X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedsobscollectsummary.cpp;h=204b61c64d779ebe2946d537e5803d9ed36d3d76;hb=250e3b11b1c9c1e1ad458ab6c7e71ac2e67e11d9;hp=c64c8259ca25d0a3c585113049ff4877d6630555;hpb=74844a60d80c6dd06e3fb02ee9b928424f9019b0;p=mothur.git

diff --git a/sharedsobscollectsummary.cpp b/sharedsobscollectsummary.cpp
index c64c825..204b61c 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++) {
@@ -38,5 +38,35 @@ EstOutput SharedSobsCS::getValues(vector<SharedRAbundVector*> shared){
 		exit(1);
 	}
 }
+/***********************************************************************/
+//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->currentSharedBinLabels[i]); }
+		}
+        
+		data[0] = observed;
+		return data;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SharedSobsCS", "getValues");
+		exit(1);
+	}
+}
 
 /***********************************************************************/