added count file to trim.seqs, get.groups, get.lineage, get.seqs, heatmap.sim, list...

[mothur.git] / sharedsobscollectsummary.cpp

diff --git a/sharedsobscollectsummary.cpp b/sharedsobscollectsummary.cpp
index 6815d875fa6d0bf5f1ad88f0fa7e26aeda20568b..fffed0290b1136da46e42d31c99542da19ec9a0a 100644 (file)
--- a/sharedsobscollectsummary.cpp
+++ b/sharedsobscollectsummary.cpp
@@ -16,10 +16,10 @@
 EstOutput SharedSobsCS::getValues(vector<SharedRAbundVector*> shared){
        try {
                data.resize(1,0);
-               int observed = 0;
+               double observed = 0;
                int numGroups = shared.size();
 
-               for (int i = 0; i < shared[0]->size(); i++) {
+               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++) {
@@ -34,13 +34,9 @@ EstOutput SharedSobsCS::getValues(vector<SharedRAbundVector*> shared){
                return data;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedSobsCS class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "SharedSobsCS", "getValues");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedSobsCS class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }
 
-/***********************************************************************/
\ No newline at end of file
+/***********************************************************************/