mods to trim.seqs

[mothur.git] / engine.cpp

diff --git a/engine.cpp b/engine.cpp
index fbf986dc6965de7d9d269c31f35e99ed85467a9d..dd61de67d36974af09bf700879c8b59821ebd83f 100644 (file)
--- a/engine.cpp
+++ b/engine.cpp
@@ -49,7 +49,7 @@ InteractEngine::InteractEngine(string path){
                
                //break apart path variable by ':'
                vector<string> dirs;
-               splitAtChar(envPath, dirs, delim);
+               mout->splitAtChar(envPath, dirs, delim);
                
                //get path related to mothur
                string mothurPath = "";
@@ -152,6 +152,10 @@ bool InteractEngine::getInput(){
                                        //executes valid command
                                        Command* command = cFactory->getCommand(commandName, options);
                                        quitCommandCalled = command->execute();
+                                                       
+                                       //if we aborted command
+                                       if (quitCommandCalled == 2) {  mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); }
+
                                        mout->control_pressed = 0;
                                        mout->executing = false;
                                                                                
@@ -181,7 +185,7 @@ string Engine::getCommand()  {
                                
                                if(nextCommand != NULL) {  add_history(nextCommand);  } 
                                else{ //^D causes null string and we want it to quit mothur
-                                       nextCommand = "quit"; 
+                                       strcpy(nextCommand, "quit"); 
                                        mout->mothurOut(nextCommand);
                                }       
                                
@@ -218,7 +222,7 @@ BatchEngine::BatchEngine(string path, string batchFileName){
        try {
                globaldata = GlobalData::getInstance();
        
-               openedBatch = openInputFile(batchFileName, inputBatchFile);
+               openedBatch = mout->openInputFile(batchFileName, inputBatchFile);
                
                string temppath = path.substr(0, (path.find_last_of('m')));
        
@@ -237,7 +241,7 @@ BatchEngine::BatchEngine(string path, string batchFileName){
                        
                        //break apart path variable by ':'
                        vector<string> dirs;
-                       splitAtChar(envPath, dirs, delim);
+                       mout->splitAtChar(envPath, dirs, delim);
                        
                        //get path related to mothur
                        string mothurPath = "";
@@ -291,7 +295,7 @@ bool BatchEngine::getInput(){
                //CommandFactory cFactory;
                int quitCommandCalled = 0;
            int count = 0;
-               while(quitCommandCalled == 0){
+               while(quitCommandCalled != 1){
                        
                        #ifdef USE_MPI
                                int pid, processors;
@@ -358,6 +362,10 @@ bool BatchEngine::getInput(){
                                        //executes valid command
                                        Command* command = cFactory->getCommand(commandName, options);
                                        quitCommandCalled = command->execute();
+                                                       
+                                       //if we aborted command
+                                       if (quitCommandCalled == 2) {  mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); }
+
                                        mout->control_pressed = 0;
                                        mout->executing = false;
                                                                                
@@ -370,7 +378,7 @@ bool BatchEngine::getInput(){
                                }
                                
                        }
-                       gobble(inputBatchFile);
+                       mout->gobble(inputBatchFile);
                }
                
                inputBatchFile.close();
@@ -388,7 +396,7 @@ string BatchEngine::getNextCommand(ifstream& inputBatchFile) {
                string nextcommand = "";
                
                if (inputBatchFile.eof()) { nextcommand = "quit()"; }
-               else { nextcommand = getline(inputBatchFile); }
+               else { nextcommand = mout->getline(inputBatchFile); }
                
                return nextcommand;
        }
@@ -425,7 +433,7 @@ ScriptEngine::ScriptEngine(string path, string commandString){
                        
                        //break apart path variable by ':'
                        vector<string> dirs;
-                       splitAtChar(envPath, dirs, delim);
+                       mout->splitAtChar(envPath, dirs, delim);
                        
                        //get path related to mothur
                        string mothurPath = "";
@@ -474,7 +482,7 @@ bool ScriptEngine::getInput(){
                //CommandFactory cFactory;
                int quitCommandCalled = 0;
        
-               while(quitCommandCalled == 0){
+               while(quitCommandCalled != 1){
                        
                        #ifdef USE_MPI
                                int pid, processors;
@@ -531,7 +539,6 @@ bool ScriptEngine::getInput(){
                                        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); 
@@ -543,6 +550,10 @@ bool ScriptEngine::getInput(){
                                        //executes valid command
                                        Command* command = cFactory->getCommand(commandName, options);
                                        quitCommandCalled = command->execute();
+                                       
+                                       //if we aborted command
+                                       if (quitCommandCalled == 2) {  mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); }
+                                                       
                                        mout->control_pressed = 0;
                                        mout->executing = false;
                                                                        
@@ -571,11 +582,16 @@ string ScriptEngine::getNextCommand(string& commandString) {
                
                string nextcommand = "";
                int count = 0;
+               bool ignoreSemiColons = false;
                
                //go through string until you reach ; or end
                while (count < commandString.length()) { 
                        
-                       if (commandString[count] == ';') {  break;   }
+                        //you want to ignore any ; until you reach the next '
+                       if ((commandString[count] == '\'') && (!ignoreSemiColons)) {  ignoreSemiColons = true;  } 
+                       else if ((commandString[count] == '\'') && (ignoreSemiColons)) {  ignoreSemiColons = false;  } 
+                               
+                       if ((commandString[count] == ';') && (!ignoreSemiColons)) {  break;   }
                        else {          nextcommand += commandString[count];    }
                        
                        count++;