X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=engine.cpp;h=e4e107168c5723c82b90a7f103ccb8d9ee83cb60;hp=7bacec5c0e757c7b77d3c8801970c17bd3cc5a4a;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=9013e13ecfb2fda3c2664a76f76cc99b8c7fa74c diff --git a/engine.cpp b/engine.cpp index 7bacec5..e4e1071 100644 --- a/engine.cpp +++ b/engine.cpp @@ -25,14 +25,19 @@ Engine::Engine(){ exit(1); } } +/***********************************************************************/ /***********************************************************************/ InteractEngine::InteractEngine(string path){ - globaldata = GlobalData::getInstance(); - globaldata->argv = path; + 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 = mout->findProgramPath("mothur"); } + + mout->argv = path; } /***********************************************************************/ @@ -60,7 +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(); @@ -110,8 +117,24 @@ 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(); + 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(); } + mout->control_pressed = 0; mout->executing = false; @@ -134,14 +157,14 @@ bool InteractEngine::getInput(){ string Engine::getCommand() { try { - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) #ifdef USE_READLINE char* nextCommand = NULL; nextCommand = readline("mothur > "); if(nextCommand != NULL) { add_history(nextCommand); } else{ //^D causes null string and we want it to quit mothur - nextCommand = "quit"; + nextCommand = strdup("quit"); mout->mothurOut(nextCommand); } @@ -176,10 +199,15 @@ string Engine::getCommand() { //This function opens the batchfile to be used by BatchEngine::getInput. BatchEngine::BatchEngine(string path, string batchFileName){ try { - globaldata = GlobalData::getInstance(); - openedBatch = openInputFile(batchFileName, inputBatchFile); - globaldata->argv = path; + openedBatch = mout->openInputFile(batchFileName, inputBatchFile); + + 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 = mout->findProgramPath("mothur"); } + + mout->argv = path; } catch(exception& e) { @@ -210,7 +238,7 @@ bool BatchEngine::getInput(){ //CommandFactory cFactory; int quitCommandCalled = 0; int count = 0; - while(quitCommandCalled == 0){ + while(quitCommandCalled != 1){ #ifdef USE_MPI int pid, processors; @@ -251,7 +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(); @@ -275,8 +303,25 @@ 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(); + + 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(); } + mout->control_pressed = 0; mout->executing = false; @@ -289,7 +334,7 @@ bool BatchEngine::getInput(){ } } - gobble(inputBatchFile); + mout->gobble(inputBatchFile); } inputBatchFile.close(); @@ -303,11 +348,11 @@ bool BatchEngine::getInput(){ /***********************************************************************/ string BatchEngine::getNextCommand(ifstream& inputBatchFile) { try { - + string nextcommand = ""; if (inputBatchFile.eof()) { nextcommand = "quit()"; } - else { nextcommand = getline(inputBatchFile); } + else { nextcommand = mout->getline(inputBatchFile); } return nextcommand; } @@ -322,12 +367,16 @@ string BatchEngine::getNextCommand(ifstream& inputBatchFile) { //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)); + + string temppath = path.substr(0, (path.find_last_of("othur")-5)); - globaldata->argv = path; + //this will happen if you set the path variable to contain mothur's exe location + if (temppath == "") { path = mout->findProgramPath("mothur"); } + + mout->argv = path; } catch(exception& e) { @@ -353,7 +402,7 @@ bool ScriptEngine::getInput(){ //CommandFactory cFactory; int quitCommandCalled = 0; - while(quitCommandCalled == 0){ + while(quitCommandCalled != 1){ #ifdef USE_MPI int pid, processors; @@ -368,10 +417,16 @@ 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"); } - 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 @@ -410,7 +465,6 @@ bool ScriptEngine::getInput(){ mout->executing = true; #ifdef USE_MPI int pid, numProcesses; - MPI_Status status; MPI_Comm_rank(MPI_COMM_WORLD, &pid); MPI_Comm_size(MPI_COMM_WORLD, &numProcesses); @@ -420,8 +474,24 @@ 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(); + 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(); } + mout->control_pressed = 0; mout->executing = false; @@ -450,11 +520,16 @@ string ScriptEngine::getNextCommand(string& commandString) { string nextcommand = ""; int count = 0; + bool ignoreSemiColons = false; //go through string until you reach ; or end while (count < commandString.length()) { - if (commandString[count] == ';') { break; } + //you want to ignore any ; until you reach the next ' + if ((commandString[count] == '\'') && (!ignoreSemiColons)) { ignoreSemiColons = true; } + else if ((commandString[count] == '\'') && (ignoreSemiColons)) { ignoreSemiColons = false; } + + if ((commandString[count] == ';') && (!ignoreSemiColons)) { break; } else { nextcommand += commandString[count]; } count++;