sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / sharedsobscollectsummary.cpp

diff --git a/sharedsobscollectsummary.cpp b/sharedsobscollectsummary.cpp
index fffed0290b1136da46e42d31c99542da19ec9a0a..b53b09afc0091e91baf6609aa9c8d5b0ab528b63 100644 (file)
--- a/sharedsobscollectsummary.cpp
+++ b/sharedsobscollectsummary.cpp
@@ -38,5 +38,35 @@ EstOutput SharedSobsCS::getValues(vector<SharedRAbundVector*> shared){
                exit(1);
        }
 }
+/***********************************************************************/
+//This returns the number of shared species observed in several groups.  
+//The shared vector is each groups sharedrabundvector.
+
+EstOutput SharedSobsCS::getValues(vector<SharedRAbundVector*> shared, vector<string>& labels){
+       try {
+               data.resize(1,0);
+               double observed = 0;
+               int numGroups = shared.size();
+        labels.clear();
+        
+               for (int i = 0; i < shared[0]->getNumBins(); i++) {
+                       //get bin values and set sharedByAll 
+                       bool sharedByAll = true;
+                       for (int j = 0; j < numGroups; j++) {
+                               if (shared[j]->getAbundance(i) == 0) { sharedByAll = false; }
+                       }
+                       
+                       //they are shared
+                       if (sharedByAll == true) {  observed++;  labels.push_back(m->currentBinLabels[i]); }
+               }
+        
+               data[0] = observed;
+               return data;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SharedSobsCS", "getValues");
+               exit(1);
+       }
+}
 
 /***********************************************************************/