added chimera.uchime

[mothur.git] / engine.cpp

diff --git a/engine.cpp b/engine.cpp
index dbdcc36300f2fd5d3f5ea6135dbc8666f328bba0..d595be332eed785c27037710396d1a7dd46c845e 100644 (file)
--- a/engine.cpp
+++ b/engine.cpp
@@ -179,6 +179,13 @@ bool InteractEngine::getInput(){
                                        //cout << pid << " is in execute " << commandName << endl;
                                        #endif
                                        //executes valid command
+                                       mout->runParse = true;
+                                       mout->Groups.clear();
+                                       mout->namesOfGroups.clear();
+                                       mout->Treenames.clear();
+                                       mout->names.clear();
+                                       mout->saveNextLabel = "";
+                                                       
                                        Command* command = cFactory->getCommand(commandName, options);
                                        quitCommandCalled = command->execute();
                                                        
@@ -353,6 +360,13 @@ bool BatchEngine::getInput(){
                                                if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
                                        #endif
                                        //executes valid command
+                                       mout->runParse = true;
+                                       mout->Groups.clear();
+                                       mout->namesOfGroups.clear();
+                                       mout->Treenames.clear();
+                                       mout->names.clear();
+                                       mout->saveNextLabel = "";
+                                                       
                                        Command* command = cFactory->getCommand(commandName, options);
                                        quitCommandCalled = command->execute();
                                                        
@@ -455,9 +469,13 @@ bool ScriptEngine::getInput(){
                        
                        if (input == "") { input = "quit()"; }
                        
-                       mout->mothurOutEndLine();
-                       mout->mothurOut("mothur > " + input);
-                       mout->mothurOutEndLine();
+                       if (mout->gui) {
+                               if ((input.find("quit") != string::npos) || (input.find("set.logfile") != string::npos)) {}
+                               else if ((input.find("get.current") != string::npos) && (!mout->hasCurrentFiles())) {}
+                               else { mout->mothurOutEndLine(); mout->mothurOut("mothur > " + input); mout->mothurOutEndLine(); }
+                       }else{
+                               mout->mothurOutEndLine(); mout->mothurOut("mothur > " + input); mout->mothurOutEndLine();
+                       }
                        
                        #ifdef USE_MPI
                                //send commandName
@@ -505,6 +523,13 @@ bool ScriptEngine::getInput(){
                                                        //cout << pid << " is in execute" << endl;      
                                        #endif
                                        //executes valid command
+                                       mout->runParse = true;
+                                       mout->Groups.clear();
+                                       mout->namesOfGroups.clear();
+                                       mout->Treenames.clear();
+                                       mout->names.clear();
+                                       mout->saveNextLabel = "";
+                                                       
                                        Command* command = cFactory->getCommand(commandName, options);
                                        quitCommandCalled = command->execute();