changes while testing

[mothur.git] / sharedjackknife.cpp

diff --git a/sharedjackknife.cpp b/sharedjackknife.cpp
index c1e5ff4ec4c56a1f5eddad239a9b21f6e0deb72c..0998db8fe3106bbb40c26dc8621d37030fb275c3 100644 (file)
--- a/sharedjackknife.cpp
+++ b/sharedjackknife.cpp
@@ -88,8 +88,7 @@ EstOutput SharedJackknife::getValues(vector<SharedRAbundVector*> vectorShared){
                SharedRAbundVector* shared1 = vectorShared[0];
                SharedRAbundVector* shared2 = vectorShared[1];
                if(numGroups == -1) {
-                       globaldata = GlobalData::getInstance();
-                       numGroups = globaldata->Groups.size();
+                       numGroups = m->getNumGroups();
                }
 
                if(callCount == numGroups*(numGroups-1)/2) {
@@ -116,17 +115,11 @@ EstOutput SharedJackknife::getValues(vector<SharedRAbundVector*> vectorShared){
                        data[0] = rdata[0];
                        data[1] = rdata[1];
                        data[2] = rdata[2];
-                       
-                       //cout << "sT = " << data[0] << "    lower confLimit = " << data[1] << "     upper confLimit = " << data[2] << "\n";
+               
                        if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
                        if (isnan(data[1]) || isinf(data[1])) { data[1] = 0; }
                        if (isnan(data[2]) || isinf(data[0])) { data[2] = 0; }
                        
-                       /*for(int i = 0; i < groups.size(); i++)
-                               cout << groups.at(i)->getGroup() << " ";
-                       cout << "\n";
-                       cout << groups.size() << "     " << data[0] << "    " << data[1] << "     " << data[2] << "\n\n";*/
-                       
                        return data;
                }
                
@@ -142,13 +135,9 @@ EstOutput SharedJackknife::getValues(vector<SharedRAbundVector*> vectorShared){
        }
                
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedJackknife class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "SharedJackknife", "getValues");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedJackknife class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }
 
 /***********************************************************************/