X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sharedsobscollectsummary.cpp;h=b53b09afc0091e91baf6609aa9c8d5b0ab528b63;hp=d39e66e58a7bb79b9d4cc5f326b53d169778d181;hb=70491a12902e89b85cfa6b44a7b7fbe066ee2ac1;hpb=44c1323a88b2a697c7047df1b3bb8c59eadd15b1

diff --git a/sharedsobscollectsummary.cpp b/sharedsobscollectsummary.cpp
index d39e66e..b53b09a 100644
--- a/sharedsobscollectsummary.cpp
+++ b/sharedsobscollectsummary.cpp
@@ -13,34 +13,60 @@
 //This returns the number of shared species observed in several groups.  
 //The shared vector is each groups sharedrabundvector.
 
-EstOutput SharedSobsCS::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2){
+EstOutput SharedSobsCS::getValues(vector<SharedRAbundVector*> shared){
 	try {
 		data.resize(1,0);
-		int observed = 0;
-		int tempA, tempB;
+		double observed = 0;
+		int numGroups = shared.size();
 
-		//loop through the species in each group
-		for (int k = 0; k < shared1->size(); k++) {
-			tempA = shared1->getAbundance(k); //store in temps to avoid calling getAbundance multiple times
-			tempB = shared2->getAbundance(k);
-
-			//if you have found a new species
-			if ((tempA != 0) && (tempB != 0)) {//they are shared
-				observed++;
+		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++;  }
 		}
 
 		data[0] = observed;
 		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
+/***********************************************************************/