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

[mothur.git] / sharedbraycurtis.cpp

diff --git a/sharedbraycurtis.cpp b/sharedbraycurtis.cpp
deleted file mode 100644 (file)
index 3711ce7..0000000
--- a/sharedbraycurtis.cpp
+++ /dev/null
@@ -1,52 +0,0 @@
-/*
- *  sharedbraycurtis.cpp
- *  Mothur
- *
- *  Created by Sarah Westcott on 3/24/09.
- *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "sharedbraycurtis.h"
-
-/***********************************************************************/
-//This is used by SharedJAbund and SharedSorAbund
-EstOutput BrayCurtis::getValues(vector<SharedRAbundVector*> shared) {
-       try {   
-               data.resize(1,0);
-               
-               double sumSharedA, sumSharedB, sumSharedAB, tempA, tempB;
-               sumSharedA = 0; sumSharedB = 0; sumSharedAB = 0; 
-               
-               /*Xi, Yi = abundance of the ith shared OTU in A and B 
-               sumSharedA = the number of otus in A
-               sumSharedB = the sum of all shared otus in B
-               sumSharedAB = the sum of the minimum otus int all shared otus in AB.
-               */
-               
-               for (int i = 0; i < shared[0]->getNumBins(); i++) {
-                       //store in temps to avoid multiple repetitive function calls
-                       tempA = shared[0]->getAbundance(i);
-                       tempB = shared[1]->getAbundance(i);
-                       
-                       sumSharedA += tempA;
-                       sumSharedB += tempB;
-                               
-                       //sum the min of tempA and tempB
-                       if (tempA < tempB) { sumSharedAB += tempA; }
-                       else  { sumSharedAB += tempB; }                         
-               }
-               
-               data[0] = 1.0 - (2 * sumSharedAB) / (float)( sumSharedA + sumSharedB);
-               
-               if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
-                               
-               return data;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "BrayCurtis", "getValues");
-               exit(1);
-       }
-}
-
-/***********************************************************************/