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[mothur.git] / sharedlennon.cpp

diff --git a/sharedlennon.cpp b/sharedlennon.cpp
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+/*
+ *  sharedlennon.cpp
+ *  Mothur
+ *
+ *  Created by Sarah Westcott on 3/24/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "sharedlennon.h"
+
+/***********************************************************************/
+
+EstOutput Lennon::getValues(vector<SharedRAbundVector*> shared) {
+       try {
+               double S1, S2, S12, tempA, tempB, min;
+               S1 = 0; S2 = 0; S12 = 0; tempA = 0; tempB = 0; min = 0;
+               
+               /*S1, S2 = number of OTUs observed or estimated in A and B 
+               S12=number of OTUs shared between A and B */
+
+               data.resize(1,0);
+               
+               for (int i = 0; i < shared[0]->getNumBins(); i++) {
+                       //store in temps to avoid multiple repetitive function calls
+                       tempA = shared[0]->getAbundance(i);
+                       tempB = shared[1]->getAbundance(i);
+                       
+                       if (tempA != 0) { S1++; }
+                       if (tempB != 0) { S2++; } 
+
+                       //they are shared
+                       if ((tempA != 0) && (tempB != 0)) {     S12++; }
+               }
+               
+               
+               tempA = S1 - S12;  tempB = S2 - S12;
+               
+               if (tempA < tempB) { min = tempA; }
+               else { min = tempB; }
+               
+               data[0] = 1.0 - S12 / (float)(S12 + min);
+               
+               if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+               
+               return data;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "Lennon", "getValues");
+               exit(1);
+       }
+}
+
+/***********************************************************************/