created mothurOut class to handle logfiles

[mothur.git] / engine.cpp

diff --git a/engine.cpp b/engine.cpp
index 18e1a595c06343a521d9bcd6458b95db4d863db7..fdd017ab34c7a083b3f09bc270498155b3cb3766 100644 (file)
--- a/engine.cpp
+++ b/engine.cpp
@@ -18,9 +18,10 @@
 Engine::Engine(){
        try {
                cFactory = CommandFactory::getInstance();
+               mout = MothurOut::getInstance();
        }
        catch(exception& e) {
-               errorOut(e, "Engine", "Engine");
+               mout->errorOut(e, "Engine", "Engine");
                exit(1);
        }
 }
@@ -31,6 +32,7 @@ InteractEngine::InteractEngine(string path){
 
        globaldata = GlobalData::getInstance();
        globaldata->argv = path;
+       
 }
 
 /***********************************************************************/
@@ -49,9 +51,10 @@ bool InteractEngine::getInput(){
                
                while(quitCommandCalled != 1){
 
-                       mothurOutEndLine();
+                       mout->mothurOutEndLine();
                        
-                       input = getCommand();                   
+                       input = getCommand();   
+                       mout->mothurOutEndLine();               
                        
                        //allow user to omit the () on the quit command
                        if (input == "quit") { input = "quit()"; }
@@ -68,14 +71,14 @@ bool InteractEngine::getInput(){
                                quitCommandCalled = command->execute();
                                
                        }else {
-                               mothurOut("Your input contains errors. Please try again."); 
-                               mothurOutEndLine();
+                               mout->mothurOut("Your input contains errors. Please try again."); 
+                               mout->mothurOutEndLine();
                        }
                }       
                return 1;
        }
        catch(exception& e) {
-               errorOut(e, "InteractEngine", "getInput");
+               mout->errorOut(e, "InteractEngine", "getInput");
                exit(1);
        }
 }
@@ -93,28 +96,28 @@ string Engine::getCommand()  {
                                        cout << nextCommand << endl;
                                }       
                                
-                               mothurOutJustToLog("mothur > " + toString(nextCommand));
+                               mout->mothurOutJustToLog("mothur > " + toString(nextCommand));
                                return nextCommand;
                        #else
                                string nextCommand = "";
-                               mothurOut("mothur > ");
+                               mout->mothurOut("mothur > ");
                                getline(cin, nextCommand);
-                               mothurOutJustToLog("mothur > " + toString(nextCommand));
+                               mout->mothurOutJustToLog("mothur > " + toString(nextCommand));
                                return nextCommand;
                        #endif
                #else
                        string nextCommand = "";
-                       mothurOut("mothur > ");
+                       mout->mothurOut("mothur > ");
                        getline(cin, nextCommand);
-                       mothurOutJustToLog("mothur > " + toString(nextCommand));
+                       mout->mothurOutJustToLog("mothur > " + toString(nextCommand));
                        return nextCommand;
                #endif
                
-               mothurOutEndLine();
+               mout->mothurOutEndLine();
                                                
        }
        catch(exception& e) {
-               errorOut(e, "Engine", "getCommand");
+               mout->errorOut(e, "Engine", "getCommand");
                exit(1);
        }
 }
@@ -129,7 +132,7 @@ BatchEngine::BatchEngine(string path, string batchFileName){
                                
        }
        catch(exception& e) {
-               errorOut(e, "BatchEngine", "BatchEngine");
+               mout->errorOut(e, "BatchEngine", "BatchEngine");
                exit(1);
        }
 }
@@ -144,8 +147,8 @@ bool BatchEngine::getInput(){
        try {
                //check if this is a valid batchfile
                if (openedBatch == 1) {  
-                       mothurOut("unable to open batchfile");  
-                       mothurOutEndLine();
+                       mout->mothurOut("unable to open batchfile");  
+                       mout->mothurOutEndLine();
                        return 1; 
                }
        
@@ -163,9 +166,9 @@ bool BatchEngine::getInput(){
                        
                        if (input[0] != '#') {
                                
-                               mothurOutEndLine();
-                               mothurOut("mothur > " + input);
-                               mothurOutEndLine();
+                               mout->mothurOutEndLine();
+                               mout->mothurOut("mothur > " + input);
+                               mout->mothurOutEndLine();
                                
                                
                                //allow user to omit the () on the quit command
@@ -181,8 +184,8 @@ bool BatchEngine::getInput(){
                                        Command* command = cFactory->getCommand(commandName, options);
                                        quitCommandCalled = command->execute();
                                }else {         
-                                       mothurOut("Invalid."); 
-                                       mothurOutEndLine();
+                                       mout->mothurOut("Invalid."); 
+                                       mout->mothurOutEndLine();
                                }
                                
                        }
@@ -193,7 +196,7 @@ bool BatchEngine::getInput(){
                return 1;
        }
        catch(exception& e) {
-               errorOut(e, "BatchEngine", "getInput");
+               mout->errorOut(e, "BatchEngine", "getInput");
                exit(1);
        }
 }
@@ -210,10 +213,10 @@ ScriptEngine::ScriptEngine(string path, string commandString){
                listOfCommands = commandString.substr(1, (commandString.length()-1));
 
                globaldata->argv = path;
-               
+                               
        }
        catch(exception& e) {
-               errorOut(e, "ScriptEngine", "ScriptEngine");
+               mout->errorOut(e, "ScriptEngine", "ScriptEngine");
                exit(1);
        }
 }
@@ -242,9 +245,9 @@ bool ScriptEngine::getInput(){
                        if (input == "") { input = "quit()"; }
                        
                        
-                       mothurOutEndLine();
-                       mothurOut("mothur > " + input);
-                       mothurOutEndLine();
+                       mout->mothurOutEndLine();
+                       mout->mothurOut("mothur > " + input);
+                       mout->mothurOutEndLine();
 
                                
                        //allow user to omit the () on the quit command
@@ -260,8 +263,8 @@ bool ScriptEngine::getInput(){
                                Command* command = cFactory->getCommand(commandName, options);
                                quitCommandCalled = command->execute();
                        }else {         
-                               mothurOut("Invalid."); 
-                               mothurOutEndLine();
+                               mout->mothurOut("Invalid."); 
+                               mout->mothurOutEndLine();
                        }
                        
                }
@@ -269,7 +272,7 @@ bool ScriptEngine::getInput(){
                return 1;
        }
        catch(exception& e) {
-               errorOut(e, "ScriptEngine", "getInput");
+               mout->errorOut(e, "ScriptEngine", "getInput");
                exit(1);
        }
 }
@@ -304,7 +307,7 @@ string ScriptEngine::getNextCommand(string& commandString) {
                return nextcommand;
        }
        catch(exception& e) {
-               errorOut(e, "ScriptEngine", "getNextCommand");
+               mout->errorOut(e, "ScriptEngine", "getNextCommand");
                exit(1);
        }
 }