X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=nseqs.h;h=e82684b645041a10095c681061d4b16fa6929a9f;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=0a7b0c355dec5eaf4cddc1206bf9b0339d2781e2;hpb=9ca2caadbeac83bb84b3330d9204b1b659d62941;p=mothur.git

diff --git a/nseqs.h b/nseqs.h
index 0a7b0c3..e82684b 100644
--- a/nseqs.h
+++ b/nseqs.h
@@ -19,13 +19,32 @@
 class NSeqs : public Calculator {
 
 public:
-	NSeqs() : Calculator("NSeqs", 1) {};
+	NSeqs() : Calculator("nseqs", 1, false) {};
 	EstOutput getValues(SAbundVector* rank){
 		data.resize(1,0);
 		data[0] = (double)rank->getNumSeqs();
 		return data;
 	}
-	EstOutput getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2) {return data;};
+	
+	EstOutput getValues(vector<SharedRAbundVector*> shared) { //return number of sequences in the sharedotus
+		
+		int numGroups = shared.size();
+		data.clear(); data.resize(numGroups,0);
+
+		for (int i = 0; i < shared[0]->size(); 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) {  for (int j = 0; j < numGroups; j++) {  data[j] += shared[j]->getAbundance(i);  } }
+		}
+
+		return data;
+	}
+	string getCitation() { return "http://www.mothur.org/wiki/Nseqs"; }
 };
 
 /***********************************************************************/