InteractEngine::InteractEngine(string path){
- globaldata = GlobalData::getInstance();
string temppath = path.substr(0, (path.find_last_of("othur")-5));
//this will happen if you set the path variable to contain mothur's exe location
if (temppath == "") { path = findMothursPath(); }
- globaldata->argv = path;
+ mout->argv = path;
}
/***********************************************************************/
//cout << pid << " is in execute " << commandName << endl;
#endif
//executes valid command
+ mout->runParse = true;
+ mout->Groups.clear();
+ mout->namesOfGroups.clear();
+ mout->Treenames.clear();
+ mout->names.clear();
+ mout->saveNextLabel = "";
+
Command* command = cFactory->getCommand(commandName, options);
quitCommandCalled = command->execute();
//This function opens the batchfile to be used by BatchEngine::getInput.
BatchEngine::BatchEngine(string path, string batchFileName){
try {
- globaldata = GlobalData::getInstance();
openedBatch = mout->openInputFile(batchFileName, inputBatchFile);
//this will happen if you set the path variable to contain mothur's exe location
if (temppath == "") { path = findMothursPath(); }
- globaldata->argv = path;
+ mout->argv = path;
}
catch(exception& e) {
if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
#endif
//executes valid command
+ mout->runParse = true;
+ mout->Groups.clear();
+ mout->namesOfGroups.clear();
+ mout->Treenames.clear();
+ mout->names.clear();
+ mout->saveNextLabel = "";
+
Command* command = cFactory->getCommand(commandName, options);
quitCommandCalled = command->execute();
//This function opens the batchfile to be used by BatchEngine::getInput.
ScriptEngine::ScriptEngine(string path, string commandString){
try {
- globaldata = GlobalData::getInstance();
//remove quotes
listOfCommands = commandString.substr(1, (commandString.length()-1));
//this will happen if you set the path variable to contain mothur's exe location
if (temppath == "") { path = findMothursPath(); }
- globaldata->argv = path;
+ mout->argv = path;
}
catch(exception& e) {
if (input == "") { 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
//send commandName
//cout << pid << " is in execute" << endl;
#endif
//executes valid command
+ mout->runParse = true;
+ mout->Groups.clear();
+ mout->namesOfGroups.clear();
+ mout->Treenames.clear();
+ mout->names.clear();
+ mout->saveNextLabel = "";
+
Command* command = cFactory->getCommand(commandName, options);
quitCommandCalled = command->execute();