modified read.otu and shared command

[mothur.git] / engine.cpp

diff --git a/engine.cpp b/engine.cpp
index 38429b972d1d04a6543330ae1d67c6f63bcc094c..55617bc3f80a97e1832ff61c3e09678de8eca1ca 100644 (file)
--- 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.1.4.1" << endl;
-               cout << "Last updated: 6/23/2009" << 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";
-               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";
+               errorOut(e, "InteractEngine", "getInput");
                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);
        }
 }
@@ -136,12 +111,15 @@ 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;
@@ -151,11 +129,14 @@ bool BatchEngine::getInput(){
                        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()"; }
@@ -170,7 +151,10 @@ bool BatchEngine::getInput(){
                                        CommandFactory cFactory;
                                        Command* command = cFactory.getCommand(commandName, options);
                                        quitCommandCalled = command->execute();
-                               }else {         cout << "Invalid." << endl;             }
+                               }else {         
+                                       mothurOut("Invalid."); 
+                                       mothurOutEndLine();
+                               }
                                
                        }
                        gobble(inputBatchFile);
@@ -180,11 +164,7 @@ bool BatchEngine::getInput(){
                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);
        }
 }
@@ -201,16 +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);
        }
 }
@@ -221,14 +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;
@@ -238,9 +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()"; }
@@ -255,18 +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);
        }
 }
@@ -293,11 +271,7 @@ string ScriptEngine::getNextCommand(string& commandString) {
                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);
        }
 }