changing command name classify.shared to classifyrf.shared

[mothur.git] / nseqs.h

diff --git a/nseqs.h b/nseqs.h
index 1382add6e58b78ba88c6459168df9d554d45e71d..c0f9549c87584bbf99e503388ff737c9f5343e8e 100644 (file)
--- a/nseqs.h
+++ b/nseqs.h
@@ -19,13 +19,32 @@
 class NSeqs : public Calculator {
 
 public:
-       NSeqs() : Calculator("NSeqs", 1, false) {};
+       NSeqs() : Calculator("nseqs", 1, false) {};
        EstOutput getValues(SAbundVector* rank){
                data.resize(1,0);
                data[0] = (double)rank->getNumSeqs();
                return data;
        }
-       EstOutput getValues(vector<SharedRAbundVector*>) {return data;};
+       
+       EstOutput getValues(vector<SharedRAbundVector*> shared) { //return number of sequences in the sharedotus
+               
+               int numGroups = shared.size();
+               data.clear(); data.resize(numGroups,0);
+
+               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) {  for (int j = 0; j < numGroups; j++) {  data[j] += shared[j]->getAbundance(i);  } }
+               }
+
+               return data;
+       }
+       string getCitation() { return "http://www.mothur.org/wiki/Nseqs"; }
 };
 
 /***********************************************************************/