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 3108f3733d59078c9c5273b0a2a2f1c145cd33d0..a80eba4292f8ca32abb9a612cd7ef3cb7f8226a4 100644 (file)
--- a/engine.cpp
+++ b/engine.cpp
@@ -180,12 +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();
@@ -362,12 +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();
@@ -526,12 +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();