added odum, canberra, structchi2, structchord, structeuclidean, gower, hellinger...

[mothur.git] / structchord.cpp

diff --git a/structchord.cpp b/structchord.cpp
new file mode 100644 (file)
index 0000000..e85846f
--- /dev/null
+++ b/structchord.cpp
@@ -0,0 +1,55 @@
+/*
+ *  structchord.cpp
+ *  Mothur
+ *
+ *  Created by westcott on 12/15/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "structchord.h"
+
+/***********************************************************************/
+EstOutput StructChord::getValues(vector<SharedRAbundVector*> shared) {
+       try {
+               data.resize(1,0);
+               
+               double sumAj2 = 0.0;
+               double sumBj2 = 0.0;
+               
+               //calc the 2 denominators
+               for (int i = 0; i < shared[0]->getNumBins(); i++) { 
+                       
+                       int Aij = shared[0]->getAbundance(i);
+                       int Bij = shared[1]->getAbundance(i);
+                       
+                       //(Aij) ^ 2
+                       sumAj2 += (Aij * Aij);
+                       sumBj2 += (Bij * Bij);
+               }
+               
+               sumAj2 = sqrt(sumAj2);
+               sumBj2 = sqrt(sumBj2);
+               
+               //calc sum
+               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);
+                       
+                       sum += (((Aij / sumAj2) - (Bij / sumBj2)) * ((Aij / sumAj2) - (Bij / sumBj2)));
+               }
+               
+               data[0] = sqrt(sum);
+               
+               if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+               
+               return data;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "StructChord", "getValues");
+               exit(1);
+       }
+}
+/***********************************************************************/