X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=engine.cpp;h=d6be4e4f1a16e00af29cfe36052c98e3a6e98efb;hp=a90bb7e0588baee4f8d922687f99063c8d961387;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=ca0785e447ca7aa7e2f0ab8bb1155db126b551ea diff --git a/engine.cpp b/engine.cpp index a90bb7e..d6be4e4 100644 --- a/engine.cpp +++ b/engine.cpp @@ -25,54 +25,19 @@ Engine::Engine(){ exit(1); } } +/***********************************************************************/ /***********************************************************************/ InteractEngine::InteractEngine(string path){ - globaldata = GlobalData::getInstance(); - string temppath = path.substr(0, (path.find_last_of('m'))); + 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 == "") { - - string envPath = getenv("PATH"); - - //delimiting path char - char delim; - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) - delim = ':'; - #else - delim = ';'; - #endif - - //break apart path variable by ':' - vector dirs; - mout->splitAtChar(envPath, dirs, delim); - - //get path related to mothur - string mothurPath = ""; - for (int i = 0; i < dirs.size(); i++) { - //to lower so we can find it - string tempLower = ""; - for (int j = 0; j < dirs[i].length(); j++) { tempLower += tolower(dirs[i][j]); } - - //is this mothurs path? - if (tempLower.find("mothur") != -1) { mothurPath = dirs[i]; break; } - } - - //add mothur so it looks like what argv would look like - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) - mothurPath += "/mothur"; - #else - mothurPath += "\\mothur"; - #endif - - path = mothurPath; - } + if (temppath == "") { path = mout->findProgramPath("mothur"); } - globaldata->argv = path; + mout->argv = path; } /***********************************************************************/ @@ -100,7 +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(); @@ -150,8 +117,26 @@ 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->commandInputsConvertError = false; + mout->printedSharedHeaders = false; + mout->currentSharedBinLabels.clear(); + mout->sharedBinLabelsInFile.clear(); + mout->printedListHeaders = false; + mout->listBinLabelsInFile.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; @@ -174,14 +159,14 @@ 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); } @@ -216,51 +201,15 @@ 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 = mout->openInputFile(batchFileName, inputBatchFile); - string temppath = path.substr(0, (path.find_last_of('m'))); + 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 == "") { + if (temppath == "") { path = mout->findProgramPath("mothur"); } - string envPath = getenv("PATH"); - - //delimiting path char - char delim; - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) - delim = ':'; - #else - delim = ';'; - #endif - - //break apart path variable by ':' - vector dirs; - mout->splitAtChar(envPath, dirs, delim); - - //get path related to mothur - string mothurPath = ""; - for (int i = 0; i < dirs.size(); i++) { - //to lower so we can find it - string tempLower = ""; - for (int j = 0; j < dirs[i].length(); j++) { tempLower += tolower(dirs[i][j]); } - - //is this mothurs path? - if (tempLower.find("mothur") != -1) { mothurPath = dirs[i]; break; } - } - - //add mothur so it looks like what argv would look like - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) - mothurPath += "/mothur"; - #else - mothurPath += "\\mothur"; - #endif - - path = mothurPath; - } - - globaldata->argv = path; + mout->argv = path; } catch(exception& e) { @@ -291,7 +240,7 @@ bool BatchEngine::getInput(){ //CommandFactory cFactory; int quitCommandCalled = 0; int count = 0; - while(quitCommandCalled == 0){ + while(quitCommandCalled != 1){ #ifdef USE_MPI int pid, processors; @@ -332,7 +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(); @@ -356,8 +305,27 @@ 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->commandInputsConvertError = false; + mout->printedSharedHeaders = false; + mout->currentSharedBinLabels.clear(); + mout->sharedBinLabelsInFile.clear(); + mout->printedListHeaders = false; + mout->listBinLabelsInFile.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; @@ -384,7 +352,7 @@ bool BatchEngine::getInput(){ /***********************************************************************/ string BatchEngine::getNextCommand(ifstream& inputBatchFile) { try { - + string nextcommand = ""; if (inputBatchFile.eof()) { nextcommand = "quit()"; } @@ -403,52 +371,16 @@ 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('m'))); - + 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 == "") { + if (temppath == "") { path = mout->findProgramPath("mothur"); } - string envPath = getenv("PATH"); - - //delimiting path char - char delim; - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) - delim = ':'; - #else - delim = ';'; - #endif - - //break apart path variable by ':' - vector dirs; - mout->splitAtChar(envPath, dirs, delim); - - //get path related to mothur - string mothurPath = ""; - for (int i = 0; i < dirs.size(); i++) { - //to lower so we can find it - string tempLower = ""; - for (int j = 0; j < dirs[i].length(); j++) { tempLower += tolower(dirs[i][j]); } - - //is this mothurs path? - if (tempLower.find("mothur") != -1) { mothurPath = dirs[i]; break; } - } - - //add mothur so it looks like what argv would look like - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) - mothurPath += "/mothur"; - #else - mothurPath += "\\mothur"; - #endif - - path = mothurPath; - } - - globaldata->argv = path; + mout->argv = path; } catch(exception& e) { @@ -474,7 +406,7 @@ bool ScriptEngine::getInput(){ //CommandFactory cFactory; int quitCommandCalled = 0; - while(quitCommandCalled == 0){ + while(quitCommandCalled != 1){ #ifdef USE_MPI int pid, processors; @@ -489,10 +421,16 @@ bool ScriptEngine::getInput(){ input = getNextCommand(listOfCommands); if (input == "") { input = "quit()"; } - - mout->mothurOutEndLine(); - mout->mothurOut("mothur > " + input); - mout->mothurOutEndLine(); + + 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)) {} + 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 @@ -531,7 +469,6 @@ 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); @@ -541,8 +478,26 @@ 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->commandInputsConvertError = false; + mout->printedSharedHeaders = false; + mout->currentSharedBinLabels.clear(); + mout->sharedBinLabelsInFile.clear(); + mout->printedListHeaders = false; + mout->listBinLabelsInFile.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;