added logfile feature

[mothur.git] / getlabelcommand.cpp

diff --git a/getlabelcommand.cpp b/getlabelcommand.cpp
index 40c656bb0286122f013ec9dfe65a6da2ea42244a..be2a989d7a953be7b68a29ceca1a88c4d514bd20 100644 (file)
--- a/getlabelcommand.cpp
+++ b/getlabelcommand.cpp
@@ -20,40 +20,31 @@ GetlabelCommand::GetlabelCommand(string option){
                if(option == "help") { help(); abort = true; }
                
                else {
-                       if (option != "") { cout << "There are no valid parameters for the get.label command." << endl; abort = true; }
+                       if (option != "") { mothurOut("There are no valid parameters for the get.label command."); mothurOutEndLine(); abort = true; }
                        
-                       if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { cout << "You must read a list, sabund or rabund before you can use the get.label command." << endl; abort = true; }                              
+                       if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { mothurOut("You must read a list, sabund or rabund before you can use the get.label command."); mothurOutEndLine(); abort = true; }                               
                }
 
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the GetlabelCommand class Function GetlabelCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "GetlabelCommand", "GetlabelCommand");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the GetlabelCommand class function GetlabelCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
-                       
 }
 //**********************************************************************************************************************
 
 void GetlabelCommand::help(){
        try {
-               cout << "The get.label command can only be executed after a successful read.otu command." << "\n";
-               cout << "You may not use any parameters with the get.label command." << "\n";
-               cout << "The get.label command should be in the following format: " << "\n";
-               cout << "get.label()" << "\n";
-               cout << "Example get.label()." << "\n";
+               mothurOut("The get.label command can only be executed after a successful read.otu command.\n");
+               mothurOut("You may not use any parameters with the get.label command.\n");
+               mothurOut("The get.label command should be in the following format: \n");
+               mothurOut("get.label()\n");
+               mothurOut("Example get.label().\n");
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the GetlabelCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "GetlabelCommand", "help");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the GetlabelCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }
 
 //**********************************************************************************************************************
@@ -78,7 +69,7 @@ int GetlabelCommand::execute(){
                        if(count > numBins)
                                count = 0;
                        if(count == 0) {
-                               cout << label << "\n";
+                               mothurOut(label); mothurOutEndLine();
                                in >> numBins;
                        }
                        in >> label;
@@ -90,12 +81,8 @@ int GetlabelCommand::execute(){
        }
 
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the GetlabelCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "GetlabelCommand", "execute");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the GetlabelCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }