moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / memchord.cpp

diff --git a/memchord.cpp b/memchord.cpp
deleted file mode 100644 (file)
index 380ddbe..0000000
--- a/memchord.cpp
+++ /dev/null
@@ -1,55 +0,0 @@
-/*
- *  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);
-       }
-}
-/***********************************************************************/
-