X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=nseqs.h;fp=nseqs.h;h=c0f9549c87584bbf99e503388ff737c9f5343e8e;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

diff --git a/nseqs.h b/nseqs.h
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+++ b/nseqs.h
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+#ifndef NSEQS_H
+#define NSEQS_H
+
+/*
+ *  nseqs.h
+ *  Mothur
+ *
+ *  Created by Sarah Westcott on 3/16/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+
+
+#include "calculator.h"
+
+/***********************************************************************/
+
+class NSeqs : public Calculator {
+
+public:
+	NSeqs() : Calculator("nseqs", 1, false) {};
+	EstOutput getValues(SAbundVector* rank){
+		data.resize(1,0);
+		data[0] = (double)rank->getNumSeqs();
+		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]->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) {  for (int j = 0; j < numGroups; j++) {  data[j] += shared[j]->getAbundance(i);  } }
+		}
+
+		return data;
+	}
+	string getCitation() { return "http://www.mothur.org/wiki/Nseqs"; }
+};
+
+/***********************************************************************/
+
+#endif