added Jensen-Shannon calc. working on get.communitytype command. fixed bug in get...

[mothur.git] / shannonrange.cpp

diff --git a/shannonrange.cpp b/shannonrange.cpp
new file mode 100644 (file)
index 0000000..f26f08a
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+++ b/shannonrange.cpp
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+//
+//  shannonrange.cpp
+//  Mothur
+//
+//  Created by SarahsWork on 1/3/14.
+//  Copyright (c) 2014 Schloss Lab. All rights reserved.
+//
+
+#include "shannonrange.h"
+
+/***********************************************************************/
+
+EstOutput RangeShannon::getValues(vector<SharedRAbundVector*> shared) {
+       try {
+        data.resize(3,0);
+        
+        double commSize = 1e20;
+        
+        SAbundVector sabund1 = shared[0]->getSAbundVector();
+        SAbundVector sabund2 = shared[1]->getSAbundVector();
+        
+        double sampleSize = 0;
+        for (int i = 0; i < sabund1.getNumBins(); i++) {  sampleSize += (sabund1.get(i) * sabund2.get(i));  }
+        int aux = ceil(pow((sampleSize+1), 0.33333));
+               
+               if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+               
+               return data;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "RangeShannon", "getValues");
+               exit(1);
+       }
+}
+/***********************************************************************/