X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=engine.cpp;h=d6be4e4f1a16e00af29cfe36052c98e3a6e98efb;hb=6b32d112bb60e9f7eb6d4407a4eed4c49b67bced;hp=48f782ab2a590d71a292e7b83125ba8ce0f3fffe;hpb=05c52893c6c2467381fe7e7b769d86b6209af2e1;p=mothur.git

diff --git a/engine.cpp b/engine.cpp
index 48f782a..d6be4e4 100644
--- a/engine.cpp
+++ b/engine.cpp
@@ -65,7 +65,9 @@ bool InteractEngine::getInput(){
 				if (pid == 0) {
 				
 			#endif
-			
+                    
+			if (mout->changedSeqNames) { mout->mothurOut("[WARNING]: your sequence names contained ':'.  I changed them to '_' to avoid problems in your downstream analysis.\n"); }
+                    
 			mout->mothurOutEndLine();
 			
 			input = getCommand();	
@@ -115,15 +117,18 @@ bool InteractEngine::getInput(){
 					//cout << pid << " is in execute " << commandName << endl;
 					#endif
 					//executes valid command
+                    mout->changedSeqNames = false;
 					mout->runParse = true;
 					mout->clearGroups();
 					mout->clearAllGroups();
 					mout->Treenames.clear();
 					mout->saveNextLabel = "";
-					mout->printedHeaders = false;
-					mout->commandInputsConvertError = false;
-					mout->currentBinLabels.clear();
-					mout->binLabelsInFile.clear();
+                    mout->commandInputsConvertError = false;
+					mout->printedSharedHeaders = false;
+					mout->currentSharedBinLabels.clear();
+					mout->sharedBinLabelsInFile.clear();
+                    mout->printedListHeaders = false;
+                    mout->listBinLabelsInFile.clear();
 							
 					Command* command = cFactory->getCommand(commandName, options);
 					if (mout->commandInputsConvertError) { quitCommandCalled = 2; }
@@ -276,7 +281,7 @@ bool BatchEngine::getInput(){
 			
 			
 			if (input[0] != '#') {
-				
+				if (mout->changedSeqNames) { mout->mothurOut("[WARNING]: your sequence names contained ':'.  I changed them to '_' to avoid problems in your downstream analysis.\n"); }
 				mout->mothurOutEndLine();
 				mout->mothurOut("mothur > " + input);
 				mout->mothurOutEndLine();
@@ -300,15 +305,18 @@ bool BatchEngine::getInput(){
 						if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
 					#endif
 					//executes valid command
+                    mout->changedSeqNames = false;
 					mout->runParse = true;
 					mout->clearGroups();
 					mout->clearAllGroups();
 					mout->Treenames.clear();
 					mout->saveNextLabel = "";
-					mout->printedHeaders = false;
 					mout->commandInputsConvertError = false;
-					mout->currentBinLabels.clear();
-					mout->binLabelsInFile.clear();
+                    mout->printedSharedHeaders = false;
+                    mout->currentSharedBinLabels.clear();
+                    mout->sharedBinLabelsInFile.clear();
+                    mout->printedListHeaders = false;
+                    mout->listBinLabelsInFile.clear();
 
 							
 					Command* command = cFactory->getCommand(commandName, options);
@@ -413,6 +421,8 @@ bool ScriptEngine::getInput(){
 			input = getNextCommand(listOfCommands);	
 			
 			if (input == "") { input = "quit()"; }
+                    
+            if (mout->changedSeqNames) { mout->mothurOut("[WARNING]: your sequence names contained ':'.  I changed them to '_' to avoid problems in your downstream analysis.\n"); }
 			
 			if (mout->gui) {
 				if ((input.find("quit") != string::npos) || (input.find("set.logfile") != string::npos)) {}
@@ -468,15 +478,18 @@ bool ScriptEngine::getInput(){
 							//cout << pid << " is in execute" << endl;	
 					#endif
 					//executes valid command
+                    mout->changedSeqNames = false;
 					mout->runParse = true;
 					mout->clearGroups();
 					mout->clearAllGroups();
 					mout->Treenames.clear();
 					mout->saveNextLabel = "";
-					mout->printedHeaders = false;
-					mout->commandInputsConvertError = false;
-					mout->currentBinLabels.clear();
-					mout->binLabelsInFile.clear();
+                    mout->commandInputsConvertError = false;
+                    mout->printedSharedHeaders = false;
+                    mout->currentSharedBinLabels.clear();
+                    mout->sharedBinLabelsInFile.clear();
+                    mout->printedListHeaders = false;
+                    mout->listBinLabelsInFile.clear();
 
 					Command* command = cFactory->getCommand(commandName, options);
 					if (mout->commandInputsConvertError) { quitCommandCalled = 2; }