added concensus command and updated calcs

[mothur.git] / sharedsobs.cpp

diff --git a/sharedsobs.cpp b/sharedsobs.cpp
index 9c3f4ddb1d47f1518791d6d95e3f94200823f175..388356ea927c02cee168918026115c010c6d705f 100644 (file)
--- a/sharedsobs.cpp
+++ b/sharedsobs.cpp
@@ -13,16 +13,16 @@
 //This returns the number of unique species observed in several groups.  
 //The shared vector is each groups sharedrabundvector.
 
-EstOutput SharedSobs::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2){
+EstOutput SharedSobs::getValues(vector<SharedRAbundVector*> shared){
        try {
                data.resize(1,0);
                int observed = 0;
 
                //loop through the species in each group
-               for (int k = 0; k < shared1->size(); k++) {
+               for (int k = 0; k < shared[0]->size(); k++) {
                        //if you have found a new species
-                       if (shared1->getAbundance(k) != 0) { observed++; } 
-                       else if ((shared1->getAbundance(k) == 0) && (shared2->getAbundance(k) != 0)) { observed++; }
+                       if (shared[0]->getAbundance(k) != 0) { observed++; } 
+                       else if ((shared[0]->getAbundance(k) == 0) && (shared[1]->getAbundance(k) != 0)) { observed++; }
                }
 
                data[0] = observed;