changed groupfile in classify.seqs to reflect multiple fasta files

[mothur.git] / engine.cpp

diff --git a/engine.cpp b/engine.cpp
index 811236003b5089171536c7e075b10b506baf670a..9e5801b1b057b2f2a1cc4a986e105ae3e73f14b5 100644 (file)
--- a/engine.cpp
+++ b/engine.cpp
@@ -14,6 +14,17 @@
 
 #include "engine.hpp"
 
+/***********************************************************************/
+Engine::Engine(){
+       try {
+               cFactory = CommandFactory::getInstance();
+               mout = MothurOut::getInstance();
+       }
+       catch(exception& e) {
+               mout->errorOut(e, "Engine", "Engine");
+               exit(1);
+       }
+}
 
 /***********************************************************************/
 
@@ -21,6 +32,7 @@ InteractEngine::InteractEngine(string path){
 
        globaldata = GlobalData::getInstance();
        globaldata->argv = path;
+       
 }
 
 /***********************************************************************/
@@ -38,13 +50,13 @@ bool InteractEngine::getInput(){
                int quitCommandCalled = 0;
                
                while(quitCommandCalled != 1){
+
+                       mout->mothurOutEndLine();
                        
-                       mothurOutEndLine();
-                       
-                       input = getCommand();                   
+                       input = getCommand();   
+                       mout->mothurOutEndLine();       
                        
-                       mothurOutJustToLog("mothur > " + input);
-                       mothurOutEndLine();
+                       if (mout->control_pressed) { input = "quit()"; }
                        
                        //allow user to omit the () on the quit command
                        if (input == "quit") { input = "quit()"; }
@@ -55,46 +67,73 @@ bool InteractEngine::getInput(){
                        options = parser.getOptionString();
                        
                        if (commandName != "") {
-                       
+                               mout->executing = true;
+                               
+                               #ifdef USE_MPI
+                                       int pid;
+                                       MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+                                       
+                                       if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
+                               #endif
                                //executes valid command
                                Command* command = cFactory->getCommand(commandName, options);
                                quitCommandCalled = command->execute();
+                               mout->control_pressed = 0;
+                               mout->executing = false;
                                
+                               #ifdef USE_MPI
+                                       }
+                               #endif
                        }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);
        }
 }
 /***********************************************************************/
 string Engine::getCommand()  {
        try {
-               char* nextCommand = NULL;
-               
-               nextCommand = readline("mothur > ");
-               if(nextCommand != NULL) {  add_history(nextCommand);  }
+               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+                       #ifdef USE_READLINE
+                               char* nextCommand = NULL;
+                               nextCommand = readline("mothur > ");
+                               
+                               if(nextCommand != NULL) {  add_history(nextCommand);  } 
+                               else{ //^D causes null string and we want it to quit mothur
+                                       nextCommand = "quit"; 
+                                       mout->mothurOut(nextCommand);
+                               }       
+                               
+                               mout->mothurOutJustToLog("mothur > " + toString(nextCommand));
+                               return nextCommand;
+                       #else
+                               string nextCommand = "";
+                               mout->mothurOut("mothur > ");
+                               getline(cin, nextCommand);
+                               mout->mothurOutJustToLog("mothur > " + toString(nextCommand));
+                               
+                               return nextCommand;
+                       #endif
+               #else
+                               string nextCommand = "";
+                               
+                               mout->mothurOut("mothur > ");
+                               getline(cin, nextCommand);
+                               mout->mothurOutJustToLog(toString(nextCommand));
+                               
+                               return nextCommand;
+               #endif
+       
                                                
-               return nextCommand;
        }
        catch(exception& e) {
-               errorOut(e, "Engine", "getCommand");
-               exit(1);
-       }
-}
-/***********************************************************************/
-void Engine::terminateCommand(int dummy)  {
-       try {
-               mothurOut("Stopping command."); mothurOutEndLine();
-               cFactory->getCommand();  //terminates command
-       }
-       catch(exception& e) {
-               errorOut(e, "Engine", "terminateCommand");
+               mout->errorOut(e, "Engine", "getCommand");
                exit(1);
        }
 }
@@ -109,7 +148,7 @@ BatchEngine::BatchEngine(string path, string batchFileName){
                                
        }
        catch(exception& e) {
-               errorOut(e, "BatchEngine", "BatchEngine");
+               mout->errorOut(e, "BatchEngine", "BatchEngine");
                exit(1);
        }
 }
@@ -124,8 +163,8 @@ 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; 
                }
        
@@ -143,10 +182,11 @@ bool BatchEngine::getInput(){
                        
                        if (input[0] != '#') {
                                
-                               mothurOutEndLine();
-                               mothurOut("mothur > " + input);
-                               mothurOutEndLine();
-                               
+                               mout->mothurOutEndLine();
+                               mout->mothurOut("mothur > " + input);
+                               mout->mothurOutEndLine();
+                                                       
+                               if (mout->control_pressed) { input = "quit()"; }
                                
                                //allow user to omit the () on the quit command
                                if (input == "quit") { input = "quit()"; }
@@ -156,13 +196,25 @@ bool BatchEngine::getInput(){
                                options = parser.getOptionString();
                                                                                
                                if (commandName != "") {
-
+                                       mout->executing = true;
+                                       #ifdef USE_MPI
+                                               int pid;
+                                               MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+                                       
+                                               if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
+                                       #endif
                                        //executes valid command
                                        Command* command = cFactory->getCommand(commandName, options);
                                        quitCommandCalled = command->execute();
+                                       mout->control_pressed = 0;
+                                       mout->executing = false;
+                               
+                                       #ifdef USE_MPI
+                                               }
+                                       #endif
                                }else {         
-                                       mothurOut("Invalid."); 
-                                       mothurOutEndLine();
+                                       mout->mothurOut("Invalid."); 
+                                       mout->mothurOutEndLine();
                                }
                                
                        }
@@ -173,7 +225,7 @@ bool BatchEngine::getInput(){
                return 1;
        }
        catch(exception& e) {
-               errorOut(e, "BatchEngine", "getInput");
+               mout->errorOut(e, "BatchEngine", "getInput");
                exit(1);
        }
 }
@@ -190,10 +242,10 @@ 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);
        }
 }
@@ -221,11 +273,11 @@ bool ScriptEngine::getInput(){
                        
                        if (input == "") { input = "quit()"; }
                        
+                       mout->mothurOutEndLine();
+                       mout->mothurOut("mothur > " + input);
+                       mout->mothurOutEndLine();
                        
-                       mothurOutEndLine();
-                       mothurOut("mothur > " + input);
-                       mothurOutEndLine();
-
+                       if (mout->control_pressed) { input = "quit()"; }
                                
                        //allow user to omit the () on the quit command
                        if (input == "quit") { input = "quit()"; }
@@ -235,13 +287,25 @@ bool ScriptEngine::getInput(){
                        options = parser.getOptionString();
                                                                                
                        if (commandName != "") {
-
+                               mout->executing = true;
+                               #ifdef USE_MPI
+                                       int pid;
+                                       MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+                                       
+                                       if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
+                               #endif
                                //executes valid command
                                Command* command = cFactory->getCommand(commandName, options);
                                quitCommandCalled = command->execute();
+                               mout->control_pressed = 0;
+                               mout->executing = false;
+                               
+                               #ifdef USE_MPI
+                                       }
+                               #endif
                        }else {         
-                               mothurOut("Invalid."); 
-                               mothurOutEndLine();
+                               mout->mothurOut("Invalid."); 
+                               mout->mothurOutEndLine();
                        }
                        
                }
@@ -249,7 +313,7 @@ bool ScriptEngine::getInput(){
                return 1;
        }
        catch(exception& e) {
-               errorOut(e, "ScriptEngine", "getInput");
+               mout->errorOut(e, "ScriptEngine", "getInput");
                exit(1);
        }
 }
@@ -284,7 +348,7 @@ string ScriptEngine::getNextCommand(string& commandString) {
                return nextcommand;
        }
        catch(exception& e) {
-               errorOut(e, "ScriptEngine", "getNextCommand");
+               mout->errorOut(e, "ScriptEngine", "getNextCommand");
                exit(1);
        }
 }