sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / sharedbraycurtis.cpp

diff --git a/sharedbraycurtis.cpp b/sharedbraycurtis.cpp
index d1b401eb78038aaa8d462678fe7bcbc3d2b13903..3711ce77cbb312e5dc2ee2aba14e1856bb942d12 100644 (file)
--- a/sharedbraycurtis.cpp
+++ b/sharedbraycurtis.cpp
@@ -10,12 +10,12 @@
 #include "sharedbraycurtis.h"
 
 /***********************************************************************/
-
-EstOutput BrayCurtis::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2) {
+//This is used by SharedJAbund and SharedSorAbund
+EstOutput BrayCurtis::getValues(vector<SharedRAbundVector*> shared) {
        try {   
                data.resize(1,0);
                
-               int sumSharedA, sumSharedB, sumSharedAB, tempA, tempB;
+               double sumSharedA, sumSharedB, sumSharedAB, tempA, tempB;
                sumSharedA = 0; sumSharedB = 0; sumSharedAB = 0; 
                
                /*Xi, Yi = abundance of the ith shared OTU in A and B 
@@ -24,10 +24,10 @@ EstOutput BrayCurtis::getValues(SharedRAbundVector* shared1, SharedRAbundVector*
                sumSharedAB = the sum of the minimum otus int all shared otus in AB.
                */
                
-               for (int i = 0; i < shared1->size(); i++) {
+               for (int i = 0; i < shared[0]->getNumBins(); i++) {
                        //store in temps to avoid multiple repetitive function calls
-                       tempA = shared1->getAbundance(i);
-                       tempB = shared2->getAbundance(i);
+                       tempA = shared[0]->getAbundance(i);
+                       tempB = shared[1]->getAbundance(i);
                        
                        sumSharedA += tempA;
                        sumSharedB += tempB;
@@ -37,22 +37,16 @@ EstOutput BrayCurtis::getValues(SharedRAbundVector* shared1, SharedRAbundVector*
                        else  { sumSharedAB += tempB; }                         
                }
                
-               data[0] = (2 * sumSharedAB) / (float)( sumSharedA + sumSharedB);
+               data[0] = 1.0 - (2 * sumSharedAB) / (float)( sumSharedA + sumSharedB);
                
                if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
                                
                return data;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the BrayCurtis class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "BrayCurtis", "getValues");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the BrayCurtis class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
-
-
 }
 
 /***********************************************************************/