X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=engine.cpp;h=55617bc3f80a97e1832ff61c3e09678de8eca1ca;hb=29c0d3ec01be5372807eb86261100d77de253787;hp=03422e20790a96159eaa68ad569ae4a15a5d94aa;hpb=786d5631d9cd5baa6ed6ef16f8b4b384cbc7470f;p=mothur.git

diff --git a/engine.cpp b/engine.cpp
index 03422e2..55617bc 100644
--- a/engine.cpp
+++ b/engine.cpp
@@ -22,12 +22,6 @@ InteractEngine::InteractEngine(string path){
 	globaldata->argv = path;
 	
 	system("clear");
-//	char buffer = ' ';
-//	ifstream header("introtext.txt");
-//	while(!header.eof()){
-//		cout << buffer;
-//		buffer = header.get();
-//	}
 }
 
 /***********************************************************************/
@@ -44,32 +38,21 @@ bool InteractEngine::getInput(){
 		string commandName = "";
 		string options = "";
 		int quitCommandCalled = 0;
-		//bool errorFree;
-		//ErrorCheck* errorCheckor = new ErrorCheck();
 		
-		cout << "mothur v.1.3.0" << endl;
-		cout << "Last updated: 5/29/2009" << endl << endl;
-		cout << "by" << endl;
-		cout << "Patrick D. Schloss" << endl << endl;
-		cout << "Department of Microbiology" << endl;
-		cout << "The University of Massachusetts" << endl;
-		cout << "pschloss@micro.umass.edu" << endl;
-		cout << "http://schloss.micro.umass.edu/mothur" << endl << endl << endl;
-		cout << "Distributed under the GNU General Public License" << endl << endl;
-		cout << "Type 'help()' for information on the commands that are available" << endl << endl;
-		cout << "Type 'quit()' to exit program" << endl;
-
+				
 		while(quitCommandCalled != 1){
-
-			cout << endl << "mothur > ";
+			
+			mothurOutEndLine();
+			mothurOut("mothur > ");
 			getline(cin, input);
 			if (cin.eof()) { input = "quit()"; }
 			
+			mothurOutJustToLog(input);
+			mothurOutEndLine();
+			
 			//allow user to omit the () on the quit command
 			if (input == "quit") { input = "quit()"; }
 			
-			//errorFree = errorCheckor->checkInput(input);
-			//if (errorFree == true) {
 			CommandOptionParser parser(input);
 			commandName = parser.getCommandString();
 			options = parser.getOptionString();
@@ -82,20 +65,16 @@ bool InteractEngine::getInput(){
 				quitCommandCalled = command->execute();
 				
 			}else {
-				cout << "Your input contains errors. Please try again." << endl;
+				mothurOut("Your input contains errors. Please try again."); 
+				mothurOutEndLine();
 			}
 		}	
 		return 1;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the InteractEngine class Function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		errorOut(e, "InteractEngine", "getInput");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the InteractEngine class function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-
 }
 
 /***********************************************************************/
@@ -106,7 +85,7 @@ BatchEngine::BatchEngine(string path, string batchFileName){
 	
 		openedBatch = openInputFile(batchFileName, inputBatchFile);
 		globaldata->argv = path;
-
+				
 		system("clear");
 	
 	//	char buffer = ' ';
@@ -117,11 +96,7 @@ BatchEngine::BatchEngine(string path, string batchFileName){
 	//	}
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the BatchEngine class Function BatchEngine. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the BatchEngine class function BatchEngine. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		errorOut(e, "BatchEngine", "BatchEngine");
 		exit(1);
 	}
 }
@@ -136,26 +111,32 @@ BatchEngine::~BatchEngine(){
 bool BatchEngine::getInput(){
 	try {
 		//check if this is a valid batchfile
-		if (openedBatch == 1) {  cout << "unable to open batchfile" << endl;  return 1; }
+		if (openedBatch == 1) {  
+			mothurOut("unable to open batchfile");  
+			mothurOutEndLine();
+			return 1; 
+		}
 	
 		string input = "";
 		string commandName = "";
 		string options = "";
-		//int count = 1;
 		
 		//CommandFactory cFactory;
 		int quitCommandCalled = 0;
 	
 		while(quitCommandCalled == 0){
-		
+	
 			if (inputBatchFile.eof()) { input = "quit()"; }
 			else { getline(inputBatchFile, input); }
 			
-			//cout << "command number" << count << endl; count++;
 			
-			if (input[0] != '#') {
 			
-				cout << endl << "mothur > " << input << endl;
+			if (input[0] != '#') {
+				
+				mothurOutEndLine();
+				mothurOut("mothur > " + input);
+				mothurOutEndLine();
+				
 				
 				//allow user to omit the () on the quit command
 				if (input == "quit") { input = "quit()"; }
@@ -170,19 +151,20 @@ bool BatchEngine::getInput(){
 					CommandFactory cFactory;
 					Command* command = cFactory.getCommand(commandName, options);
 					quitCommandCalled = command->execute();
-				}else {		cout << "Invalid." << endl;		}
+				}else {		
+					mothurOut("Invalid."); 
+					mothurOutEndLine();
+				}
 				
 			}
 			gobble(inputBatchFile);
 		}
+		
+		inputBatchFile.close();
 		return 1;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the BatchEngine class Function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the BatchEngine class function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		errorOut(e, "BatchEngine", "getInput");
 		exit(1);
 	}
 }
@@ -199,16 +181,12 @@ ScriptEngine::ScriptEngine(string path, string commandString){
 		listOfCommands = commandString.substr(1, (commandString.length()-1));
 
 		globaldata->argv = path;
-
+		
 		system("clear");
 	
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ScriptEngine class Function ScriptEngine. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the ScriptEngine class function ScriptEngine. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		errorOut(e, "ScriptEngine", "ScriptEngine");
 		exit(1);
 	}
 }
@@ -219,14 +197,14 @@ ScriptEngine::~ScriptEngine(){
 	}
 
 /***********************************************************************/
-//This Function allows the user to run a batchfile containing several commands on Dotur
+//This Function allows the user to run a batchfile containing several commands on mothur
 bool ScriptEngine::getInput(){
 	try {
 			
 		string input = "";
 		string commandName = "";
 		string options = "";
-		//int count = 1;
+		
 		
 		//CommandFactory cFactory;
 		int quitCommandCalled = 0;
@@ -236,9 +214,12 @@ bool ScriptEngine::getInput(){
 			input = getNextCommand(listOfCommands);	
 			
 			if (input == "") { input = "quit()"; }
-			//cout << "command number" << count << endl; count++;
 			
-			cout << endl << "mothur > " << input << endl;
+			
+			mothurOutEndLine();
+			mothurOut("mothur > " + input);
+			mothurOutEndLine();
+
 				
 			//allow user to omit the () on the quit command
 			if (input == "quit") { input = "quit()"; }
@@ -253,18 +234,17 @@ bool ScriptEngine::getInput(){
 				CommandFactory cFactory;
 				Command* command = cFactory.getCommand(commandName, options);
 				quitCommandCalled = command->execute();
-			}else {		cout << "Invalid." << endl;		}
+			}else {		
+				mothurOut("Invalid."); 
+				mothurOutEndLine();
+			}
 			
 		}
 		
 		return 1;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ScriptEngine class Function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the ScriptEngine class function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		errorOut(e, "ScriptEngine", "getInput");
 		exit(1);
 	}
 }
@@ -280,21 +260,19 @@ string ScriptEngine::getNextCommand(string& commandString) {
 			commandString = commandString.substr(commandString.find_first_of(';')+1, commandString.length());
 		}else { commandString = ""; } //you have reached the last command.
 		
-		//get rid of any extra spaces in between commands
-		//string space = " ";
-		
-		//while(commandString.at(0) == ' ')
-			//commandString = commandString.substr(1, commandString.length());
-			
+		//get rid of spaces in between commands if any
+		if (commandString.length() > 0) {
+			while (commandString[0] == ' ') {  
+				commandString = commandString.substr(1,commandString.length());
+				if (commandString.length() == 0) {  break;  }
+			}
+		}
+					
 		return nextcommand;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ScriptEngine class Function getNextCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the ScriptEngine class function getNextCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		errorOut(e, "ScriptEngine", "getNextCommand");
 		exit(1);
 	}
 }
-/***********************************************************************/
\ No newline at end of file
+/***********************************************************************/