modified sequence class to read fasta files with comments. this required modification...

[mothur.git] / engine.cpp

diff --git a/engine.cpp b/engine.cpp
index 0a0f5a0ce7f0f4f0a120509e2c3d5c0e51471ecb..371bda8fb83f2b8ceb4793c49f067ed5987f2094 100644 (file)
--- a/engine.cpp
+++ b/engine.cpp
@@ -20,14 +20,11 @@ InteractEngine::InteractEngine(string path){
 
        globaldata = GlobalData::getInstance();
        globaldata->argv = path;
-       
-       
 }
 
 /***********************************************************************/
 
-InteractEngine::~InteractEngine(){
-       }
+InteractEngine::~InteractEngine(){}
 
 /***********************************************************************/
 //This function allows the user to input commands one line at a time until they quit.
@@ -44,9 +41,47 @@ bool InteractEngine::getInput(){
                        
                        mothurOutEndLine();
                        mothurOut("mothur > ");
+                       
+                       //get input char by char so you can check for use of arrow keys
+                       //if (_kbhit()){
+                       //      _getch(); // edit : if you want to check the arrow-keys you must call getch twice because special-keys have two values
+                       //      return _getch();
+                       //}
+                       //return 0; // if no key is pressed
+                       //setbuf(stdin, NULL); //no buffering
+/*if(ch==0)
+{
+ch=getch();
+if(ch==72) cout<<"up";
+else if(ch==75) cout<<"left";
+else if(ch==77) cout<<"right";
+else if(ch==80) cout<<"down";
+cout<<endl;
+}
+else break;
+}
+delay(2000);
+return 0;
+}*/
+                       
+                       //int letter = 0;
+                       //while ((letter != 10) && (letter != 13)) {
+                       //      letter = getch();
+                               
+                       //      cout << "char code = " << letter << endl;
+                               
+                       //      input += char(letter);
+                       //}
+               //      input = input.substr(0, input.length()-1); //cut off newline char
+               
+       //cout << input << endl;                
+                       
                        getline(cin, input);
                        if (cin.eof()) { input = "quit()"; }
                        
+                       //save command
+                       //previousInputs.push_back(input);
+                       
                        mothurOutJustToLog(input);
                        mothurOutEndLine();
                        
@@ -55,13 +90,13 @@ bool InteractEngine::getInput(){
                        
                        CommandOptionParser parser(input);
                        commandName = parser.getCommandString();
+       //cout << " command = " << commandName << endl;
                        options = parser.getOptionString();
                        
                        if (commandName != "") {
                        
                                //executes valid command
-                               CommandFactory cFactory;
-                               Command* command = cFactory.getCommand(commandName, options);
+                               Command* command = cFactory->getCommand(commandName, options);
                                quitCommandCalled = command->execute();
                                
                        }else {
@@ -76,7 +111,17 @@ bool InteractEngine::getInput(){
                exit(1);
        }
 }
-
+/***********************************************************************/
+void Engine::terminateCommand(int dummy)  {
+       try {
+               mothurOut("Stopping command."); mothurOutEndLine();
+               cFactory->getCommand();  //terminates command
+       }
+       catch(exception& e) {
+               errorOut(e, "InteractEngine", "terminateCommand");
+               exit(1);
+       }
+}
 /***********************************************************************/
 //This function opens the batchfile to be used by BatchEngine::getInput.
 BatchEngine::BatchEngine(string path, string batchFileName){
@@ -95,8 +140,7 @@ BatchEngine::BatchEngine(string path, string batchFileName){
 
 /***********************************************************************/
 
-BatchEngine::~BatchEngine(){
-       }
+BatchEngine::~BatchEngine(){   }
 
 /***********************************************************************/
 //This Function allows the user to run a batchfile containing several commands on Dotur
@@ -138,8 +182,7 @@ bool BatchEngine::getInput(){
                                if (commandName != "") {
 
                                        //executes valid command
-                                       CommandFactory cFactory;
-                                       Command* command = cFactory.getCommand(commandName, options);
+                                       Command* command = cFactory->getCommand(commandName, options);
                                        quitCommandCalled = command->execute();
                                }else {         
                                        mothurOut("Invalid."); 
@@ -172,8 +215,6 @@ ScriptEngine::ScriptEngine(string path, string commandString){
 
                globaldata->argv = path;
                
-               
-       
        }
        catch(exception& e) {
                errorOut(e, "ScriptEngine", "ScriptEngine");
@@ -183,8 +224,7 @@ ScriptEngine::ScriptEngine(string path, string commandString){
 
 /***********************************************************************/
 
-ScriptEngine::~ScriptEngine(){
-       }
+ScriptEngine::~ScriptEngine(){         }
 
 /***********************************************************************/
 //This Function allows the user to run a batchfile containing several commands on mothur
@@ -221,8 +261,7 @@ bool ScriptEngine::getInput(){
                        if (commandName != "") {
 
                                //executes valid command
-                               CommandFactory cFactory;
-                               Command* command = cFactory.getCommand(commandName, options);
+                               Command* command = cFactory->getCommand(commandName, options);
                                quitCommandCalled = command->execute();
                        }else {         
                                mothurOut("Invalid.");