This is mothur v 1.2.0 - the April ~24, 2009 release

[mothur.git] / sharedbraycurtis.cpp

diff --git a/sharedbraycurtis.cpp b/sharedbraycurtis.cpp
index 0f29b2393f76b80f74cec7b59cb971fc58dd4a68..d1b401eb78038aaa8d462678fe7bcbc3d2b13903 100644 (file)
--- a/sharedbraycurtis.cpp
+++ b/sharedbraycurtis.cpp
@@ -10,17 +10,16 @@
 #include "sharedbraycurtis.h"
 
 /***********************************************************************/
-//This is used by SharedJAbund and SharedSorAbund
+
 EstOutput BrayCurtis::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2) {
        try {   
-               EstOutput data;
                data.resize(1,0);
                
                int 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 sum of all shared otus in A
+               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.
                */
@@ -29,16 +28,13 @@ EstOutput BrayCurtis::getValues(SharedRAbundVector* shared1, SharedRAbundVector*
                        //store in temps to avoid multiple repetitive function calls
                        tempA = shared1->getAbundance(i);
                        tempB = shared2->getAbundance(i);
-
                        
-                       if ((tempA != 0) && (tempB != 0)) {//they are shared
-                               sumSharedA += tempA;
-                               sumSharedB += tempB;
+                       sumSharedA += tempA;
+                       sumSharedB += tempB;
                                
-                               //sum the min of tempA and tempB
-                               if (tempA < tempB) { sumSharedAB += tempA; }
-                               else  { sumSharedAB += tempB; }                         
-                       }
+                       //sum the min of tempA and tempB
+                       if (tempA < tempB) { sumSharedAB += tempA; }
+                       else  { sumSharedAB += tempB; }                         
                }
                
                data[0] = (2 * sumSharedAB) / (float)( sumSharedA + sumSharedB);