sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / sharedbraycurtis.cpp

diff --git a/sharedbraycurtis.cpp b/sharedbraycurtis.cpp
index 0f29b2393f76b80f74cec7b59cb971fc58dd4a68..3711ce77cbb312e5dc2ee2aba14e1856bb942d12 100644 (file)
--- a/sharedbraycurtis.cpp
+++ b/sharedbraycurtis.cpp
@@ -11,52 +11,42 @@
 
 /***********************************************************************/
 //This is used by SharedJAbund and SharedSorAbund
-EstOutput BrayCurtis::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2) {
+EstOutput BrayCurtis::getValues(vector<SharedRAbundVector*> shared) {
        try {   
-               EstOutput data;
                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 
-               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.
                */
                
-               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);
                        
-                       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);
+               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);
-       }       
-
-
 }
 
 /***********************************************************************/