X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=engine.cpp;h=98d730c31c2d03e3222057f8cef3da571aca0877;hb=2009a1a1f47e7467094d844e7c07ab8ddf7bb447;hp=fbf986dc6965de7d9d269c31f35e99ed85467a9d;hpb=11c115c802602be50e106aae56969e15d2c49a62;p=mothur.git diff --git a/engine.cpp b/engine.cpp index fbf986d..98d730c 100644 --- a/engine.cpp +++ b/engine.cpp @@ -25,23 +25,16 @@ Engine::Engine(){ exit(1); } } - /***********************************************************************/ - -InteractEngine::InteractEngine(string path){ - - globaldata = GlobalData::getInstance(); - - string temppath = path.substr(0, (path.find_last_of('m'))); - - //this will happen if you set the path variable to contain mothur's exe location - if (temppath == "") { - +string Engine::findMothursPath(){ + try { + string envPath = getenv("PATH"); + string mothurPath = ""; //delimiting path char char delim; - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) delim = ':'; #else delim = ';'; @@ -49,11 +42,15 @@ InteractEngine::InteractEngine(string path){ //break apart path variable by ':' vector dirs; - splitAtChar(envPath, dirs, delim); + mout->splitAtChar(envPath, dirs, delim); + if (mout->debug) { mout->mothurOut("[DEBUG]: dir's in path: \n"); } + //get path related to mothur - string mothurPath = ""; for (int i = 0; i < dirs.size(); i++) { + + if (mout->debug) { mout->mothurOut("[DEBUG]: " + dirs[i] + "\n"); } + //to lower so we can find it string tempLower = ""; for (int j = 0; j < dirs[i].length(); j++) { tempLower += tolower(dirs[i][j]); } @@ -61,18 +58,57 @@ InteractEngine::InteractEngine(string path){ //is this mothurs path? if (tempLower.find("mothur") != -1) { mothurPath = dirs[i]; break; } } + + if (mout->debug) { mout->mothurOut("[DEBUG]: mothurPath = " + mothurPath + "\n"); } + + if (mothurPath != "") { + //add mothur so it looks like what argv would look like + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) + mothurPath += "/mothur"; + #else + mothurPath += "\\mothur"; + #endif + }else { + //okay mothur is not in the path, so the folder mothur is in must be in the path + //lets find out which one + + //get path related to mothur + for (int i = 0; i < dirs.size(); i++) { + + //is this mothurs path? + ifstream in; + string tempIn = dirs[i]; + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) + tempIn += "/mothur"; + #else + tempIn += "\\mothur"; + #endif + mout->openInputFile(tempIn, in, ""); + + //if this file exists + if (in) { in.close(); mothurPath = tempIn; break; if (mout->debug) { mout->mothurOut("[DEBUG]: found it, mothurPath = " + mothurPath + "\n"); } } + } + } - //add mothur so it looks like what argv would look like - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) - mothurPath += "/mothur"; - #else - mothurPath += "\\mothur"; - #endif + return mothurPath; - path = mothurPath; } + catch(exception& e) { + mout->errorOut(e, "Engine", "findMothursPath"); + exit(1); + } +} +/***********************************************************************/ + +InteractEngine::InteractEngine(string 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 = findMothursPath(); } - globaldata->argv = path; + mout->argv = path; } /***********************************************************************/ @@ -150,8 +186,23 @@ bool InteractEngine::getInput(){ //cout << pid << " is in execute " << commandName << endl; #endif //executes valid command + 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; @@ -174,14 +225,14 @@ 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 +267,15 @@ 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); + 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 = findMothursPath(); } - 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; - 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 +306,7 @@ bool BatchEngine::getInput(){ //CommandFactory cFactory; int quitCommandCalled = 0; int count = 0; - while(quitCommandCalled == 0){ + while(quitCommandCalled != 1){ #ifdef USE_MPI int pid, processors; @@ -356,8 +371,24 @@ bool BatchEngine::getInput(){ if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) { #endif //executes valid command + 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; @@ -370,7 +401,7 @@ bool BatchEngine::getInput(){ } } - gobble(inputBatchFile); + mout->gobble(inputBatchFile); } inputBatchFile.close(); @@ -384,11 +415,11 @@ 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; } @@ -403,52 +434,16 @@ 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 = findMothursPath(); } - 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; - 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 +469,7 @@ bool ScriptEngine::getInput(){ //CommandFactory cFactory; int quitCommandCalled = 0; - while(quitCommandCalled == 0){ + while(quitCommandCalled != 1){ #ifdef USE_MPI int pid, processors; @@ -490,9 +485,13 @@ bool ScriptEngine::getInput(){ 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 @@ -531,7 +530,6 @@ 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 +539,23 @@ bool ScriptEngine::getInput(){ //cout << pid << " is in execute" << endl; #endif //executes valid command + 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; @@ -571,11 +584,16 @@ 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++;