changes while testing

[mothur.git] / engine.cpp

diff --git a/engine.cpp b/engine.cpp
index 48f782ab2a590d71a292e7b83125ba8ce0f3fffe..e4e107168c5723c82b90a7f103ccb8d9ee83cb60 100644 (file)
--- 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();   
@@ -115,6 +117,7 @@ bool InteractEngine::getInput(){
                                        //cout << pid << " is in execute " << commandName << endl;
                                        #endif
                                        //executes valid command
+                    mout->changedSeqNames = false;
                                        mout->runParse = true;
                                        mout->clearGroups();
                                        mout->clearAllGroups();
@@ -276,7 +279,7 @@ 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();
@@ -300,6 +303,7 @@ bool BatchEngine::getInput(){
                                                if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
                                        #endif
                                        //executes valid command
+                    mout->changedSeqNames = false;
                                        mout->runParse = true;
                                        mout->clearGroups();
                                        mout->clearAllGroups();
@@ -413,6 +417,8 @@ 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)) {}
@@ -468,6 +474,7 @@ bool ScriptEngine::getInput(){
                                                        //cout << pid << " is in execute" << endl;      
                                        #endif
                                        //executes valid command
+                    mout->changedSeqNames = false;
                                        mout->runParse = true;
                                        mout->clearGroups();
                                        mout->clearAllGroups();