removing chime source files from mother project.

[mothur.git] / engine.cpp

diff --git a/engine.cpp b/engine.cpp
index d595be332eed785c27037710396d1a7dd46c845e..24adcb53b59f39f049269d74b4da953a5f387262 100644 (file)
--- a/engine.cpp
+++ b/engine.cpp
@@ -34,7 +34,7 @@ string Engine::findMothursPath(){
                
                //delimiting path char
                char delim;
-               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                        delim = ':';
                #else
                        delim = ';';
@@ -56,7 +56,7 @@ string Engine::findMothursPath(){
                
                if (mothurPath != "") {
                        //add mothur so it looks like what argv would look like
-                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                                mothurPath += "/mothur";
                        #else
                                mothurPath += "\\mothur";
@@ -71,7 +71,7 @@ string Engine::findMothursPath(){
                                //is this mothurs path?
                                ifstream in;
                                string tempIn = dirs[i];
-                               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+                               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                                        tempIn += "/mothur";
                                #else
                                        tempIn += "\\mothur";
@@ -180,14 +180,18 @@ bool InteractEngine::getInput(){
                                        #endif
                                        //executes valid command
                                        mout->runParse = true;
-                                       mout->Groups.clear();
-                                       mout->namesOfGroups.clear();
+                                       mout->clearGroups();
+                                       mout->clearAllGroups();
                                        mout->Treenames.clear();
-                                       mout->names.clear();
                                        mout->saveNextLabel = "";
+                                       mout->printedHeaders = false;
+                                       mout->commandInputsConvertError = false;
+                                       mout->currentBinLabels.clear();
+                                       mout->binLabelsInFile.clear();
                                                        
                                        Command* command = cFactory->getCommand(commandName, options);
-                                       quitCommandCalled = command->execute();
+                                       if (mout->commandInputsConvertError) { quitCommandCalled = 2; }
+                                       else { quitCommandCalled = command->execute(); }
                                                        
                                        //if we aborted command
                                        if (quitCommandCalled == 2) {  mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); }
@@ -214,14 +218,14 @@ bool InteractEngine::getInput(){
 string Engine::getCommand()  {
        try {
        
-               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                        #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
-                                       strcpy(nextCommand, "quit"); 
+                                       nextCommand = strdup("quit");
                                        mout->mothurOut(nextCommand);
                                }       
                                
@@ -361,14 +365,19 @@ bool BatchEngine::getInput(){
                                        #endif
                                        //executes valid command
                                        mout->runParse = true;
-                                       mout->Groups.clear();
-                                       mout->namesOfGroups.clear();
+                                       mout->clearGroups();
+                                       mout->clearAllGroups();
                                        mout->Treenames.clear();
-                                       mout->names.clear();
                                        mout->saveNextLabel = "";
+                                       mout->printedHeaders = false;
+                                       mout->commandInputsConvertError = false;
+                                       mout->currentBinLabels.clear();
+                                       mout->binLabelsInFile.clear();
+
                                                        
                                        Command* command = cFactory->getCommand(commandName, options);
-                                       quitCommandCalled = command->execute();
+                                       if (mout->commandInputsConvertError) { quitCommandCalled = 2; }
+                                       else { quitCommandCalled = command->execute(); }
                                                        
                                        //if we aborted command
                                        if (quitCommandCalled == 2) {  mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); }
@@ -399,7 +408,7 @@ bool BatchEngine::getInput(){
 /***********************************************************************/
 string BatchEngine::getNextCommand(ifstream& inputBatchFile) {
        try {
-               
+                       
                string nextcommand = "";
                
                if (inputBatchFile.eof()) { nextcommand = "quit()"; }
@@ -524,14 +533,18 @@ bool ScriptEngine::getInput(){
                                        #endif
                                        //executes valid command
                                        mout->runParse = true;
-                                       mout->Groups.clear();
-                                       mout->namesOfGroups.clear();
+                                       mout->clearGroups();
+                                       mout->clearAllGroups();
                                        mout->Treenames.clear();
-                                       mout->names.clear();
                                        mout->saveNextLabel = "";
-                                                       
+                                       mout->printedHeaders = false;
+                                       mout->commandInputsConvertError = false;
+                                       mout->currentBinLabels.clear();
+                                       mout->binLabelsInFile.clear();
+
                                        Command* command = cFactory->getCommand(commandName, options);
-                                       quitCommandCalled = command->execute();
+                                       if (mout->commandInputsConvertError) { quitCommandCalled = 2; }
+                                       else { quitCommandCalled = command->execute(); }
                                        
                                        //if we aborted command
                                        if (quitCommandCalled == 2) {  mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); }