added sequence name to error string in fastq.info. Changed np_shannon to npshannon.

[mothur.git] / engine.cpp

diff --git a/engine.cpp b/engine.cpp
index f128c4684040346110d519c56f45c9506e953866..ea1c0e14dc9f89fe0157d24828a2e9552297389c 100644 (file)
--- a/engine.cpp
+++ b/engine.cpp
@@ -180,14 +180,19 @@ 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->commandInputsConvertError = false;
+                                       mout->currentBinLabels.clear();
+                                       mout->binLabelsInFile.clear();
                                                        
                                        Command* command = cFactory->getCommand(commandName, options);
-                                       quitCommandCalled = command->execute();
+                                       if (mout->commandInputsConvertError) { quitCommandCalled = 2; }
+                                       else { quitCommandCalled = command->execute(); }
                                                        
                                        //if we aborted command
                                        if (quitCommandCalled == 2) {  mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); }
@@ -221,7 +226,7 @@ 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);
                                }       
                                
@@ -361,14 +366,20 @@ 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->commandInputsConvertError = false;
+                                       mout->currentBinLabels.clear();
+                                       mout->binLabelsInFile.clear();
+
                                                        
                                        Command* command = cFactory->getCommand(commandName, options);
-                                       quitCommandCalled = command->execute();
+                                       if (mout->commandInputsConvertError) { quitCommandCalled = 2; }
+                                       else { quitCommandCalled = command->execute(); }
                                                        
                                        //if we aborted command
                                        if (quitCommandCalled == 2) {  mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); }
@@ -399,7 +410,7 @@ bool BatchEngine::getInput(){
 /***********************************************************************/
 string BatchEngine::getNextCommand(ifstream& inputBatchFile) {
        try {
-               
+                       
                string nextcommand = "";
                
                if (inputBatchFile.eof()) { nextcommand = "quit()"; }
@@ -469,10 +480,12 @@ 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
@@ -522,14 +535,19 @@ 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->commandInputsConvertError = false;
+                                       mout->currentBinLabels.clear();
+                                       mout->binLabelsInFile.clear();
+
                                        Command* command = cFactory->getCommand(commandName, options);
-                                       quitCommandCalled = command->execute();
+                                       if (mout->commandInputsConvertError) { quitCommandCalled = 2; }
+                                       else { quitCommandCalled = command->execute(); }
                                        
                                        //if we aborted command
                                        if (quitCommandCalled == 2) {  mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); }