changing command name classify.shared to classifyrf.shared

[mothur.git] / sharedbraycurtis.cpp

diff --git a/sharedbraycurtis.cpp b/sharedbraycurtis.cpp
index e8512d4b95bf3d2d32e058ca5c0b250d25609979..3711ce77cbb312e5dc2ee2aba14e1856bb942d12 100644 (file)
--- a/sharedbraycurtis.cpp
+++ b/sharedbraycurtis.cpp
@@ -15,7 +15,7 @@ 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 
@@ -24,7 +24,7 @@ EstOutput BrayCurtis::getValues(vector<SharedRAbundVector*> shared) {
                sumSharedAB = the sum of the minimum otus int all shared otus in AB.
                */
                
-               for (int i = 0; i < shared[0]->size(); i++) {
+               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);
@@ -37,7 +37,7 @@ EstOutput BrayCurtis::getValues(vector<SharedRAbundVector*> shared) {
                        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; }