a few changes to chimera classes

[mothur.git] / readotu.cpp

diff --git a/readotu.cpp b/readotu.cpp
index a99f343c83e35cd42724ddef6b32d26f4d0c88a6..1f64919825bbd8692043b4e8d16feaaf5e727e12 100644 (file)
--- a/readotu.cpp
+++ b/readotu.cpp
@@ -31,24 +31,29 @@ void ReadOTUFile::read(GlobalData* globaldata){
                }else {//there is an orderfile
                        input = new InputData(philFile, globaldata->getOrderFile(), globaldata->getFormat());
                }
-//cout << "made it here"       << endl;        
+       
                //memory leak prevention
                //if (globaldata->ginput != NULL) { delete globaldata->ginput;  }
                globaldata->ginput = input;     //saving to be used by collector and rarefact commands.
-//cout << "after input" << endl;               
+       
                if ((globaldata->getFormat() == "list") || (globaldata->getFormat() == "rabund") || (globaldata->getFormat() == "sabund")) {//you are reading a list, rabund or sabund file for collect, rarefaction or summary.
+
+//cout << input << '\t' << globaldata << endl;
                        order = input->getOrderVector();
                        //memory leak prevention
+
                        //if (globaldata->gorder != NULL) { delete globaldata->gorder;  }
                        globaldata->gorder = order;     //saving to be used by collect and rarefact commands.
                        sabund = inputSabund->getSAbundVector(); 
                        //if (globaldata->sabund != NULL) { delete globaldata->sabund;  }
                        globaldata->sabund = sabund; //saving to be used by summary command.
                        delete inputSabund;
+
                        rabund = inputRabund->getRAbundVector(); 
                        //if (globaldata->rabund != NULL) { delete globaldata->rabund;  }
                        globaldata->rabund = rabund; //saving to be used by heatmap.bin command.
                        delete inputRabund;
+
                        list = inputList->getListVector();
                        //if (globaldata->gListVector != NULL) { delete globaldata->gListVector;  }
                        globaldata->gListVector = list;
@@ -62,11 +67,7 @@ void ReadOTUFile::read(GlobalData* globaldata){
                }
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the ReadOTUFile class Function read. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the ReadOTUFile class function read. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "ReadOTUFile", "read");
                exit(1);
        }
 }