Revert to previous commit

[mothur.git] / canberra.cpp

diff --git a/canberra.cpp b/canberra.cpp
new file mode 100644 (file)
index 0000000..9ab6234
--- /dev/null
+++ b/canberra.cpp
@@ -0,0 +1,47 @@
+/*
+ *  canberra.cpp
+ *  Mothur
+ *
+ *  Created by westcott on 12/14/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "canberra.h"
+
+/***********************************************************************/
+
+EstOutput Canberra::getValues(vector<SharedRAbundVector*> shared) {
+       try {
+               data.resize(1,0);
+               
+               int numSharedOTUS = 0;
+               
+               double sum = 0.0;
+               
+               for (int i = 0; i < shared[0]->getNumBins(); i++) { 
+                       
+                       int Aij = shared[0]->getAbundance(i);
+                       int Bij = shared[1]->getAbundance(i);
+                       
+                       //is this otu shared
+                       if ((Aij != 0) && (Bij != 0)) { numSharedOTUS++; }
+                       
+                       if ((Aij + Bij) != 0) { 
+                               sum += ((abs(Aij - Bij)) / (float) (Aij + Bij));
+                       }
+               }
+               
+               data[0] = (1 / (float) shared[0]->getNumBins()) * sum;
+               
+               if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+               
+               return data;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "Canberra", "getValues");
+               exit(1);
+       }
+}
+
+/***********************************************************************/