added logfile feature

[mothur.git] / getlinecommand.cpp

diff --git a/getlinecommand.cpp b/getlinecommand.cpp
index 800f9d816eab2230d2f543321d0ddb5c97e1ee63..f1ec55cab12261a5b91f425553bf34bc71393727 100644 (file)
--- a/getlinecommand.cpp
+++ b/getlinecommand.cpp
@@ -19,40 +19,31 @@ GetlineCommand::GetlineCommand(string option){
                if(option == "help") { help(); abort = true; }
                
                else {
-                       if (option != "") { cout << "There are no valid parameters for the get.line command." << endl; abort = true; }
+                       if (option != "") { mothurOut("There are no valid parameters for the get.line 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.line 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.line command."); mothurOutEndLine(); abort = true; }                                
                }
 
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the GetlineCommand class Function GetlineCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "GetlineCommand", "GetlineCommand");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the GetlineCommand class function GetlineCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
-                       
 }
 //**********************************************************************************************************************
 
 void GetlineCommand::help(){
        try {
-               cout << "The get.line command can only be executed after a successful read.otu command." << "\n";
-               cout << "You may not use any parameters with the get.line command." << "\n";
-               cout << "The get.line command should be in the following format: " << "\n";
-               cout << "get.line()" << "\n";
-               cout << "Example get.line()." << "\n";
+               mothurOut("The get.line command can only be executed after a successful read.otu command.\n");
+               mothurOut("You may not use any parameters with the get.line command.\n");
+               mothurOut("The get.line command should be in the following format: \n");
+               mothurOut("get.line()\n");
+               mothurOut("Example get.line().\n");
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the GetlineCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "GetlineCommand", "help");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the GetlineCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }
 
 //**********************************************************************************************************************
@@ -77,7 +68,7 @@ int GetlineCommand::execute(){
                        if(count > numBins)
                                count = 0;
                        if(count == 0) {
-                               cout << line << "\n";
+                               mothurOut(toString(line)); mothurOutEndLine();
                                in >> numBins;
                                line++;
                        }
@@ -90,13 +81,9 @@ int GetlineCommand::execute(){
        }
 
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the GetlineCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "GetlineCommand", "execute");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the GetlineCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }