added logfile feature

[mothur.git] / sharedcommand.cpp

diff --git a/sharedcommand.cpp b/sharedcommand.cpp
index 6ca1ed63585463d92ac8dc7aa65f921ca1070308..4857a3482737a2b305b5a9ad381e228328289c19 100644 (file)
--- a/sharedcommand.cpp
+++ b/sharedcommand.cpp
@@ -22,21 +22,16 @@ SharedCommand::SharedCommand(){
                openOutputFile(filename, out);
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedCommand class Function SharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SharedCommand", "SharedCommand");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedCommand class function SharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-
 }
 //**********************************************************************************************************************
 
 int SharedCommand::execute(){
        try {
                
-               cout << "creating sharedfile...";
+               mothurOut("creating sharedfile..."); mothurOutEndLine();
                //lookup.clear();
                int count = 1;
                string errorOff = "no error";
@@ -94,12 +89,8 @@ int SharedCommand::execute(){
                set<string>::iterator it;
                bool needToRun = false;
                for (it = userLabels.begin(); it != userLabels.end(); it++) {  
-                       //cout << "Your file does not include the label "<< *it; 
                        if (processedLabels.count(lastLabel) != 1) {
-                               //cout << ". I will use " << lastList->getLabel() << "." << endl;
                                needToRun = true;
-                       }else {
-                               //cout << ". Please refer to " << lastList->getLabel() << "." << endl;
                        }
                }
                
@@ -119,18 +110,13 @@ int SharedCommand::execute(){
                
                out.close();
                
-               cout << "complete." << endl;
+               mothurOut("complete."); mothurOutEndLine();
                return 0;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SharedCommand", "execute");
                exit(1);
        }
-
 }
 //**********************************************************************************************************************
 void SharedCommand::printSharedData(vector<SharedRAbundVector*> thislookup) {
@@ -144,14 +130,9 @@ void SharedCommand::printSharedData(vector<SharedRAbundVector*> thislookup) {
  
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedCommand class Function printSharedData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedCommand class function printSharedData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SharedCommand", "printSharedData");
                exit(1);
        }
-       
 }
 
 //**********************************************************************************************************************