fixed bug with trim.flows that was adding flow files names to the .flow.files file...

[mothur.git] / engine.cpp

diff --git a/engine.cpp b/engine.cpp
index f128c4684040346110d519c56f45c9506e953866..a80eba4292f8ca32abb9a612cd7ef3cb7f8226a4 100644 (file)
--- a/engine.cpp
+++ b/engine.cpp
@@ -180,11 +180,14 @@ 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->currentBinLabels.clear();
+                                       mout->binLabelsInFile.clear();
                                                        
                                        Command* command = cFactory->getCommand(commandName, options);
                                        quitCommandCalled = command->execute();
@@ -221,7 +224,7 @@ string Engine::getCommand()  {
                                
                                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);
                                }       
                                
@@ -361,11 +364,15 @@ 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->currentBinLabels.clear();
+                                       mout->binLabelsInFile.clear();
+
                                                        
                                        Command* command = cFactory->getCommand(commandName, options);
                                        quitCommandCalled = command->execute();
@@ -469,10 +476,12 @@ bool ScriptEngine::getInput(){
                        
                        if (input == "") { input = "quit()"; }
                        
-                       if ((!mout->gui) || (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
@@ -522,11 +531,15 @@ 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->currentBinLabels.clear();
+                                       mout->binLabelsInFile.clear();
+
                                                        
                                        Command* command = cFactory->getCommand(commandName, options);
                                        quitCommandCalled = command->execute();