+//This returns the number of shared species observed in several groups.  
+//The shared vector is each groups sharedrabundvector.
+
+EstOutput SharedSobsCS::getValues(vector<SharedRAbundVector*> shared, vector<string>& labels){
+	try {
+		data.resize(1,0);
+		double observed = 0;
+		int numGroups = shared.size();
+        labels.clear();
+        
+		for (int i = 0; i < shared[0]->getNumBins(); i++) {
+			//get bin values and set sharedByAll 
+			bool sharedByAll = true;
+			for (int j = 0; j < numGroups; j++) {
+				if (shared[j]->getAbundance(i) == 0) { sharedByAll = false; }
+			}
+			
+			//they are shared
+			if (sharedByAll == true) {  observed++;  labels.push_back(m->currentBinLabels[i]); }
+		}
+        
+		data[0] = observed;
+		return data;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SharedSobsCS", "getValues");
 		exit(1);
-	}	
+	}
 }
 
-/***********************************************************************/
\ No newline at end of file
+/***********************************************************************/