changed the daughterLevels in classifiers summary file to reflect the classifications...

[mothur.git] / engine.cpp

diff --git a/engine.cpp b/engine.cpp
index fdd017ab34c7a083b3f09bc270498155b3cb3766..2ed819f9661fe728526c5e9ba59ba661f58027e9 100644 (file)
--- a/engine.cpp
+++ b/engine.cpp
@@ -54,7 +54,9 @@ bool InteractEngine::getInput(){
                        mout->mothurOutEndLine();
                        
                        input = getCommand();   
-                       mout->mothurOutEndLine();               
+                       mout->mothurOutEndLine();       
+                       
+                       if (mout->control_pressed) { input = "quit()"; }
                        
                        //allow user to omit the () on the quit command
                        if (input == "quit") { input = "quit()"; }
@@ -65,15 +67,27 @@ bool InteractEngine::getInput(){
                        options = parser.getOptionString();
                        
                        if (commandName != "") {
-                       
-                               //executes valid command
-                               Command* command = cFactory->getCommand(commandName, options);
-                               quitCommandCalled = command->execute();
-                               
-                       }else {
-                               mout->mothurOut("Your input contains errors. Please try again."); 
-                               mout->mothurOutEndLine();
-                       }
+                                       mout->executing = true;
+                                       #ifdef USE_MPI
+                                               int pid;
+                                               MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+ 
+cout << pid << " is here " << commandName << endl;
+                                               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 {         
+                                       mout->mothurOut("Invalid."); 
+                                       mout->mothurOutEndLine();
+                               }
                }       
                return 1;
        }
@@ -85,6 +99,10 @@ bool InteractEngine::getInput(){
 /***********************************************************************/
 string Engine::getCommand()  {
        try {
+               #ifdef USE_MPI
+                       MPI_Barrier(MPI_COMM_WORLD);
+               #endif
+       
                #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
                        #ifdef USE_READLINE
                                char* nextCommand = NULL;
@@ -93,7 +111,7 @@ string Engine::getCommand()  {
                                if(nextCommand != NULL) {  add_history(nextCommand);  } 
                                else{ //^D causes null string and we want it to quit mothur
                                        nextCommand = "quit"; 
-                                       cout << nextCommand << endl;
+                                       mout->mothurOut(nextCommand);
                                }       
                                
                                mout->mothurOutJustToLog("mothur > " + toString(nextCommand));
@@ -103,17 +121,19 @@ string Engine::getCommand()  {
                                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("mothur > " + toString(nextCommand));
-                       return nextCommand;
+                               string nextCommand = "";
+                               
+                               mout->mothurOut("mothur > ");
+                               getline(cin, nextCommand);
+                               mout->mothurOutJustToLog(toString(nextCommand));
+                               
+                               return nextCommand;
                #endif
-               
-               mout->mothurOutEndLine();
+       
                                                
        }
        catch(exception& e) {
@@ -158,18 +178,19 @@ bool BatchEngine::getInput(){
                
                //CommandFactory cFactory;
                int quitCommandCalled = 0;
-       
+           int count = 0;
                while(quitCommandCalled == 0){
        
-                       if (inputBatchFile.eof()) { input = "quit()"; }
-                       else { input = getline(inputBatchFile); }
+                       input = getNextCommand(inputBatchFile);
+                       count++;
                        
                        if (input[0] != '#') {
                                
                                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()"; }
@@ -179,10 +200,23 @@ bool BatchEngine::getInput(){
                                options = parser.getOptionString();
                                                                                
                                if (commandName != "") {
-
+                                       mout->executing = true;
+                                       #ifdef USE_MPI
+                                               int pid;
+                                               MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+                                               
+cout << pid << " is here " << commandName << '\t' << count << endl;
+                                               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 {         
                                        mout->mothurOut("Invalid."); 
                                        mout->mothurOutEndLine();
@@ -200,7 +234,27 @@ bool BatchEngine::getInput(){
                exit(1);
        }
 }
-
+/***********************************************************************/
+string BatchEngine::getNextCommand(ifstream& inputBatchFile) {
+       try {
+               
+               #ifdef USE_MPI
+                       int err = MPI_Barrier(MPI_COMM_WORLD);
+//cout << "barrier = " << err << '\t' << MPI_SUCCESS << endl;
+               #endif
+               
+               string nextcommand = "";
+               
+               if (inputBatchFile.eof()) { nextcommand = "quit()"; }
+               else { nextcommand = getline(inputBatchFile); }
+               
+               return nextcommand;
+       }
+       catch(exception& e) {
+               mout->errorOut(e, "BatchEngine", "getNextCommand");
+               exit(1);
+       }
+}
 
 /***********************************************************************/
 /***********************************************************************/
@@ -244,11 +298,11 @@ bool ScriptEngine::getInput(){
                        
                        if (input == "") { input = "quit()"; }
                        
-                       
                        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()"; }
@@ -258,14 +312,33 @@ bool ScriptEngine::getInput(){
                        options = parser.getOptionString();
                                                                                
                        if (commandName != "") {
+                                       mout->executing = true;
+                                       #ifdef USE_MPI
+                                               int pid, numProcesses;
+                                               MPI_Status status; 
+                                               
+                                               MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+                                               MPI_Comm_size(MPI_COMM_WORLD, &numProcesses); 
+                                       
+cout << pid << " is here " << commandName  << endl;
+                                               if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
+                                                       cout << pid << " is in execute" << endl;        
+                                       #endif
+                                       //executes valid command
+                                       Command* command = cFactory->getCommand(commandName, options);
+                                       quitCommandCalled = command->execute();
+                                       mout->control_pressed = 0;
+                                       mout->executing = false;
+                                                                       
+                                       #ifdef USE_MPI
+                                       cout << pid << " is done in execute" << endl;
+                                               }
+                                       #endif
+                               }else {         
+                                       mout->mothurOut("Invalid."); 
+                                       mout->mothurOutEndLine();
+                               }
 
-                               //executes valid command
-                               Command* command = cFactory->getCommand(commandName, options);
-                               quitCommandCalled = command->execute();
-                       }else {         
-                               mout->mothurOut("Invalid."); 
-                               mout->mothurOutEndLine();
-                       }
                        
                }
                
@@ -279,6 +352,11 @@ bool ScriptEngine::getInput(){
 /***********************************************************************/
 string ScriptEngine::getNextCommand(string& commandString) {
        try {
+               
+               #ifdef USE_MPI
+                       MPI_Barrier(MPI_COMM_WORLD);
+               #endif
+               
                string nextcommand = "";
                int count = 0;
                
@@ -303,7 +381,7 @@ string ScriptEngine::getNextCommand(string& commandString) {
                                if (commandString.length() == 0) {  break;  }
                        }
                }
-                                       
+               
                return nextcommand;
        }
        catch(exception& e) {