created mothurOut class to handle logfiles

[mothur.git] / systemcommand.cpp

diff --git a/systemcommand.cpp b/systemcommand.cpp
index 489a2f11f7c3a13df14bedf42a05339e86fcaeb2..708724a4e5cd46643e7ec29464b61c1f34c7cd41 100644 (file)
--- a/systemcommand.cpp
+++ b/systemcommand.cpp
@@ -11,7 +11,7 @@
 
 //**********************************************************************************************************************
 
-SystemCommand::SystemCommand(string option){
+SystemCommand::SystemCommand(string option)  {
        try {
                abort = false;
                
@@ -19,7 +19,7 @@ SystemCommand::SystemCommand(string option){
                if(option == "help") { help(); abort = true; }
                
                else {
-                       if (option == "") { mothurOut("You must enter a command to run."); mothurOutEndLine(); abort = true; }
+                       if (option == "") { m->mothurOut("You must enter a command to run."); m->mothurOutEndLine(); abort = true; }
                        else { 
                                //check for outputdir and inputdir parameters
                                int commaPos = option.find_first_of(',');
@@ -35,7 +35,7 @@ SystemCommand::SystemCommand(string option){
 
        }
        catch(exception& e) {
-               errorOut(e, "SystemCommand", "SystemCommand");
+               m->errorOut(e, "SystemCommand", "SystemCommand");
                exit(1);
        }
 }
@@ -43,13 +43,13 @@ SystemCommand::SystemCommand(string option){
 
 void SystemCommand::help(){
        try {
-               mothurOut("The system command allows you to execute a system command from within mothur.\n");
-               mothurOut("The system has no parameters.\n");
-               mothurOut("The system command should be in the following format: system(yourCommand).\n");
-               mothurOut("Example system(clear).\n");
+               m->mothurOut("The system command allows you to execute a system command from within mothur.\n");
+               m->mothurOut("The system has no parameters.\n");
+               m->mothurOut("The system command should be in the following format: system(yourCommand).\n");
+               m->mothurOut("Example system(clear).\n");
        }
        catch(exception& e) {
-               errorOut(e, "SystemCommand", "help");
+               m->errorOut(e, "SystemCommand", "help");
                exit(1);
        }
 }
@@ -67,7 +67,7 @@ int SystemCommand::execute(){
        }
 
        catch(exception& e) {
-               errorOut(e, "SystemCommand", "execute");
+               m->errorOut(e, "SystemCommand", "execute");
                exit(1);
        }
 }