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

[mothur.git] / memchord.cpp

diff --git a/memchord.cpp b/memchord.cpp
new file mode 100644 (file)
index 0000000..380ddbe
--- /dev/null
+++ b/memchord.cpp
@@ -0,0 +1,55 @@
+/*
+ *  memchord.cpp
+ *  Mothur
+ *
+ *  Created by westcott on 12/17/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "memchord.h"
+
+/***********************************************************************/
+EstOutput MemChord::getValues(vector<SharedRAbundVector*> shared) {
+       try {
+               data.resize(1,0);
+               
+               double nonZeroA = 0;
+               double nonZeroB = 0;
+               
+               //for each otu
+               for (int i = 0; i < shared[0]->getNumBins(); i++) {
+                       if (shared[0]->getAbundance(i) != 0) { nonZeroA++; }
+                       if (shared[1]->getAbundance(i) != 0) { nonZeroB++; }
+               }
+               
+               nonZeroA = sqrt(nonZeroA);
+               nonZeroB = sqrt(nonZeroB);
+               
+               double sum = 0.0;
+               for (int i = 0; i < shared[0]->getNumBins(); i++) {
+                       int A = shared[0]->getAbundance(i);
+                       int B = shared[1]->getAbundance(i);
+                       
+                       if (A > 0) { A = 1; }
+                       if (B > 0) { B = 1; }
+                       
+                       double Aterm = A / nonZeroA;
+                       double Bterm = B / nonZeroB;
+                       
+                       sum += ((Aterm-Bterm)*(Aterm-Bterm));
+               }
+               
+               data[0] = sqrt(sum);
+               
+               if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+               
+               return data;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "MemChord", "getValues");
+               exit(1);
+       }
+}
+/***********************************************************************/
+