done testing 1.13.0

[mothur.git] / getlabelcommand.cpp

diff --git a/getlabelcommand.cpp b/getlabelcommand.cpp
index e0c17204e7c732ed180fd134a1a7c0d05a105c40..971feb4b33f70f44bcfbabdf6de55caf17bda3cd 100644 (file)
--- a/getlabelcommand.cpp
+++ b/getlabelcommand.cpp
@@ -11,7 +11,7 @@
 
 //**********************************************************************************************************************
 
-GetlabelCommand::GetlabelCommand(string option){
+GetlabelCommand::GetlabelCommand(string option)  {
        try {
                globaldata = GlobalData::getInstance();
                abort = false;
@@ -20,40 +20,29 @@ 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 ((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() == "")) { m->mothurOut("You must read a list, sabund or rabund before you can use the get.label command."); m->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";
+               m->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";
+               m->mothurOut("The get.label command can only be executed after a successful read.otu command.\n");
+               m->mothurOut("You may not use any parameters with the get.label command.\n");
+               m->mothurOut("The get.label command should be in the following format: \n");
+               m->mothurOut("get.label()\n");
+               m->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";
+               m->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);
-       }       
 }
 
 //**********************************************************************************************************************
@@ -70,30 +59,31 @@ int GetlabelCommand::execute(){
                
                filename = globaldata->inputFileName;
                ifstream in;
-               openInputFile(filename, in);
+               m->openInputFile(filename, in);
                string label;
                int numBins = 0;
                int count = -1;
                while(in.good()) {
+                       
+                       if (m->control_pressed) { in.close();  return 0; }
+                       
                        if(count > numBins)
                                count = 0;
                        if(count == 0) {
-                               cout << label << "\n";
+                               m->mothurOut(label); m->mothurOutEndLine();
                                in >> numBins;
                        }
                        in >> label;
                        count++;
                }       
+               
+               in.close();
                return 0;       
        }
 
        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";
+               m->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);
-       }       
 }